https://cyana.org/w/api.php?action=feedcontributions&feedformat=atom&user=GuentertCYANA Wiki - User contributions [en]2026-04-09T16:33:11ZUser contributionsMediaWiki 1.45.1https://cyana.org/w/index.php?title=INCLAN:_intrinsics&diff=9958INCLAN: intrinsics2026-01-20T09:49:52Z<p>Guentert: </p>
<hr />
<div>The following functions can be used in Fortran-77 expressions in addition to the standard Fortran-77 intrinsic functions or anywhere on the command line in the form '''$'''''function'''''('''''parameter''''','''''parameter''''','''...''')''' if there are<br />
parameters or in the form '''$'''''function'' without parameters. In the alphabetical list below, ''i'' and ''n'' denote integer expressions, and ''s'' and ''t'' denote character expressions. The result type of the function is given in parentheses.<br />
<br />
;cputime: CPU time in seconds since the start of the program (real)<br />
<br />
;date: current date in the form dd-mm-yy (character)<br />
<br />
;def(''s''): does a variable with name ''s'' exist and have a value different from NULL? (logical)<br />
<br />
;exist(''s''): does a variable with name ''s'' exist? (logical)<br />
<br />
;existfile(''s''): does a file with name ''s'' exist? (logical)<br />
<br />
;external(''s''): value of the external (i.e. non-local) variable with name ''s'' (even if it is hidden by a local variable with the same name), or a blank string if no external variable with this name exists. (character)<br />
<br />
;external(''s'',''t''): value of the external (i.e. non-local) variable with name ''s'' (even if it is hidden by a local variable with the same name), or ''t'' if no external variable with this name exists. (character)<br />
<br />
;fitchisq: ''&chi;''<sup>2</sup> value of the last linear least-squares fit (real)<br />
<br />
;fiterr(''n''): standard deviation of the ''n''-th fit parameter of the last linear least-squares fit (real)<br />
<br />
;fitpar(''n''): optimal value of the ''n''-th fit parameter of the last linear least-squares fit (real)<br />
<br />
;fitprob: probability that the ''&chi;''<sup>2</sup> value of the last linear least-squares fit would be exceeded by chance (real)<br />
<br />
;getenv(''s''): value of Unix environment variable with name ''s'' (character)<br />
<br />
;getpid: Unix PID of current process (integer)<br />
<br />
;global(''s''): value of the global with name ''s'' (even if it is hidden by a local variable with the same name), or a blank string if no global variable with this name exists. (character)<br />
<br />
;global(''s'',''t''): value of the global with name ''s'' (even if it is hidden by a local variable with the same name), or ''t'' if no global variable with this name exists. (character)<br />
<br />
;if(''n'',''x1'',''x2''): argument ''x1'' if the condition ''n'' is true, or ''x2'' otherwise. The arguments ''x1'' and ''x2'' can have any type.<br />
<br />
;length(''s''): number of elements of the variable with name ''s'' (integer)<br />
<br />
;lenstr(''s''): length of string s (without trailing blanks) (integer)<br />
<br />
;macro(''s''): does a macro with name ''s'' exist in the search path? (logical)<br />
<br />
;match(''s'',''t''): does the string ''s'' match the string ''t''? The string ''t'' may contain wildcards: an asterisk matches zero or more characters, and a question mark matches exactly one character. (logical)<br />
<br />
;mtime(''s''): time of last modification (in seconds since a reference date) of the file with name ''s'' (integer)<br />
<br />
;opened(''s''): is the file with name ''s'' open? (logical)<br />
<br />
;plotx0, ploty0, plotx1, ploty1: coordinates of the two reference points in the user coordinate system used for graphics (real)<br />
<br />
;rand: random number between 0 and 1 (real)<br />
<br />
;rand(''i''): random number between 0 and 1, using seed ''i'' (real)<br />
<br />
;rand(''i'',''n''): ''n''-th random number between 0 and 1, using seed ''i'' (real)<br />
<br />
;time: current time in the form hh:mm:ss (character)<br />
<br />
;val(''s''): value of the variable with name s, or a blank string if no variable with this name exists. (character)<br />
<br />
;val(''s'',''t''): value of the variable with name ''s'', or ''t'' if no variable with this name exists. (character)<br />
<br />
;walltime: wallclock time in s since the start of the program (integer)</div>Guenterthttps://cyana.org/w/index.php?title=INCLAN:_Expressions&diff=9957INCLAN: Expressions2026-01-20T08:43:09Z<p>Guentert: </p>
<hr />
<div>The command interpreter can evaluate general Fortran-77 integer, real, complex, logical and character expressions. Expressions can appear in eval statements, as conditions of if statements, as command parameters when a numeric value is expected, and as substring and element index expressions.<br />
<br />
An expression is built according to the rules of Fortran-77 from constants, variables, and function calls. These basic items can be combined by operators (“+”, “–”, “*”, “/”, “**”, “.eq.”, “.ne.”, “.lt.”, “.le.”, “.ge.”, “.gt.”, “.and.”, “.or.”, “.not.”, “.eqv.”, “.neqv.”, “==”, “!=”, “<”, “<=”, “>=”, “>”) and grouped by parentheses. <br />
<br />
There are the following differences to the rules of Fortran-77:<br />
* The data type “double precision” is not supported.<br />
* The data type “logical” is represented by the integer values 0 (false) and 1 (true). Any integer expression can be used in place of a logical expression, with 0 representing “false”, and all other values representing “true”.<br />
* Variable, function and operator names are case sensitive. The names of logical operators and intrinsic functions must be written in lower case.<br />
* The logical operators “==”, “!=”, “<”, “<=”, “>=”, “>”, “&&”, “||”, and “!” can be used in place of its respective Fortran-77 equivalents “.eq.”, “.ne.”, “.lt.”, “.le.”, “.ge.”, “.gt.”, “.and.”, “.or.”, and “.not.”.<br />
* All [http://www.fortran.com/F77_std/rjcnf-15.html#sh-15.10 Fortran-77 intrinsic functions] (except “dble”, “dprod”, “lge”, “lgt”, “lle” and “llt”) are available by their generic names but not under special names. For example, the absolute value function is known by the name “abs” but not by the special names “iabs” or “cabs”. <br />
* There are additional [[INCLAN: intrinsics|intrinsic functions]].<br />
* Blanks can only appear at “reasonable” places but not within numbers, variable names, etc. There must be no blanks between the name of a function and the opening parenthesis of its parameter list.</div>Guenterthttps://cyana.org/w/index.php?title=INCLAN_Reference_Manual&diff=9956INCLAN Reference Manual2026-01-20T08:33:14Z<p>Guentert: </p>
<hr />
<div>The user interface of the program CYANA is based on INCLAN, a powerful interactive command language that allows the use of variables, mathematical and character expressions, macros, flow control (loops, conditional statements, jumps), parallelization on shared-memory and distributed-memory systems, and the production of graphics. <br />
<br />
INCLAN separates the user interface from the specific functions of the underlying program. It allows new commands to be implemented quickly, either in the compiled source code of the program or as interpreted INCLAN scripts (macros). In both cases the command line syntax follows the same, uniform rules, and is automatically checked by INCLAN for consistency and correct data typing. The output of the program is controlled and formatted by INCLAN, which allows the amount and destination of informative output to be defined in a uniform way. The INCLAN command language is an interpreted language that combines features of Unix shell scripts, e.g. the use variable substitutions in the command line, with those of high-level programming languages, e.g. sophisticated mathematical functions and expressions.<br />
<br />
The current version of INCLAN is implemented in Fortran, and is used as the command interpreter of several program packages written in Fortran and C++, including [[Main Page|CYANA]], [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/DYANA DYANA], [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/GARANT, GARANT], [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/OPALp OPALp], and [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/PROSA PROSA].<br />
<br />
In the following, literal INCLAN input and output is shown in Courier font. Non-literal input is shown in italics. Optional arguments are enclosed in square brackets “[…]”. In an argument list the ellipsis “…” indicates that the preceding parameter can be repeated.<br />
<br />
* [[INCLAN: Special characters|Special characters]]<br />
<br />
== INCLAN Commands ==<br />
<br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: Commands|Introduction]]<br />
</div><br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: abort|abort]]<br />
* [[INCLAN: alias|alias]]<br />
* [[INCLAN: ask|ask]]<br />
* [[INCLAN: break|break]]<br />
* [[INCLAN: cd, chdir|cd, chdir]]<br />
* [[INCLAN: command|command]]<br />
* [[INCLAN: do|do]]<br />
* [[INCLAN: else|else]]<br />
* [[INCLAN: else if|else if]]<br />
* [[INCLAN: end|end]]<br />
* [[INCLAN: end do|end do]]<br />
* [[INCLAN: end if|end if]]<br />
* [[INCLAN: error|error]]<br />
* [[INCLAN: eval|eval]]<br />
* [[INCLAN: external|external]]<br />
* [[INCLAN: eval, show, set, unset, external|eval, show, set, unset, external]]<br />
* [[INCLAN: exit|exit]]<br />
* [[INCLAN: goto, go to|goto, go to]]<br />
* [[INCLAN: help|help]]<br />
* [[INCLAN: if|if]]<br />
* [[INCLAN: label|label]]<br />
* [[INCLAN: parameter|parameter]]<br />
* [[INCLAN: plot|plot]]<br />
* [[INCLAN: print|print]]<br />
* [[INCLAN: print, error|print, error]]<br />
* [[INCLAN: quit|quit]]<br />
* [[INCLAN: readline|readline]]<br />
* [[INCLAN: remove|remove]]<br />
* [[INCLAN: return|return]]<br />
* [[INCLAN: safe|safe]]<br />
* [[INCLAN: set|set]]<br />
* [[INCLAN: show|show]]<br />
* [[INCLAN: sleep|sleep]]<br />
* [[INCLAN: special characters|special characters]]<br />
* [[INCLAN: subroutine|subroutine]]<br />
* [[INCLAN: subroutine, command|subroutine, command]]<br />
* [[INCLAN: synchronize|synchronize]]<br />
* [[INCLAN: syntax|syntax]]<br />
* [[INCLAN: system|system]]<br />
* [[INCLAN: type|type]]<br />
* [[INCLAN: unset|unset]]<br />
* [[INCLAN: var|var]]<br />
</div><br />
<br />
== INCLAN Variables==<br />
<br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: Variables|Introduction]]<br />
* [[INCLAN: Variable substitutions|Variable substitutions]]<br />
</div><br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: echo|echo]]<br />
* [[INCLAN: erract|erract]]<br />
* [[INCLAN: info|info]]<br />
* [[INCLAN: label|label]]<br />
* [[INCLAN: nparam|nparam]]<br />
* [[INCLAN: nproc|nproc]]<br />
* [[INCLAN: p1, p2,...|p1, p2,...]]<br />
* [[INCLAN: path|path]]<br />
* [[INCLAN: prompt|prompt]]<br />
* [[INCLAN: protocol|protocol]]<br />
* [[INCLAN: timing|timing]]<br />
</div><br />
<br />
== Expressions and functions ==<br />
<br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: Expressions|Expressions]]<br />
* [[INCLAN: intrinsics|Intrinsic functions]]<br />
</div><br />
<br />
== INCLAN Graphics ==<br />
<br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: Graphics|Introduction]]<br />
</div><br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN Graphics: plot arc|plot arc]]<br />
* [[INCLAN Graphics: plot caro|plot caro]]<br />
* [[INCLAN Graphics: plot clip|plot clip]]<br />
* [[INCLAN Graphics: plot close|plot close]]<br />
* [[INCLAN Graphics: plot comment|plot comment]]<br />
* [[INCLAN Graphics: plot cross|plot cross]]<br />
* [[INCLAN Graphics: plot curve|plot curve]]<br />
* [[INCLAN Graphics: plot dot|plot dot]]<br />
* [[INCLAN Graphics: plot errorbar|plot errorbar]]<br />
* [[INCLAN Graphics: plot file|plot file]]<br />
* [[INCLAN Graphics: plot fit|plot fit]]<br />
* [[INCLAN Graphics: plot frame|plot frame]]<br />
* [[INCLAN Graphics: plot function|plot function]]<br />
* [[INCLAN Graphics: plot label|plot label]]<br />
* [[INCLAN Graphics: plot layout|plot layout]]<br />
* [[INCLAN Graphics: plot line|plot line]]<br />
* [[INCLAN Graphics: plot plus|plot plus]]<br />
* [[INCLAN Graphics: plot polygon|plot polygon]]<br />
* [[INCLAN Graphics: plot ps|plot ps]]<br />
* [[INCLAN Graphics: plot rectangle|plot rectangle]]<br />
* [[INCLAN Graphics: plot scale|plot scale]]<br />
* [[INCLAN Graphics: plot set|plot set]]<br />
* [[INCLAN Graphics: plot shape|plot shape]]<br />
* [[INCLAN Graphics: plot spline|plot spline]]<br />
* [[INCLAN Graphics: plot square|plot square]]<br />
* [[INCLAN Graphics: plot text|plot text]]<br />
* [[INCLAN Graphics: plot triangle|plot triangle]]<br />
* [[INCLAN Graphics: plot write|plot write]]<br />
</div><br />
<br />
== INCLAN Plot Parameters ==<br />
<br />
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"><br />
* [[INCLAN: align|align]]<br />
* [[INCLAN: angle|angle]]<br />
* [[INCLAN: autoscale|autoscale]]<br />
* [[INCLAN: border|border]]<br />
* [[INCLAN: color|color]]<br />
* [[INCLAN: dash|dash]]<br />
* [[INCLAN: fill|fill]]<br />
* [[INCLAN: font|font]]<br />
* [[INCLAN: linewidth|linewidth]]<br />
* [[INCLAN: marksize|marksize]]<br />
* [[INCLAN: mode|mode]]<br />
* [[INCLAN: rotate|rotate]]<br />
* [[INCLAN: textsize|textsize]]<br />
* [[INCLAN: weight|weight]]<br />
* [[INCLAN: x0, y0, x1, y1|x0, y0, x1, y1]]<br />
* [[INCLAN: X0, Y0, X1, Y1|X0, Y0, X1, Y1]]<br />
<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9955CYANA courses2026-01-20T08:29:07Z<p>Guentert: </p>
<hr />
<div>== Upcoming courses ==<br />
<br />
* [https://embo2026.bnmrz.org/ EMBO Practical Course: Structural dynamics, interactions and function of biological macromolecules by NMR], Munich, Germany, July 24-31, 2026<br />
<br />
== Past courses ==<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-ai-perspective Biomolecular NMR: Advanced Tools, AI perspective. Advanced hands-on PhD course], Gothenburg University, Sweden, September 29-October 3, 2025 <br />
<br />
* [https://meetings.embo.org/event/24-nmr EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Grenoble, France, August 30-September 6, 2024<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-machine-learning Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course], Gothenburg University, Sweden, September 26-30, 2022 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Biozentrum Basel, Switzerland, August 5-12, 2022<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9954CYANA courses2026-01-19T21:10:15Z<p>Guentert: </p>
<hr />
<div>== Upcoming courses ==<br />
<br />
* [https://embo2026.bnmrz.org/ EMBO Practical Course: Structural dynamics, interactions and function of biological macromolecules by NMR], Munich, Germany, July 24-31, 2026<br />
<br />
== Past courses ==<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-ai-perspective Biomolecular NMR: Advanced Tools, AI perspective. Advanced hands-on PhD course], Gothenburg University, Sweden, September 29-October 3, 2025 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Grenoble, France, August 30-September 6, 2024<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-machine-learning Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course], Gothenburg University, Sweden, September 26-30, 2022 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Biozentrum Basel, Switzerland, August 5-12, 2022<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9953CYANA courses2026-01-19T21:06:47Z<p>Guentert: </p>
<hr />
<div>== Upcoming courses ==<br />
<br />
* [https://embo2026.bnmrz.org/ EMBO Practical Course: Structural dynamics, interactions and function of biological macromolecules by NMR], Munich, Germany, July 24-31, 2026<br />
<br />
== Past courses ==<br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Grenoble, France, August 30-September 6, 2024<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-machine-learning Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course], Gothenburg University, Sweden, September 26-30, 2022 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Biozentrum Basel, Switzerland, August 5-12, 2022<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=Atom_selection&diff=9952Atom selection2025-12-28T09:40:24Z<p>Guentert: /* Examples */</p>
<hr />
<div>== Volatile and temporary selections ==<br />
<br />
Selections can either be volatile, i.e. be used temporarily for the current command, or persistent, i.e. be used for the following commands. Persistent selections are made with the commands [[CYANA Command: atoms select|atoms select]], [[CYANA Command: angles select|angles select]], [[CYANA Command: distances select|distances select]], [[CYANA Command: peaks select|peaks select]], [[CYANA Command: couplings select|couplings select]], [[CYANA Command: rdc select|rdc select]], [[CYANA Command: pcs select|pcs select]], and [[CYANA Command: structures select|structures select]]. Selections made by other commands are always volatile. <br />
<br />
== General form ==<br />
<br />
Atom selections are enclosed in double quotes and have the following general form:<br />
<br />
<br />
:'''"[''[[#Operators|operator]]''] {''atom''} [''residue''] {''[[#Conditions|condition]]''} {''operator'' {''atom''} [''residue''] {''condition''}}"'''<br />
<br />
<br />
Items in square brackets are optional and items in curly braces can occur zero or more times. <br />
<br />
An atom selection can have the following elements:<br />
<br />
;''operator'': An operator to combine the selection that follows it with the previous selection<br />
;''atom'': An atom name, possibly containing wildcards ("?" or "*" replace exactly one or any number of characters, respectively)<br />
;~''atom'': An atom name, possibly containing wildcards, as in the residue library, i.e. before a possible renaming with the library rename command<br />
;&''atomtype'': An atom type, possibly containing wildcards, as given in the residue library<br />
;''residue'': A [[#Residue selection|residue selection]], as explained below<br />
;''condition'': An additional [[#condition|condition]], as explained below<br />
<br />
== Special atom names ==<br />
<br />
The following special atom names can be used to select groups of atoms:<br />
<br />
;AMIDE: nitrogen atoms and hydrogen and pseudo atoms connected to nitrogens <br />
;ASSIGNED: atoms with assigned chemical shift values (in the first chemical shift list)<br />
;BACKBONE: main chain atoms (in proteins: N, CA, C)<br />
;BB: atoms whose position does not depend on side-chain torsion angles (in proteins: N, H, CA, HA, CB, C, O)<br />
;CARBON: carbon atoms<br />
;CBOUND: atoms covalently bound to carbon atoms<br />
;HBOUND: atoms covalently bound to hydrogen atoms<br />
;HEAVY: all atoms except hydrogen or pseudo atoms<br />
;HYDROGEN: hydrogen atoms<br />
;HYDROXYL: oxygen atoms and hydrogen and pseudo atoms connected to oxygens <br />
;METHINE: methine (CH1) groups, including the carbon and the hydrogen atom<br />
;METHYL: methyl (CH3) groups, including the carbon atom, three hydrogen atoms and the pseudo atom. In the case of isopropyl groups, e.g. in valine and leucine, the pseudo atom that represents both methyl groups is also selected.<br />
;METHYLENE: methylene (CH2) groups, including for each methylene group the carbon atom, two hydrogen atoms and the pseudo atom<br />
;NBOUND: atoms covalently bound to nitrogen atoms<br />
;NH3: NH3 groups, including for each NH3 group the nitrogen atom, three hydrogen atoms and the pseudo atom <br />
;NITROGEN: nitrogen atoms<br />
;OBOUND: atoms covalently bound to oxygen atoms<br />
;OXYGEN: oxygen atoms<br />
;PBOUND: atoms covalently bound to phosphorus atoms<br />
;PHOSPHOR: phosphorus atoms<br />
;PSEUDO: pseudo atoms<br />
;RENAMED: atoms for which an external name is defined<br />
;SBOUND: atoms covalently bound to sulfur atoms<br />
;SELBOUND: atoms bound to a selected atom<br />
;SELECTED: already selected atoms<br />
;SULFUR: sulfur atoms<br />
;WITHCOORD: atoms for which Cartesian coordinates are present<br />
<br />
== Residue selection ==<br />
<br />
A residue selection consists of one or several of the following elements:<br />
<br />
;@''name'': a residue name, possibly containing wildcards<br />
;@~''name'': a residue name, possibly containing wildcards, as in the residue library, i.e. before a possible renaming with the library rename command<br />
;@FIRST: the first residue<br />
;@LAST: the last residue<br />
;@first: the first residue of every fragment with contiguous resi¬due numbers<br />
;@last: the last residue of every fragment with contiguous resi¬due numbers<br />
;range: a residue number range<br />
<br />
<br />
Ranges of numbers in selections, e.g. residue number ranges, can be specified in one of the following ways:<br />
<br />
;''m'': a number<br />
;''m''..''n'': a range of numbers<br />
;''m''-''n'': alternative format for a range of numbers (only for ''n'' ≥ 0)<br />
;''m''..: from number ''m'' onwards<br />
;''m''-: from number ''m'' onwards; alternative format<br />
;..''n'': from the first up to number ''n''.<br />
<br />
== Operators ==<br />
<br />
Atom selections can be combined using the following operators:<br />
<br />
;=: atoms in the new set (default)<br />
;!: atoms not in the new set<br />
;+: atoms in the current set or in the new set<br />
;–: atoms in the current set, but not in the new set<br />
;/: atoms in the current set and in the new set<br />
<br />
Operators are always evaluated from left to right. The current atom set is the set of atoms defined by what precedes the operator. The new atom set is the set of atoms defined by what follows the operator. An empty atom selection selects all atoms.<br />
<br />
== Conditions ==<br />
<br />
Additional conditions can be applied to atom selections:<br />
<br />
;random=''p'': Select randomly only a fraction ''p'' of all atoms that would normally be selected. <br />
<br />
;shift=''shiftmin''..''shiftmax'': Select only atoms with an assigned chemical shift value between ''shiftmin'' and ''shiftmax'' ppm in the first chemical shift list.<br />
<br />
;tolerance=''tolmin''..''tolmax'': Select only assigned atoms with a chemical shift tolerance value between ''tolmin'' and ''tolmax'' ppm in the first chemical shift list.<br />
<br />
== Examples ==<br />
<br />
All atoms called HA:<br />
<br />
HA<br />
<br />
Atom HA of residue 5:<br />
<br />
"HA 5"<br />
<br />
All atoms called HA or whose name starts with HB: <br />
<br />
"HA HB*"<br />
<br />
Atoms HA in ALA residues with numbers 10-20:<br />
<br />
"HA @ALA 10..20"<br />
<br />
Atoms HA in ALA except in residues with numbers 10-20:<br />
<br />
"HA @ALA - 10..20"<br />
<br />
All atoms N, CA, C, and the side-chain heavy atoms of residues 15 and 17:<br />
<br />
"N CA C + 15 17 - H* Q*" <br />
<br />
The previous selection except for atoms whose name starts with C:<br />
<br />
"- C*"<br />
<br />
Atoms in the previous selection that are bound to carbon atoms'<br />
<br />
"/ CBOUND"<br />
<br />
Assigned carbon atoms:<br />
<br />
"CARBON / ASSIGNED"<br />
<br />
Hydrogens and pseudo atoms, except hydroxyls and side-chain amides, whose atom type either starts with H_ or is PSEUD:<br />
<br />
"H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" <br />
<br />
The commands [[CYANA Command: atoms list|atoms list]] and [[CYANA Command: atoms select|atoms select]] (with the parameter info=full) can be used to check atom selections.</div>Guenterthttps://cyana.org/w/index.php?title=Using_INCLAN_variables&diff=9945Using INCLAN variables2025-12-15T15:58:51Z<p>Guentert: </p>
<hr />
<div>In INCLAN, string variables can be used in a similar way as in a Unix shell:<br />
<br />
cyana> name:=Cyana<br />
cyana> print "My name is $name."<br />
My name is Cyana.<br />
<br />
The operator “:=” assigns a string (“Cyana”) to a variable (“name”). $''variable'' substitutes the value of a variable into the command line. In addition, variables with numeric values can be used in expressions in the same way as in Fortran or other programming languages:<br />
<br />
cyana> x=7<br />
cyana> y=5*x<br />
cyana> z=sqrt(y-10.0)<br />
cyana> show x y z<br />
x = 7<br />
y = 35<br />
z = 5.0<br />
<br />
(The INCLAN command [[INCLAN: show|'''show''']] displays the values of variables.) Here a different assignment sign, “=” instead of “:=”, was used. Assignments with “=” have the meaning: “Evaluate the expression on the right hand side and assign the result value to the variable on the left hand side.” Note the difference to a string assignment with “:=”:<br />
<br />
cyana> y:=5*x<br />
cyana> show y<br />
y = 5*x<br />
cyana> y=5*x<br />
cyana> show y<br />
y = 35<br />
Expressions formed according to the rules of Fortran-77 may contain integer, real and complex numbers, logicals (Boolean values), and character strings. Within expressions, character strings must be enclosed in single quotes:<br />
<br />
cyana> s:=cyana<br />
cyana> l=lenstr(s)<br />
*** ERROR: Illegal expression "lenstr(s)".<br />
<br />
This is an error because the variable s does not contain a quoted string (lenstr is an INCLAN function that returns the length of a string, i. e. the index of its last non-blank character). The correct use of simple, unquoted strings in an expression is:<br />
<br />
cyana> l=lenstr('$s')<br />
cyana> show l<br />
l = 5<br />
<br />
Single quotes do not inhibit variable substitutions.</div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9944Tutorials2025-12-15T15:57:43Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-250921Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (21.09.2025)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Frequently_Asked_Questions&diff=9943Frequently Asked Questions2025-09-30T05:30:50Z<p>Guentert: /* General */</p>
<hr />
<div>== General ==<br />
# [https://www.las.jp/english/cyana.html How can I get CYANA?]<br />
# [[Benchmarks|How fast is CYANA?]]<br />
<!--# [[Users Map|Where are the CYANA users?]]--><br />
<br />
== CYANA releases ==<br />
# [[New Features in CYANA 3.0|What is new in CYANA 3.0?]]<br />
# [[New Features in CYANA 2.1|What is new in CYANA 2.1?]]<br />
# [[New Features in CYANA 2.0|What is new in CYANA 2.0?]]<br />
# [[How to extend the licensing period for CYANA 2.1?]]<br />
<br />
== CYANA Features ==<br />
# [[Standard CYANA nomenclature|What is the standard CYANA nomenclature for amino acids and nucleotides?]]<br />
# [[CYANA Commands|Which commands are available in CYANA 3.0?]]<br />
# [[CYANA System Functions|Which system functions are available in CYANA 3.0?]]</div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-250921Demo.tgz&diff=9942File:Cyana-3.98.15bin-250921Demo.tgz2025-09-21T15:01:31Z<p>Guentert: CYANA 3.98.15 demo version</p>
<hr />
<div>== Summary ==<br />
CYANA 3.98.15 demo version</div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9941Tutorials2025-09-21T14:53:22Z<p>Guentert: /* Downloads */</p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-250921Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (21.09.2025)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]https://cyana.org/w/index.php?title=Tutorials&action=edit<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-250806Demo.tgz&diff=9940File:Cyana-3.98.15bin-250806Demo.tgz2025-08-06T17:09:57Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9939Tutorials2025-08-06T17:07:38Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-250806Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (06.08.2025)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]https://cyana.org/w/index.php?title=Tutorials&action=edit<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Defining_non-standard_residues&diff=9938Defining non-standard residues2024-11-21T16:08:13Z<p>Guentert: </p>
<hr />
<div>Non-standard residue types can be added to the residue library as additional<br />
entries. The procedure to add a new residue type to the library is<br />
as follows (see also the description of the format of<br />
the [[residue library file]]):<br />
<br />
Create Cartesian coordinates for all atoms of the residue, for example<br />
with a molecular graphics program or using the attach and insert commands<br />
of the program [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/COFIMA COFIMA]. <br />
Bond lengths, bond angles, and chiralities<br />
of this structure must be correct but the conformation, i.e. the values<br />
of the dihedral angles, does not matter. The coordinates of the overlap atoms<br />
at the beginning and at the end of the residue (for example N, CA,<br />
and C in amino acids) will also be needed. If the new residue type results<br />
from a slight modification of an existing residue type, it is usually most<br />
convenient to start from the coordinates of the existing residue type and<br />
to modify them. Order the atoms such that their order is compatible with<br />
the tree structure of dihedral angles that will be defined, i.e. such that the<br />
following two rules are fulfilled:<br />
<br />
* A change of a dihedral angle must not affect the positions of the first, second, third, or fourth atom in any preceding dihedral angle definition.<br />
<br />
* The set of atoms whose positions will be affected by a change of a dihedral angle consists of all atoms following the third atom in the dihedral angle definition up to the fifth (last) atom in the dihedral angle definition (or the end of the main chain for backbone dihedral angles).<br />
<br />
Convert the coordinates into the format of the library file (for example<br />
with a text editor). Add atom types, connectivities, and the information<br />
about diastereotopic partners. Add the dihedral angle definitions to the<br />
new entry. These two steps are best done using the library format in<br />
which connectivities and angle definitions are given by atom names rather<br />
than by atom numbers (see the option '''names''' of the [[CYANA Command: write lib|'''write lib''']] command).<br />
Make sure that the header line starting with RESIDUE is correct.<br />
Add the new entry to (a copy of) the residue library file. Test the new entry,<br />
for example in the following way:<br />
<br />
* Create a sequence file that contains the new residue type, preferably in the interior of the chain, i.e. not as the first or last residue.<br />
* Using this sequence file and the new residue library in the program CYANA, create angle and coordinate files for a conformer with randomized dihedral angles.<br />
* Start CYANA again (with the same sequence and residue library file), read the previously produced coordinate file, and write again angle and coordinate files without making any minimization.<br />
* Check whether the angles and coordinates produced by the second run of CYANA coincide closely with those from the first run. If this test fails, then there is probably a format error in the new library entry or the ordering rules listed above are violated. However, this test does not detect errors in nomenclature, connectivities, or pointers to pseudo atoms.<br />
* Check the coordinates produced by CYANA on a molecular graphics system, for example with the program MOLMOL (Koradi et al., 1996).<br />
<br />
== See also ==<br />
<br />
* [[Residue library file]]</div>Guenterthttps://cyana.org/w/index.php?title=Frequently_Asked_Questions&diff=9937Frequently Asked Questions2024-11-03T22:38:13Z<p>Guentert: </p>
<hr />
<div>== General ==<br />
# [http://www.las.jp/english/products/cyana.html How can I get CYANA?]<br />
# [[Benchmarks|How fast is CYANA?]]<br />
<!--# [[Users Map|Where are the CYANA users?]]--><br />
== CYANA releases ==<br />
# [[New Features in CYANA 3.0|What is new in CYANA 3.0?]]<br />
# [[New Features in CYANA 2.1|What is new in CYANA 2.1?]]<br />
# [[New Features in CYANA 2.0|What is new in CYANA 2.0?]]<br />
# [[How to extend the licensing period for CYANA 2.1?]]<br />
<br />
== CYANA Features ==<br />
# [[Standard CYANA nomenclature|What is the standard CYANA nomenclature for amino acids and nucleotides?]]<br />
# [[CYANA Commands|Which commands are available in CYANA 3.0?]]<br />
# [[CYANA System Functions|Which system functions are available in CYANA 3.0?]]</div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9936Tutorials2024-09-20T09:34:24Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240809Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (09.08.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9933Tutorials2024-09-09T10:06:39Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240909Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (09.09.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-240809Demo.tgz&diff=9932File:Cyana-3.98.15bin-240809Demo.tgz2024-08-09T02:31:53Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9931Tutorials2024-08-09T02:30:02Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240809Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (09.08.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9930Tutorials2024-04-10T14:44:08Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240312Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (12.03.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)<br />
* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9929Tutorials2024-04-10T14:43:23Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240312Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (12.03.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biological macromolecules by NMR ===<br />
<br />
Grenoble, 30 August – 6 September 2024 ([https://meetings.embo.org/event/24-nmr course homepage])<br />
<br />
<!--<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-240312Demo.tgz&diff=9928File:Cyana-3.98.15bin-240312Demo.tgz2024-03-12T22:54:48Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9927Tutorials2024-03-12T22:53:26Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-240312Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (12.03.2024)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=CYANA_Publications&diff=9926CYANA Publications2024-02-12T13:36:18Z<p>Guentert: /* All CYANA-related publications */</p>
<hr />
<div>== The key publications on CYANA ==<br />
<br />
* Klukowski, P., Riek, R. & Güntert, P. Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Klukowski22-ARTINA.pdf .] [http://doi.org/10.1038/s41467-022-33879-5 Nat. Commun. 13, 6151 (2022)]<br />
<br />
* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]<br />
<br />
* Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt12-AssignmentAlgorithm.pdf .] [http://dx.doi.org/10.1021/ja305091n J. Am. Chem. Soc. 134, 12817–12829 (2012)]<br />
<br />
* Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]<br />
<br />
* Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. [http://dx.doi.org/10.1006/jmbi.1997.1284 J. Mol. Biol. 273, 283–298 (1997)] <br />
<br />
* Güntert, P., Braun, W. & Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. [http://dx.doi.org/10.1016/0022-2836(91)90754-T J. Mol. Biol. 217, 517–530 (1991)]<br />
<br />
== All CYANA-related publications ==<br />
<br />
In reverse chronological order.<br />
<br />
* Klukowski, P., Riek, R. & Güntert, P. Time-optimized protein NMR assignment with an integrative deep learning approach using AlphaFold and chemical shift prediction[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Klukowski23-ARTINAAlphaFold.pdf .] [http://doi.org/10.1126/sciadv.adi9323 Sci. Adv. 9, eadi9323 (2023)]<br />
<br />
* Wetton, H, Klukowski, P., Riek, R. & Güntert, P. Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Wetton23-ShiftTransfer.pdf .] [http://doi.org/10.3389/fmolb.2023.1244029 Front. Mol. Biosci. 10, 1244029 (2023)]<br />
<br />
* Kuschert, S., Stroet, M., Chin, Y. K. Y., Conibear, A. C., Jia, X., Lee, T., Bartling, C. R. O., Strømgaard, K., Güntert, P., Rosengren, K. J., Mark, A. E. & Mobli, M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Kuschert23-ncAAs.pdf .] [https://doi.org/10.5194/mr-4-57-2023 Magn. Reson. 4, 57-72 (2023)]<br />
<br />
* Klukowski, P., Riek, R. & Güntert, P. NMRtist: an online platform for automated biomolecular NMR spectra analysis[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Klukowski23-NMRtist.pdf .] [http://doi.org/10.1093/bioinformatics/btad066 Bioinformatics 39, btad066 (2023)]<br />
<br />
* Klukowski, P., Riek, R. & Güntert, P. Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Klukowski22-ARTINA.pdf .] [http://doi.org/10.1038/s41467-022-33879-5 Nat. Commun. 13, 6151 (2022)]<br />
<br />
* Cucuzza, S., Güntert, P., Plückthun, A. & Zerbe, O. An automated iterative approach for protein structure refinement using pseudocontact shifts[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Cucuzza21-PCS.pdf .] [http://doi.org/10.1007/s10858-021-00376-8 J. Biomol. NMR 75, 319-334 (2021)]<br />
<br />
* Pritišanac, I., Alderson, T. R. & Güntert, P. Automated assignment of methyl NMR spectra from large proteins. Prog. NMR Spectrosc. 118–119, 54–73 (2020)<br />
<br />
* Pritišanac, I., Würz, J. M., Alderson, T. R., Güntert, P. Automatic structure-based NMR methyl resonance assignment in large proteins. Nat. Commun. 10, 4922 (2019)<br />
<br />
* Pritišanac, I., Würz, J. M. & Güntert, P. Fully automated assignment of methyl resonances of a 36 kDa protein dimer from sparse NOESY data. J. Phys Conf. Ser. 1036, 012008 (2018)<br />
<br />
* Würz, J. M., Kazemi, S., Schmidt, E., Bagaria, A. & Güntert, P. NMR-based automated protein structure determination[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Wuerz17-ReviewArchBiochemBiophys.pdf .] [http://doi.org/10.1016/j.abb.2017.02.011 Arch. Biochem. Biophys. 628, 24-32 (2017)] <br />
<br />
* Würz, J. M. & Güntert, P. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Wuerz17-CYPICK.pdf .] [http://dx.doi.org/10.1007/s10858-016-0084-3 J. Biomol. NMR. 67, 63–76 (2017)]<br />
<br />
* Kazemi, S., Würz, J. M., Schmidt, E., Bagaria, A. & Güntert, P. Automated structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Kazemi17-ModMagnResonReview.pdf .] In [http://doi.org/10.1007/978-3-319-28275-6_32-1 Modern Magnetic Resonance 2nd Ed. (Ed. G. Webb), Springer.]<br />
<br />
* Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Maden15-Cylib.pdf .] [http://dx.doi.org/10.1007/s10858-015-9959-y J. Biomol. NMR 63, 21-37 (2015)]<br />
<br />
* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]<br />
<br />
* Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Buchner15-NoeassignEvaluation.pdf .] [http://dx.doi.org/10.1007/s10858-015-9921-z J. Biomol. NMR 62, 81–95 (2015)]<br />
<br />
* Buchner, L. & Güntert, P. Increased reliability of NMR protein structures by consensus structure bundles[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Buchner15-ConsensusBundles.pdf .] [http://dx.doi.org/10.1016/j.str.2014.11.014 Structure 23, 425–434 (2015)]<br />
<br />
* Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt15-AutomatedNMR.pdf .] [http://dx.doi.org/10.1007/978-1-4939-2230-7_16 Meth. Mol. Biol. 1261, 303–329 (2015)]<br />
<br />
* Lin, Y. J., Ikeya, T., Kirchner, D. K. & Güntert, P. Influence of incomplete NOESY peaks of the interface residues on structure determinations of homodimeric proteins[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Lin14-Homodimer.pdf .] [http://dx.doi.org/10.1002/jccs.201400095 J. Chin. Chem. Soc. 61, 1297-1306 (2014)]<br />
<br />
* Krähenbühl, B., El Bakkali, I., Schmidt, E., Güntert, P. & Wider, G. Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Kraehenbuehl14-APSYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-014-9829-z J. Biomol. NMR 59, 87-93 (2014)]<br />
<br />
* Orts, J., Vögeli, B., Riek, R. & Güntert, P. Stereospecific assignments in proteins using exact NOEs[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Orts13-eNOEStereoassignment.pdf .] [http://dx.doi.org/10.1007/s10858-013-9780-4 J. Biomol. NMR 57, 211-218 (2013)]<br />
<br />
* Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Aeschbacher13-RNAFLYA.pdf .] [http://dx.doi.org/10.1093/nar/gkt665 Nucl. Acids Res. 41, e172 (2013)]<br />
<br />
* Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt13-NOESYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9779-x J. Biomol. NMR 57, 193-204 (2013)]<br />
<br />
* Schmidt, E., Gath, J., Habenstein, B., Ravotti, F., Székely, K., Huber, M., Buchner, L., Böckmann, A., Meier, B. H. & Güntert, P. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt13-SolidStateFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9742-x J. Biomol. NMR 56, 243–254 (2013)]<br />
<br />
* Buchner, L., Schmidt, E. & Güntert, P. Peakmatch: a simple and robust method for peak list matching[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Buchner13-Peakmatch.pdf .] [http://dx.doi.org/10.1007/s10858-013-9708-z J. Biomol. NMR. 55, 267–277 (2013)]<br />
<br />
* Vögeli, B., Güntert, P., & Riek, R. Multiple-state ensemble structure determination from eNOE spectroscopy[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Voegeli13-eNOEMultipleStates.pdf .] [http://dx.doi.org/10.1080/00268976.2012.728257 Mol. Phys. 111, 437–454 (2013)]<br />
<br />
* Vögeli, B., Kazemi, S., Güntert, P. & Riek, R. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Voegeli12-eNOEsMotion.pdf .] [http://dx.doi.org/10.1038/nsmb.2355 Nature Struct. Mol. Biol. 19, 1053–1057 (2012)]<br />
<br />
* Gottstein, D., Kirchner, D. K. & Güntert, P. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Gottstein12-REGMEAN.pdf .] [http://dx.doi.org/10.1007/s10858-012-9615-8 J. Biomol. NMR 52, 351-364 (2012)]<br />
<br />
* Rosato, A., Aramini, J. M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J. F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Güntert, P., He. Y. F., Herrmann, T., Huang, Y. J., Jaravine, V., Jonker, H. R. A., Kennedy, M. A., Lange, O. F., Liu, G., Malliavin, T. E., Mani, R., Mao, B., Montelione, G. T., Nilges, M., Rossi, P., van der Schot, G., Schwalbe, H., Szyperski, T., Vendruscolo, M., Vernon, R., Vranken, W. F., de Vries, S., Vuister, G. W., Wu, B. Yang, Y. & Bonvin, A. M. J. J. Blind testing of routine, fully automated determination of protein structures from NMR data[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Rosato12-CASDNMR.pdf .] [http://dx.doi.org/10.1016/j.str.2012.01.002 Structure 20, 227–236 (2012)] <br />
<br />
* Güntert, P. Calculation of structures from NMR restraints. In [http://dx.doi.org/10.1002/9781119972006.ch5 Protein NMR Spectroscopy: Practical Techniques and Applications (Eds. G. Roberts & L.-Y. Lian), Wiley, New York, pp. 159–192 (2011).]<br />
<br />
* Kirchner, D. K. & Güntert, P. Objective identification of residue ranges for the superposition of protein structures. [http://dx.doi.org/10.1186/1471-2105-12-170 BMC Bioinformatics 12, 170 (2011)]<br />
<br />
* Ikeya, T., Jee. J. G., Shigemitsu, Y., Hamatsu, J., Mishima, M., Ito, Y., Kainosho, M. & Güntert, P. Exclusively NOESY-based automated NMR assignment and structure determination of proteins. [http://dx.doi.org/10.1007/s10858-011-9502-8 J. Biomol. NMR. 50, 137–146 (2011)]<br />
<br />
* Güntert, P. Automated structure determination from NMR spectra. In Advances in Biomedical Spectroscopy. Volume 3: Biomolecular NMR Spectroscopy (Eds. A. Dingley & S. Pascal), IOS Press, Amsterdam, pp. 338–365 (2011)<br />
<br />
* Hefke, F., Bagaria, A., Reckel, S., Ullrich, S.J., Dötsch, V., Glaubitz, C. & Güntert P. Optimization of amino acid type-specific <sup>13</sup>C and <sup>15</sup>N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. [http://dx.doi.org/10.1007/s10858-010-9462-4 J. Biomol. NMR 49, 75-84 (2011)] <br />
<br />
* Kainosho, M. & Güntert, P. SAIL – Stereo-array isotope labeling. [http://dx.doi.org/10.1017/S0033583510000016 Q. Rev. Biophys. 42, 247-300 (2009)]<br />
<br />
* Ikeya, T., Takeda, M., Yoshida, H., Terauchi, T., Jee, J., Kainosho, M. & Güntert, P. Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. [http://dx.doi.org/10.1007/s10858-009-9339-6 J. Biomol. NMR. 44, 261-272 (2009)]<br />
<br />
* Güntert, P. Automated structure determination from NMR Spectra. [http://dx.doi.org/10.1007/s00249-008-0367-z Eur. Biophys. J. 38, 129-143 (2009)] <br />
<br />
* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://dx.doi.org/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112–13122 (2006)]<br />
<br />
* Scott, A., López-Méndez, B. & Güntert, P. Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. [http://dx.doi.org/10.1002/mrc.1813 Magn. Reson. Chem. 44, S83–S88 (2006)]<br />
<br />
* Ikeya, T., Terauchi, T., Güntert, P., Kainosho, M. Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA. [http://dx.doi.org/10.1002/mrc.1815 Magn. Reson. Chem. 44, S152–S157 (2006)]<br />
<br />
* Güntert, P. Automated NMR structure calculation with CYANA. [http://dx.doi.org/10.1385/1-59259-809-9:353 Meth. Mol. Biol. 278, 353–378 (2004)]<br />
<br />
* Güntert, P. Automated NMR protein structure calculation. [http://dx.doi.org/10.1016/S0079-6565(03)00021-9 Prog. NMR Spectrosc. 43, 105–125 (2003)]<br />
<br />
* Jee, J. G. & Güntert, P. Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. [http://dx.doi.org/10.1023/A:1026122726574 J. Struct. Funct. Genom. 4, 179–189 (2003)]<br />
<br />
* Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. [http://dx.doi.org/10.1023/A:1021614115432 J. Biomol. NMR 24, 171–189 (2002)]<br />
<br />
* Güntert, P. Structure calculation using automated techniques. Meth. Principles Med. Chem. 16, 39–66 (2002).<br />
<br />
* Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]<br />
<br />
* Güntert, P. & Wüthrich, K. Sampling of conformation space in torsion angle dynamics calculations. [http://dx.doi.org/10.1016/S0010-4655(01)00204-1 Comp. Phys. Commun. 138, 155–169 (2001)]<br />
<br />
* Güntert, P., Billeter, M., Ohlenschläger, O., Brown, L. & Wüthrich, K. Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND. [http://dx.doi.org/10.1023/A:1008391403193 J. Biomol. NMR 12, 543–548 (1998)]<br />
<br />
* Banci, L., Bertini, I., Cremonini, M. A., Gori-Savellini, G., Luchinat, C., Wüthrich, K. & Güntert, P. PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics.[http://dx.doi.org/10.1023/A:1008388614638 J. Biomol. NMR 12, 553–557 (1998)]<br />
<br />
* Güntert, P. Structure calculation of biological macromolecules from NMR data. [http://journals.cambridge.org/action/displayAbstract?aid=26555 Q. Rev. Biophys. 31, 145–237 (1998)]<br />
<br />
* Mumenthaler, C., Güntert, P., Braun, W. & Wüthrich, K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. [http://dx.doi.org/10.1023/A:1018383106236 J. Biomol. NMR 10, 351–362 (1997)]<br />
<br />
* Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. [http://dx.doi.org/10.1006/jmbi.1997.1284 J. Mol. Biol. 273, 283–298 (1997)] <br />
<br />
* Güntert, P. Calculating protein structures from NMR data. Meth. Mol. Biol. 60, 157–194 (1997).<br />
<br />
* Güntert, P. Computer–supported protein structure determination by NMR. In Statistical mechanics, protein structure and protein–substrate interactions (Ed. S. Doniach), Plenum Press, New York, pp. 197–207 (1994).<br />
<br />
* Güntert, P., Berndt, K. D. & Wüthrich, K. The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. [http://dx.doi.org/10.1007/BF00174613 J. Biomol. NMR 3, 601–606 (1993)]<br />
<br />
* Güntert, P. Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz, Ph.D. Thesis ETH 10135 [http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10135 (1993)]<br />
<br />
* Güntert, P. & Wüthrich, K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. [http://dx.doi.org/10.1007/BF02192866 J. Biomol. NMR 1, 447–456 (1991)]<br />
<br />
* Güntert, P., Braun, W. & Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. [http://dx.doi.org/10.1016/0022-2836(91)90754-T J. Mol. Biol. 217, 517–530 (1991)]<br />
<br />
* Güntert, P., Qian, Y. Q., Otting, G., Müller, M., Gehring, W. J. & Wüthrich K. Structure determination of the Antp(C39S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. [http://dx.doi.org/10.1016/0022-2836(91)90755-U J. Mol. Biol. 217, 531–540 (1991)]<br />
<br />
* Güntert, P., Braun, W., Billeter, M. & Wüthrich, K. Automated stereospecific <sup>1</sup>H NMR assignments and their impact on the precision of protein structure determinations in solution. [http://dx.doi.org/10.1021/ja00193a036 J. Am. Chem. Soc. 111, 3997–4004 (1989)]<br />
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== Further publications ==<br />
<br />
[http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Publications_of_P._G%C3%BCntert All Publications of P. Güntert]</div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-230824Demo.tgz&diff=9925File:Cyana-3.98.15bin-230824Demo.tgz2023-08-24T20:39:31Z<p>Guentert: </p>
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<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9924Tutorials2023-08-24T20:22:22Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-230824Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (01.01.2023)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=New_Features_in_CYANA_3.0&diff=9923New Features in CYANA 3.02023-03-24T09:55:50Z<p>Guentert: </p>
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<div>CYANA 3.0 is a major new release.</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9922CYANA courses2023-03-16T10:34:55Z<p>Guentert: </p>
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<div>== Upcoming courses ==<br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Grenoble, France, August 30-September 6, 2024<br />
<br />
== Past courses ==<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-machine-learning Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course], Gothenburg University, Sweden, September 26-30, 2022 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Biozentrum Basel, Switzerland, August 5-12, 2022<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9921CYANA courses2023-03-16T10:22:35Z<p>Guentert: </p>
<hr />
<div>== Upcoming courses ==<br />
<br />
<br />
<br />
== Past courses ==<br />
<br />
* [https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-machine-learning Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course], Gothenburg University, Sweden, September 26-30, 2022 <br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Biozentrum Basel, Switzerland, August 5-12, 2022<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9920CYANA courses2023-03-16T10:19:06Z<p>Guentert: /* Past courses */</p>
<hr />
<div>== Upcoming courses ==<br />
<br />
<br />
<br />
== Past courses ==<br />
<br />
* [https://www.biozentrum.unibas.ch/events/conferences-symposia/embo-practical-course-nmr-2022 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 6-13, 2021<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_courses&diff=9919CYANA courses2023-03-16T10:14:56Z<p>Guentert: </p>
<hr />
<div>== Upcoming courses ==<br />
<br />
<br />
<br />
== Past courses ==<br />
<br />
* [https://www.embo.org/pc21-22 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 6-13, 2021<br />
<br />
* [http://embo2019.bnmrz.org/ EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR], Munich, Germany, July 26 - August 2, 2019<br />
<br />
* [http://events.embo.org/coming-soon/index.php?EventID=pc17-37 EMBO Practical Course on Structure, Dynamics and Function of Biological Macromolecules by NMR], Basel, Switzerland, August 5-12, 2017<br />
<br />
* [http://www.icmrbs2016.org/conference.html 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2016), Satellite workshop on “Next generation computational methods for NMR structure determination”], Kyoto, Japan, August 24, 2016<br />
<br />
* 2nd G-NMR School, Goethe University Frankfurt am Main, Germany, February 29–March 4, 2016<br />
<br />
* [http://www.tifr.res.in/~nmr/TIFR-Kerala-Meeting/ NMR Meets Biology: An Interaction Week], Kerala, India, January 14–19, 2016<br />
<br />
* [http://www.bnmrz.org/index.php?option=com_content&view=article&id=68&Itemid=98 EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], TU München, Germany, July 31-August 7, 2015<br />
<br />
* Biomolecular NMR: A hands-on PhD Course, Swedish NMR Centre, University of Gothenburg, Sweden, October 13–17, 2014<br />
<br />
* [http://www.biozentrum.unibas.ch/embo13_nmr/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Basel, Switzerland, July 20–27, 2013<br />
<br />
* NMR Workshop, Indian Institute of Science, Bangalore, India, March 7–9, 2013<br />
<br />
* Workshop at Institute for Protein Research, Osaka University, Japan, November 12, 2012<br />
<br />
* Recent Advances in High-Resolution NMR Workshop, Hyderabad, India, December 12–17, 2011<br />
<br />
* [http://www.bnmrz.org/embo2011/ EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], München, Germany, July 29–August 5, 2011<br />
<br />
* Advanced course: Protein NMR Structure Calculation and Validation, Vilnius, Lithuania, May 17–19, 2011<br />
<br />
* NMR Structure Determination Courses: From NMR data to protein structure, The Biomolecular NMR Training Center, Vilnius, Lithuania, September 20-24, 2010<br />
<br />
* [http://www.icmrbs2010.org/index.php?option=com_content&task=view&id=41&Itemid=67 ICMRBS 2010 Satellite Meeting: Protein Structure Calculation Workshop], Brisbane Convention & Entertainment Centre, Brisbane, Australia, August 30-31, 2010<br />
<br />
* [http://training.spronknmr.eu/index.php?mact=Workshops,cntnt01,frontend_category_items,0&cntnt01category_id=1&cntnt01returnid=68 e-NMR - Extend-NMR Workshops: NMR structure calculation - GRID applications and integrated tools], The Biomolecular NMR Training Center, Vilnius, Lithuania. Given multiple times. Next course June 7-11, 2010 ([[CYANA structure calculation with automated NOESY assignment (e-NMR - Extend-NMR Workshop)|Practicals]])<br />
<br />
* [http://cwp.embo.org/wpc09-07/ Practical EMBO World Course on Structure and Dynamics of Biomolecules by NMR], Rosario/Argentina, September 21–30, 2009<br />
<br />
* [http://cwp.embo.org/pc09-22/ EMBO Practical Course on Structure, Dynamics and Function of Biomacromolecules by Solution NMR], Bayerisches NMR-Zentrum, Technische Universität München, Garching/Germany, July 27–August 3, 2009<br />
<br />
* [http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/Strukturrechnung_mit_CYANA Praktikum Biophysikalische Chemie], Beilstein-Center, Goethe University Frankfurt am Main, Germany, January 13, 2009<br />
<br />
* [http://bnmrc.pku.edu.cn/embo_2008_nmr/ EMBO World Practical Course on Structure Determination of Biological Macromolecules by Solution NMR], Peking University, Beijing, China, September 8–15, 2008<br />
<br />
* [http://www.chem.umd.edu/courses/bioNMR/ Joint National Institutes of Health and University of Maryland Practical Training Course on Structure Determination of Biological Macromolecules by Solution NMR], National Institutes of Health, Bethesda, Maryland, USA, August 17–21, 2008<br />
<br />
* [http://www.biozentrum.unibas.ch/embo07_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, July 6–13, 2007<br />
<br />
* [http://www.nmrfam.wisc.edu/workshops/2006/ NMRFAM Workshop on NMR Data Collection and Analysis], University of Madison, Wisconsin/USA, June 6–9, 2006<br />
<br />
* [http://www.biozentrum.unibas.ch/embo05_nmr/ EMBO Practical Course on Structure determination of biological macromolecules by solution NMR], Biozentrum, Universität Basel, Basel/Switzerland, September 7–14, 2005<br />
<br />
* NMRFAM Workshop on SAIL Labeling and Automation in NMR Structure Determination, University of Wisconsin-Madison, Wisconsin/USA, October 30, 2004<br />
<br />
* RRR 2004 Workshop, Institute for Protein Research, Osaka University, Osaka/Japan, August 6, 2004<br />
<br />
* [http://www.nanuc.ca/resources/workshop2004.php CYANA @ NANUC 2004 Workshop], Canadian National High Field NMR Centre (NANUC), Edmonton/Canada, June 25/26, 2004<br />
<br />
* Fifth NMR Wakate Meeting, Hakone/Japan, June 6, 2004<br />
<br />
* JASS'03-Winter School on NMR Spectroscopy at the Frontier of Progress in the Life Sciences, Osaka University, Osaka/Japan, January 29, 2004<br />
<br />
* Workshop on Recent Progress in Protein-NMR & Automation, Yonsei University, Seoul/Korea, December 12, 2003<br />
<br />
* [http://www.nmr.sinica.edu.tw/Cours/Workshop20030518-19/ Workshop on High Throughput NMR structure Determination in the Post Genomic Era], Academia Sinica, Taipei/Taiwan, November 1–2, 2003<br />
<br />
* EMBO Practical Course on Structure Determination by NMR, EMBL, Heidelberg/Germany, September 13, 2003<br />
<br />
* RRR Workshop, Yokohama City University, Yokohama/Japan, September 2, 2003<br />
<br />
* Practical Course Multidimensional NMR in Solution - 2002, University of Wollongong, Wollongong/Australia, December 8–13, 2002</div>Guenterthttps://cyana.org/w/index.php?title=CYANA_Command:_distances_modify&diff=9918CYANA Command: distances modify2023-03-01T11:00:33Z<p>Guentert: </p>
<hr />
<div><br />
== Parameters ==<br />
<br />
; pseudoonly <br />
<br />
== Description ==<br />
<br />
Modifies distance restraints. Distance limits with diastereotopic groups are adjusted and/or pseudoatoms are inserted if no stereospecific assignment is available. Unless the option '''pseudoonly''' is set, redundant and meaningless distance restraints are removed, too.<br><br />
This command cannot be used for ambiguous distance restraints.<br><br />
A detailed report of the modifications made is provided if the information level is full ('''info=full'''). A first table reports the modifications made to make distance restraints symmetric under the exchange of diastereotopic partners in order to account for the absence of stereospecific assignments (Güntert et al., 1991a; Güntert et al., 1991b). For example:<br />
<br />
Modifications for floating stereospecific assignments:<br />
Input restraint(s) modified to<br />
Atom(s) A Atom(s) B1-B1 A1-B2 A2-B1 A2-B2 Ai-Bj QA-QB<br />
Upper HA ASP 1 - HD2/3 PRO 2 3.39 3.55<br />
Upper HB2/3 ASP 1 - HD2/3 PRO 2 5.50 5.50 3.89 5.41 5.50 4.97<br />
Upper HB2 PRO 2 - HG2/3 MET 3 5.50 6.38<br />
Upper HD2/3 PRO 2 - QE TYR 19 7.63 8.51<br />
Upper HN MET 3 - HB2/3 MET 3 3.95 3.33 3.83 3.45<br />
Upper HB2/3 MET 3 - QE MET 3 6.53 6.31 6.53<br />
Upper HB2/3 MET 3 - HN THR 4 5.38 5.50 5.50<br />
Upper HB2/3 MET 3 - HA THR 4 4.69 5.54<br />
Upper HG2/3 MET 3 - HN THR 4 4.14 5.01<br />
Upper HG2/3 MET 3 - HB THR 4 5.50 6.38<br />
Upper HG2/3 MET 3 - QB ALA 8 6.53 7.40<br />
Upper HG2/3 MET 3 - QD TYR 9 7.64 8.52<br />
Upper HG2/3 MET 3 - QE TYR 19 7.63 8.51<br />
Upper QE MET 3 - HG2/3 MET 16 5.47 6.35<br />
Upper QG2 THR 4 - HE21/2 GLN 7 6.53 7.3<br />
Upper HN GLU 6 - HG2/3 GLU 6 5.04 5.50 5.50 5.14<br />
Upper HA GLU 6 - HG2/3 GLU 6 4.23<br />
<br />
Each line in the listing of distance restraint modifications treats a pair of distance restraints in case one diastereotopic pair (without stereospecific assignment) is involved, or a group of up to four distance restraints in case two diastereotopic pairs are involved. The input restraints are listed in the columns '''A1–B1''', '''A1-B2''', '''A2-B1''' and '''A2-B2''', where '''A1''' denotes the first atom of the first diastereotopic group, '''A2''' the second atom of the first diastereotopic group, '''B1''' the first atom of the second diastereotopic group, and '''B2''' the second atom of the second diastereotopic group.<br />
These will then be replaced by the distance restraints listed in the two columns '''Ai-Bj''' and '''QA-QB'''. A number in the '''Ai-Bj''' column indicates that equal distance restraints with this upper bound are applied to all two or four individual distances that involve the diastereotopic substituents. A number given in the '''QA-QB''' column indicates the single upper distance bound that is applied to the distance to the pseudoatom, or between the two pseudoatoms in the case of two prochiral groups. If the modified distance limit(s) would be meaningless, it is discarded and not reported.<br />
A second table reports redundant and meaningless restraints that are removed. For example:<br />
<br />
<br />
Meaningless distance restraints:<br />
limit diagnosis<br />
Upper HA ASP 1 - HB3 ASP 1 3.21 duplicate restraint<br />
Upper HA ASP 1 - HB3 ASP 1 3.21 no restriction<br />
Upper HA ASP 1 - HD2 PRO 2 4.20 duplicate restraint<br />
Upper HA ASP 1 - HD2 PRO 2 4.20 no restriction<br />
Upper HA ASP 1 - HD3 PRO 2 3.21 duplicate restraint<br />
Upper HB2 ASP 1 - HB3 ASP 1 2.40 duplicate restraint<br />
Upper HB2 ASP 1 - HB3 ASP 1 2.40 fixed distance<br />
Upper HB2 ASP 1 - HD2 PRO 2 5.50 duplicate restraint<br />
...<br />
Number of modified restraints: 597<br />
<br />
Distance restraints can be meaningless for one of the following reasons:<br />
<br />
:; '''fixed distance''' : The restraint concerns an interatomic distance that cannot be varied by changing the rotatable torsion angles. Examples include restraints between geminal hydrogen atoms, or between atoms of the same aromatic ring.<br />
:; '''no restriction''' : The restraint is such that no conformation exists that would violate it. The program can detect this only if the restrained distance depends on one or two torsion angles. Many meaningless intraresidual peaks can thus be eliminated.<br />
:; '''duplicate restraint''' : The same restraint occurs more than once in the input, for example because transposed peaks were present in the peak list. Only the most restrictive of these restraints is kept.<br />
<br />
<br />
The number of upper distance limits after the modifications is given at the end of the table. Depending on the extent of stereospecific assignments etc., the '''distances modify''' command may increase or decrease the number of restraints.<br />
<br />
Further reading:<br />
<br />
* Güntert et al. J. Mol. Biol. 217, 517-530 (1991).<br />
* Güntert et al. J. Mol. Biol. 217, 531-540 (1991).<br />
<br />
== See also ==<br />
<br />
* [[distance multiple]]<br />
* [[distance unique]]</div>Guenterthttps://cyana.org/w/index.php?title=Coordinate_generation&diff=9904Coordinate generation2023-02-25T11:06:26Z<p>Guentert: /* Tree structure */</p>
<hr />
<div>== Tree structure ==<br />
<br />
[[Image:TreeStructure.jpg|thumb|300px|Fig. 1. The tree structure used by the program CYANA to represent the tripeptide Val–Ser–Ile. Numbered circles stand for rigid units. Rotatable bonds are indicated by arrows that point towards the part of the tree that is moved by a rotation about the bond.]]<br />
<br />
Structure calculations with the program CYANA work in torsion angle space. Since the degrees of freedom are torsion angles but distance restraints are defined by the Cartesian coordinates of the atoms, the program has to recompute the positions of the atoms after each change of the conformation, i.e. each change of the torsion angle values, in order to compute the target function. To this end, the molecule is considered as a tree, consisting of rigid units that are connected by rotatable bonds (Abe et al., 1984; Güntert, 1993; Güntert et al., 1991). Rigid units do not contain rotatable bonds and are made up by one or several atoms whose relative positions are invariable.<br />
<br />
The torsion angles and the rigid units are numbered with monotonously increasing numbers, if the tree is traversed in the direction of the arrows, which point in the direction of that part of the tree that is moved by a rotation about a rotatable bond. A rigid unit and the (always unique) rotatable bond that leads to it have the same number ''a'' and uniquely defined predecessors ''p''(''a'') &lt; ''a''. A rigid unit a comprises all atoms, whose position depends only on the torsion angle ''a'', if all preceding torsion angles ''a’'' &lt; ''a'' are held fixed. For instance, in Fig. 1 the rigid units 1, 6 and 9 each comprise the atoms H<sup>&alpha;</sup>, C’ and C<sup>&beta;</sup>, and the rigid units 5 and 9 both comprise the atoms O, N, H and C<sup>&alpha;</sup> (the peptide bond is not rotatable).<br />
<br />
== Torsion angles ==<br />
<br />
A torsion angle a is defined by four atoms with position vectors <math>\scriptstyle r_a^{(1)}</math>, <math>\scriptstyle r_a^{(2)}</math>, <math>\scriptstyle r_a^{(3)}</math> and <math>\scriptstyle r_a^{(4)}</math>. The rotatable bond connects the second with the third atom of the torsion angle definition. The second atom of the torsion angle definition is the start point <math>\scriptstyle r_a = r_a^{(2)}</math> of the rotatable bond. The unit vector along the axis of the rotatable bond is given by <math>\scriptstyle e_a = (r_a^{(3)}-r_a^{(2)})/|r_a^{(3)}-r_a^{(2)}|</math>. The value ''&#981;<sub>a</sub>'' &isin; [-''&pi;'',''&pi;''] of the torsion angle ''a'' is related to the position vectors <math>\scriptstyle r_a^{(1)}</math>, <math>\scriptstyle r_a^{(2)}</math>, <math>\scriptstyle r_a^{(3)}</math> and <math>\scriptstyle r_a^{(4)}</math> by <br />
<br />
:<math>\cos\phi_a = (\epsilon_1\cdot\epsilon_2)/|\epsilon_1||\epsilon_2|</math>,<br />
<br />
where <math>\scriptstyle\epsilon_1 = e_a \wedge (r_a^{(1)} - r_a^{(2)})</math> and <math>\scriptstyle\epsilon_2 = e_a \wedge (r_a^{(4)} - r_a^{(3)})</math>, and ''&#981;<sub>a</sub>'' receives the same sign as ''e<sub>a</sub>''. The symbols “&sdot;” and “Λ” denote scalar and the vector product, respectively.<br />
<br />
== Coordinate generation ==<br />
<br />
Upon reading the residue library, each individual residue is rotated (as a whole) into a standard orientation:<br />
<br />
:<math>r_a' = R(r_3-r_1,r_2-r_1)(r_\alpha-r_1)\,</math><br />
<br />
The position vector of the atom ''&alpha;'' = 1,2,… in the residue library is denoted by ''r<sub>&alpha;</sub>''. The corresponding position vector in the standard orientation of the residue is <math>r_{\alpha}'</math>. ''R''(''u'',''v'')is the rotation matrix whose rows are given by the three orthonormal vectors<br />
<br />
:<math>\epsilon_1 = \frac{u}{|u|}, \epsilon_2 = \frac{u\wedge v}{|u\wedge v|}</math>, and <math>\epsilon_3 = \epsilon_1\wedge\epsilon_2</math>.<br />
<br />
To calculate the coordinates of the atoms in a conformation that is given by the torsion angle values (''&#981;''<sub>1</sub>,…,''&#981;<sub>n</sub>'') residues can be attached to a partial polypeptide chain one by one. Afterwards – before appending the next residue – the required torsion angle values must be set by rotating the appropriate atoms of the new residue. The “overlap atoms” in the residue library are used to dock a residue to the preceding one. The first three atoms of each residue entry in the residue library (the atoms C, O and N for amino acid residues in the standard residue library) are superimposed onto the final three atoms with corresponding names of the preceding residue. The coordinates <math>\scriptstyle r_\alpha''\,</math> of the atoms of the docked residue are obtained by the transformation<br />
<br />
:<math>r_\alpha'' = p_1 + R(p_3-p_1,p_2-p_1)^{-1}(r_\alpha'-r_1')\,</math>,<br />
<br />
where ''p''<sub>1</sub>, ''p''<sub>2</sub> and ''p''<sub>3</sub> are the positions of the overlap atoms of the preceding residue, and <math>\scriptstyle r_\alpha'\,</math> are the coordinates of the new residue in standard orientation defined above. The transformation<br />
<br />
:<math>r_\alpha''' = r_a + R(e_a,\phi_a-\phi_a^{(0)})(r_\alpha''-r_a)\,</math>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(&alpha; &isin; ''M<sub>a</sub>'').<br />
<br />
sets the desired torsion angle values. The transformation has to be applied for all rotatable bonds ''m'' of the newly docked residue in descending order, m,m - 1,…,1. In this equation ''r<sub>a</sub>'' denotes the position vector of the start point of the rotatable bond ''a'', and ''e<sub>a</sub>'' is a unit vector along the rotation axis of the rotatable bond ''a''. The desired torsion angle value is given by ''&#981;<sub>a</sub>'', and <math>\phi_a^{(0)}</math> is the value of the torsion angle ''a'' in the conformation whose coordinates are stored in the residue library. ''M<sub>a</sub>'' denotes the set of atoms that are moved when the torsion angle ''a'' is rotated. ''R''(''e'',''&#981;'') is the matrix for a rotation with axis ''e'' and rotation angle ''&#981;'', given by<br />
<br />
:<math>R(e,\phi)x = (e\cdot x)e + (e\wedge x)\sin\phi + (x-(e\cdot x)e)\cos\phi</math><br />
<br />
for an arbitrary vector ''x''.<br />
<br />
The generation of the atom coordinates using the above equations is inefficient because an atom is in general subjected to several coordinate transformations. The program CYANA therefore uses these equations only once after reading the residue sequence to generate the atom coordinates of the conformation with torsion angle values ''&#981;''<sub>1</sub> = … = ''&#981;<sub>n</sub>'' = 0. This conformation is the start point for the fast algorithm that is used to generate the atom coordinates during torsion angle dynamics and minimization by building the “scaffold” of the rotatable bonds followed by the positioning of the atoms by a single coordinate transformation. Starting from the conformation ''&#981;''<sub>1</sub> = … = ''&#981;<sub>n</sub>'' = 0 with atom coordinates {''r<sub>&alpha</sub>''}, the rigid units are first brought into a standard orientation:<br />
<br />
:<math>r_\alpha' = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})(r_\alpha-r_a^{(2)})</math>.<br />
<br />
<math>r_a^{(i)}</math> denotes the position vector of the ''i''<sup>th</sup> atom in the definition of the torsion angle ''a''. The transformation is applied to all atoms ''&alpha;'' in the rigid unit ''a''. In addition, for each rigid unit ''a'' a rotation matrix ''R<sub>a</sub>'' and a translation vector ''t<sub>a</sub>'' are calculated – the two quantities that form the scaffold of the tree structure.<br />
<br />
:<math>R_a = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})R(r_{p(a)}^{(1)}-r_{p(a)}^{(2)},r_{p(a)}^{(3)}-r_{p(a)}^{(2)})^{-1}</math>,<br />
<br />
<br />
:<math>t_a = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})(r_a^{(2)}-r_{p(a)}^{(2)})</math>.<br />
<br />
The quantities <math>r_\alpha'</math>, ''R<sub>a</sub>'' and ''t<sub>a</sub>'' have to be computed only once after reading the amino acid sequence. For each new conformation (''&#981;''<sub>1</sub>,…,''&#981;<sub>n</sub>'')<br />
<br />
:<math>R_a' = R(e_z,\phi_a)R_a R_{p(a)}'^{-1}\,</math>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(''e<sub>z</sub>'' = (0,0,1))<br />
<br />
:<math>t_a' = t_{p(a)}' + R_{p(a)}'^{-1}t_a\,</math><br />
<br />
Builds recursively the scaffold of rotatable bonds, and <br />
<br />
:<math>r_\alpha'' = t_a' + R_a' r_\alpha'\,</math><br />
<br />
generates the coordinates with a single transformation for each atom.<br />
<br />
== References ==<br />
<br />
ABE, H., BRAUN, W., NOGUTI, T. & GO, N. (1984). Rapid calculation of 1st and 2nd derivatives of conformational energy with respect to dihedral angles for proteins - General recurrent equations. Computers & Chemistry 8, 239–247.<br />
<br />
GÜNTERT, P. (1993). Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz. Ph.D. thesis, ETH.<br />
<br />
GÜNTERT, P., BRAUN, W. & WÜTHRICH, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. Journal of Molecular Biology 217, 517–530.</div>Guenterthttps://cyana.org/w/index.php?title=Coordinate_generation&diff=9903Coordinate generation2023-02-25T11:05:36Z<p>Guentert: </p>
<hr />
<div>== Tree structure ==<br />
<br />
[[Image:TreeStructure.jpg|thumb|300px|Fig. 1. The tree structure used by the program CYANA to represent the tripeptide Val–Ser–Ile. Numbered circles stand for rigid units. Rotatable bonds are indicated by arrows that point towards the part of the tree that is moved by a rotation about the bond.]]<br />
<br />
Structure XXXcalculations with the program CYANA work in torsion angle space. Since the degrees of freedom are torsion angles but distance restraints are defined by the Cartesian coordinates of the atoms, the program has to recompute the positions of the atoms after each change of the conformation, i.e. each change of the torsion angle values, in order to compute the target function. To this end, the molecule is considered as a tree, consisting of rigid units that are connected by rotatable bonds (Abe et al., 1984; Güntert, 1993; Güntert et al., 1991). Rigid units do not contain rotatable bonds and are made up by one or several atoms whose relative positions are invariable.<br />
<br />
The torsion angles and the rigid units are numbered with monotonously increasing numbers, if the tree is traversed in the direction of the arrows, which point in the direction of that part of the tree that is moved by a rotation about a rotatable bond. A rigid unit and the (always unique) rotatable bond that leads to it have the same number ''a'' and uniquely defined predecessors ''p''(''a'') &lt; ''a''. A rigid unit a comprises all atoms, whose position depends only on the torsion angle ''a'', if all preceding torsion angles ''a’'' &lt; ''a'' are held fixed. For instance, in Fig. 1 the rigid units 1, 6 and 9 each comprise the atoms H<sup>&alpha;</sup>, C’ and C<sup>&beta;</sup>, and the rigid units 5 and 9 both comprise the atoms O, N, H and C<sup>&alpha;</sup> (the peptide bond is not rotatable).<br />
<br />
== Torsion angles ==<br />
<br />
A torsion angle a is defined by four atoms with position vectors <math>\scriptstyle r_a^{(1)}</math>, <math>\scriptstyle r_a^{(2)}</math>, <math>\scriptstyle r_a^{(3)}</math> and <math>\scriptstyle r_a^{(4)}</math>. The rotatable bond connects the second with the third atom of the torsion angle definition. The second atom of the torsion angle definition is the start point <math>\scriptstyle r_a = r_a^{(2)}</math> of the rotatable bond. The unit vector along the axis of the rotatable bond is given by <math>\scriptstyle e_a = (r_a^{(3)}-r_a^{(2)})/|r_a^{(3)}-r_a^{(2)}|</math>. The value ''&#981;<sub>a</sub>'' &isin; [-''&pi;'',''&pi;''] of the torsion angle ''a'' is related to the position vectors <math>\scriptstyle r_a^{(1)}</math>, <math>\scriptstyle r_a^{(2)}</math>, <math>\scriptstyle r_a^{(3)}</math> and <math>\scriptstyle r_a^{(4)}</math> by <br />
<br />
:<math>\cos\phi_a = (\epsilon_1\cdot\epsilon_2)/|\epsilon_1||\epsilon_2|</math>,<br />
<br />
where <math>\scriptstyle\epsilon_1 = e_a \wedge (r_a^{(1)} - r_a^{(2)})</math> and <math>\scriptstyle\epsilon_2 = e_a \wedge (r_a^{(4)} - r_a^{(3)})</math>, and ''&#981;<sub>a</sub>'' receives the same sign as ''e<sub>a</sub>''. The symbols “&sdot;” and “Λ” denote scalar and the vector product, respectively.<br />
<br />
== Coordinate generation ==<br />
<br />
Upon reading the residue library, each individual residue is rotated (as a whole) into a standard orientation:<br />
<br />
:<math>r_a' = R(r_3-r_1,r_2-r_1)(r_\alpha-r_1)\,</math><br />
<br />
The position vector of the atom ''&alpha;'' = 1,2,… in the residue library is denoted by ''r<sub>&alpha;</sub>''. The corresponding position vector in the standard orientation of the residue is <math>r_{\alpha}'</math>. ''R''(''u'',''v'')is the rotation matrix whose rows are given by the three orthonormal vectors<br />
<br />
:<math>\epsilon_1 = \frac{u}{|u|}, \epsilon_2 = \frac{u\wedge v}{|u\wedge v|}</math>, and <math>\epsilon_3 = \epsilon_1\wedge\epsilon_2</math>.<br />
<br />
To calculate the coordinates of the atoms in a conformation that is given by the torsion angle values (''&#981;''<sub>1</sub>,…,''&#981;<sub>n</sub>'') residues can be attached to a partial polypeptide chain one by one. Afterwards – before appending the next residue – the required torsion angle values must be set by rotating the appropriate atoms of the new residue. The “overlap atoms” in the residue library are used to dock a residue to the preceding one. The first three atoms of each residue entry in the residue library (the atoms C, O and N for amino acid residues in the standard residue library) are superimposed onto the final three atoms with corresponding names of the preceding residue. The coordinates <math>\scriptstyle r_\alpha''\,</math> of the atoms of the docked residue are obtained by the transformation<br />
<br />
:<math>r_\alpha'' = p_1 + R(p_3-p_1,p_2-p_1)^{-1}(r_\alpha'-r_1')\,</math>,<br />
<br />
where ''p''<sub>1</sub>, ''p''<sub>2</sub> and ''p''<sub>3</sub> are the positions of the overlap atoms of the preceding residue, and <math>\scriptstyle r_\alpha'\,</math> are the coordinates of the new residue in standard orientation defined above. The transformation<br />
<br />
:<math>r_\alpha''' = r_a + R(e_a,\phi_a-\phi_a^{(0)})(r_\alpha''-r_a)\,</math>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(&alpha; &isin; ''M<sub>a</sub>'').<br />
<br />
sets the desired torsion angle values. The transformation has to be applied for all rotatable bonds ''m'' of the newly docked residue in descending order, m,m - 1,…,1. In this equation ''r<sub>a</sub>'' denotes the position vector of the start point of the rotatable bond ''a'', and ''e<sub>a</sub>'' is a unit vector along the rotation axis of the rotatable bond ''a''. The desired torsion angle value is given by ''&#981;<sub>a</sub>'', and <math>\phi_a^{(0)}</math> is the value of the torsion angle ''a'' in the conformation whose coordinates are stored in the residue library. ''M<sub>a</sub>'' denotes the set of atoms that are moved when the torsion angle ''a'' is rotated. ''R''(''e'',''&#981;'') is the matrix for a rotation with axis ''e'' and rotation angle ''&#981;'', given by<br />
<br />
:<math>R(e,\phi)x = (e\cdot x)e + (e\wedge x)\sin\phi + (x-(e\cdot x)e)\cos\phi</math><br />
<br />
for an arbitrary vector ''x''.<br />
<br />
The generation of the atom coordinates using the above equations is inefficient because an atom is in general subjected to several coordinate transformations. The program CYANA therefore uses these equations only once after reading the residue sequence to generate the atom coordinates of the conformation with torsion angle values ''&#981;''<sub>1</sub> = … = ''&#981;<sub>n</sub>'' = 0. This conformation is the start point for the fast algorithm that is used to generate the atom coordinates during torsion angle dynamics and minimization by building the “scaffold” of the rotatable bonds followed by the positioning of the atoms by a single coordinate transformation. Starting from the conformation ''&#981;''<sub>1</sub> = … = ''&#981;<sub>n</sub>'' = 0 with atom coordinates {''r<sub>&alpha</sub>''}, the rigid units are first brought into a standard orientation:<br />
<br />
:<math>r_\alpha' = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})(r_\alpha-r_a^{(2)})</math>.<br />
<br />
<math>r_a^{(i)}</math> denotes the position vector of the ''i''<sup>th</sup> atom in the definition of the torsion angle ''a''. The transformation is applied to all atoms ''&alpha;'' in the rigid unit ''a''. In addition, for each rigid unit ''a'' a rotation matrix ''R<sub>a</sub>'' and a translation vector ''t<sub>a</sub>'' are calculated – the two quantities that form the scaffold of the tree structure.<br />
<br />
:<math>R_a = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})R(r_{p(a)}^{(1)}-r_{p(a)}^{(2)},r_{p(a)}^{(3)}-r_{p(a)}^{(2)})^{-1}</math>,<br />
<br />
<br />
:<math>t_a = R(r_a^{(1)}-r_a^{(2)},r_a^{(3)}-r_a^{(2)})(r_a^{(2)}-r_{p(a)}^{(2)})</math>.<br />
<br />
The quantities <math>r_\alpha'</math>, ''R<sub>a</sub>'' and ''t<sub>a</sub>'' have to be computed only once after reading the amino acid sequence. For each new conformation (''&#981;''<sub>1</sub>,…,''&#981;<sub>n</sub>'')<br />
<br />
:<math>R_a' = R(e_z,\phi_a)R_a R_{p(a)}'^{-1}\,</math>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(''e<sub>z</sub>'' = (0,0,1))<br />
<br />
:<math>t_a' = t_{p(a)}' + R_{p(a)}'^{-1}t_a\,</math><br />
<br />
Builds recursively the scaffold of rotatable bonds, and <br />
<br />
:<math>r_\alpha'' = t_a' + R_a' r_\alpha'\,</math><br />
<br />
generates the coordinates with a single transformation for each atom.<br />
<br />
== References ==<br />
<br />
ABE, H., BRAUN, W., NOGUTI, T. & GO, N. (1984). Rapid calculation of 1st and 2nd derivatives of conformational energy with respect to dihedral angles for proteins - General recurrent equations. Computers & Chemistry 8, 239–247.<br />
<br />
GÜNTERT, P. (1993). Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz. Ph.D. thesis, ETH.<br />
<br />
GÜNTERT, P., BRAUN, W. & WÜTHRICH, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. Journal of Molecular Biology 217, 517–530.</div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-230101Demo.tgz&diff=9900File:Cyana-3.98.15bin-230101Demo.tgz2023-02-17T16:50:20Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9899Tutorials2023-02-17T16:48:03Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-230101Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (01.01.2023)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-220901Demo.tgz&diff=9898File:Cyana-3.98.15bin-220901Demo.tgz2022-09-01T12:59:17Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9897Tutorials2022-09-01T12:58:47Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-220901Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (01.09.2022)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.15' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.15bin-220819Demo.tgz&diff=9896File:Cyana-3.98.15bin-220819Demo.tgz2022-08-19T11:07:52Z<p>Guentert: </p>
<hr />
<div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9895Tutorials2022-08-19T11:06:58Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.15bin-220819Demo.tgz|demo version of CYANA 3.98.15]] for Linux and MacOS (19.08.2022)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.13' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
* [[Peaklist preparation for eNOE pipeline]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9878Tutorials2022-03-16T14:14:05Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.13bin-211123Demo.tgz|demo version of CYANA 3.98.13]] for Linux and MacOS (23.11.2021)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.13' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (93 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=File:Cyana-3.98.13bin-211123Demo.tgz&diff=9877File:Cyana-3.98.13bin-211123Demo.tgz2022-03-16T14:10:02Z<p>Guentert: Cyana 3.98.13 demo version (21.11.2021)</p>
<hr />
<div>Cyana 3.98.13 demo version (21.11.2021)</div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9876Tutorials2022-03-16T13:58:10Z<p>Guentert: </p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.13bin-211123Demo.tgz|demo version of CYANA 3.98.13]] for Linux and MacOS (23.11.2021)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.13' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (92 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Structure_calculation_and_automated_NOESY_assignment_with_CYANA_(Gothenburg_2021)&diff=9872Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)2021-09-28T08:52:04Z<p>Guentert: </p>
<hr />
<div>== Installation of CYANA demo version ==<br />
<br />
If not done yet, please install the [[Tutorials#Downloads|demo version of CYANA]].<br />
<br />
== Basic structure calculation with given restraints ==<br />
<br />
The basic type of structure calculation with CYANA uses already prepared input restraint files. An example is in the 'demo/basic' directory of the CYANA package. <br />
<br />
Refer to the description [[Basic structure calculation starting from given restraints|here]] to perform the structure calculation.<br />
<br />
Variants of this basic structure calculation that include other types of input data are in the directories 'demo/rdc' (with residual dipolar couplings), 'demo/pcs' (pseudocontact shifts), 'demo/dimer' (homodimer symmetry restraints), and 'demo/rna' (RNA).<br />
<br />
== Structure calculation using assigned NOESY peak lists ==<br />
<br />
CYANA can convert assigned NOESY peak lists into distance restraints, and perform a structure calculation with these (and possibly other types of restraints). An example is in the 'demo/manual' directory. <br />
<br />
Refer to the description [[Structure calculation using manually assigned NOESY peak lists|here]] to perform the structure calculation.<br />
<br />
== Combined automated NOESY assignment and structure calculation ==<br />
<br />
CYANA can automatically assign NOESY peak lists and calculate a structure in an iterative protocol comprising seven cycles of combined automated NOESY asssignment and structure calculation. <br />
<br />
Refer to the description [[Structure calculation with automated NOESY assignment|here]] to perform automated NOESY assignment and structure calculation.<br />
<br />
The protocol is described in complete detail in the following publication:<br />
<br />
* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]<br />
<br />
To speed up the calculation, you can set in the 'CALC.cya' macro:<br />
<br />
structures:=50,10<br />
steps=5000<br />
<br />
These commands tell the program to calculate, in each cycle, 50 conformers (instead of the standard of 100), and to analyze the best 10 (instead of 20) of them. 5000 (instead of 10000) torsion angle dynamics steps will be applied per conformer.<br />
<br />
Seven cycles of automated NOE assignment and structure calculation will be performed by running the command<br />
<br />
cyana "nproc=10; CALC" | tee CALC.out<br />
<br />
In this example, the structure calculations will be performed using 10 processors (if available!) in parallel. The number of processors should not be larger than the number of structures to calculate. The screen output is kept in the file 'CALC.out'. Alternatively, you can run the calculation completely in the background:<br />
<br />
cyana "nproc=10; CALC" > CALC.out &<br />
<br />
Statistics on the NOE assignment and the structure calculation can be obtained with the command 'cyanatable -l'.<br />
<br />
The final structure will be 'final.pdb'. The optimal residue range for superposition can be found with the command<br />
<br />
cyana overlay final.pdb<br />
<br />
or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].<br />
<br />
== Results ==<br />
<br />
You can download the [http://www.cyana.org/demo-results.tgz results of all CYANA demo calculations] (92 MB).</div>Guenterthttps://cyana.org/w/index.php?title=Tutorials&diff=9871Tutorials2021-09-28T08:50:47Z<p>Guentert: /* Downloads */</p>
<hr />
<div>== Downloads ==<br />
<br />
* Latest [[Media:cyana-3.98.13bin-210926Demo.tgz|demo version of CYANA 3.98.13]] for Linux and MacOS (26.09.2021)<br>The demo version has the full functionality of the program for the protein sequences that are used in the example calculations.<br />
* On certain Mac systems, you must execute the command 'xattr -r -d com.apple.quarantine cyana-3.98.13' after unpacking CYANA to allow execution of the programs.<br />
* [http://www.cyana.org/demo-results.tgz Results of all CYANA 3.98.13 demo calculations] (92 MB).<br />
<br />
== INCLAN Tutorials ==<br />
<br />
* [[Writing and using INCLAN macros]]<br />
* [[Using INCLAN variables]]<br />
* [[Using INCLAN control statements]]<br />
<br />
== CYANA Tutorials ==<br />
<br />
* [[Defining non-standard residues]]<br />
<!--<br />
* [[eNORA and multi-state structure calculations]]<br />
--><br />
<br />
== CYANA example calculations ==<br />
<br />
* [[Basic structure calculation starting from given restraints]]<br />
* [[Structure calculation using manually assigned NOESY peak lists]]<br />
* [[Structure calculation with automated NOESY assignment]]<br />
* [[Homodimer structure calculation with automated NOESY assignment]]<br />
* [[ENORA and multi-state structure calculations]]<br />
* [[Identification of key NOEs]]<br />
* [[Determination of the protein state populations]]<br />
* [[Determination of the protein number of states]]<br />
<!--<br />
* [[Structure calculations using residual dipolar coupling restraints]]<br />
* [[Structure calculations using pseudocontact shift restraints]]<br />
* [[Various additional tasks]]<br />
** [[Analyze a structure]]<br />
** [[Angle restraints based on CA chemical shifts]]<br />
** [[Create restraints for disulfide bonds]]<br />
** [[Systematic local conformation analysis]]<br />
** [[Create restraints for hydrogen bonds]]<br />
** [[Merge multiple restraints files]]<br />
** [[Migrate data from Cyana 1.x or Dyana]]<br />
** [[Migrate data from Xplor or CNS]]<br />
** [[Modify upper distance limits]]<br />
** [[NOE statistics and plots]]<br />
** [[Prepare files for PDB and BMRB deposition]]<br />
** [[Create restraints to close flexible PRO rings]]<br />
** [[Ramachandran plot and rotamer restraints]]<br />
** [[Renumber chemical shifts and peaks]]<br />
** [[Calculate RMSD values and mean structures]]<br />
** [[Angle restraints from the program TALOS]]<br />
--><br />
<br />
== Courses ==<br />
<br />
=== Biomolecular NMR: Advanced tools PhD course ===<br />
<br />
Gothenburg, 27 September - 8 October 2021 ([https://www.gu.se/en/event/biomolecular-nmr-advanced-tools-0 course homepage])<br />
<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2021)|Automated resonance assignment with FLYA]]<br />
* [[Structure calculation and automated NOESY assignment with CYANA (Gothenburg 2021)|Structure calculation and automated NOESY assignment with CYANA]]<br />
<br />
<!--<br />
=== EMBO Practical Course: Structure, dynamics and function of biomacromolecules by NMR 2019 ===<br />
<br />
Garching bei München, 26 July - 2 August 2019 ([http://embo2019.bnmrz.org/ course homepage])<br />
<br />
* [[Structure calculation and automated NOESY assignment with CYANA (EMBO 2019)|Structure calculation and automated NOESY assignment with CYANA]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2019)|Automated resonance assignment with FLYA]]<br />
<br />
* [[Automated resonance assignment with FLYA (Brazil 2018)|Complex Structure calculation]]<br />
* [[Automated resonance assignment with FLYA (EMBO 2017)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 5-12 August 2017)--><br />
<!--* [[Automated resonance assignment with FLYA (EMBO 2015)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Munich, 31 July - 7 August 2015)<br />
* [[Automated resonance assignment with FLYA (Gothenburg 2014)|Automated resonance assignment with FLYA]] (Biomolecular NMR course at the Swedish NMR Centre, Gothenburg, 15 October 2014)<br />
* [[Automated resonance assignment with FLYA (EMBO 2013)|Automated resonance assignment with FLYA]] (EMBO Practical Course NMR in Basel, 20–27 July 2013)<br />
--><br />
<br />
== Input file formats ==<br />
<br />
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"><br />
* [[Residue library file]] (.lib)<br />
* [[Sequence file]] (.seq)<br />
* [[Distance restraint file]] (.upl, .lol)<br />
* [[Torsion angle restraint file]] (.aco)<br />
* [[Residual dipolar coupling restraint file]] (.rdc)<br />
* [[Pseudocontact shift restraint file]] (.pcs)<br />
* [[DG Cartesian coordinate file]] (.cor)<br />
* [[PDB coordinate file]] (.pdb)<br />
* [[Torsion angle file]] (.ang)<br />
* [[XEASY chemical shift list file]] (.prot)<br />
* [[BMRB chemical shift list file]] (.bmrb)<br />
* [[XEASY peak list file]] (.peaks)<br />
* [[NMRView peak list file]] (.xpk)<br />
</div></div>Guenterthttps://cyana.org/w/index.php?title=Automated_resonance_assignment_with_FLYA_(Gothenburg_2021)&diff=9870Automated resonance assignment with FLYA (Gothenburg 2021)2021-09-28T08:48:38Z<p>Guentert: /* Results */</p>
<hr />
<div>In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA. <br />
<br />
== Installation of CYANA demo version ==<br />
<br />
If not done yet, please install the [[Tutorials#Downloads|demo version of CYANA]].<br />
<br />
== Experimental input data ==<br />
<br />
Example data for FLYA is in the 'demo/flya' directory of the CYANA package. <br />
<br />
The protein sequence is stored in three-letter code in the file 'demo.seq'. <br />
<br />
Experimental peak lists are available for the following spectra:<br />
* [<sup>1</sup>H,<sup>13</sup>C]-HSQC (called 'C13HSQC' in FLYA)<br />
* [<sup>1</sup>H,<sup>15</sup>N]-HSQC (called 'N15HSQC' in FLYA)<br />
* 3D [<sup>13</sup>C]-resolved NOESY (called 'C13NOESY' in FLYA)<br />
* 3D [<sup>15</sup>N]-resolved NOESY (called 'N15NOESY' in FLYA)<br />
* HNCA<br />
* HN(CO)CA (called 'HNcoCA' in FLYA)<br />
* HNCO<br />
* HN(CA)CO (called 'HNcaCO' in FLYA)<br />
* CBCANH<br />
* CBCACONH (called 'CBCAcoNH' in FLYA)<br />
* HBHACONH (called 'HBHAcoNH' in FLYA)<br />
* HCCH-TOCSY (called 'HCCHTOCSY' in FLYA)<br />
* HCCH-COSY (called 'HCCHCOSY' in FLYA)<br />
* C(CO)NH (called 'CcoNH' in FLYA)<br />
* HC(CO)NH (called 'HCcoNH' in FLYA)<br />
<br />
Peak lists in XEASY format that have been prepared by automatic peak picking with the program NMRView are stored in files ''XXX''.peaks, where ''XXX'' denotes the FLYA spectrum type.<br />
<br />
Each peak list starts with a header that defines the experiment type and the order of dimensions. For instance, for HNCA.peaks:<br />
<br />
# Number of dimensions 3<br />
#FORMAT xeasy3D<br />
#INAME 1 HN<br />
#INAME 2 C<br />
#INAME 3 N<br />
#SPECTRUM HNCA HN C N<br />
5 6.475 58.033 98.548 1 U 2.769E+02 0.000E+00 e 0 0 0 0<br />
6 6.476 62.123 98.126 1 U 2.571E+01 0.000E+00 e 0 0 0 0<br />
7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0<br />
<br />
The first line specifies the number of dimensions (3 in this case). The next 4 lines ('#FORMAT' and '#INAME') are ignored by CYANA. The '#SPECTRUM' line is crucial and gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. These labels must match those in the corresponding experiment definition in the general CYANA library (see below). After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has<br />
<br />
* Peak number 5<br />
* HN chemical shift 6.475 ppm<br />
* C (i.e. CA) chemical shift 58.033 ppm<br />
* N chemical shift 98.548 ppm<br />
<br />
The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm.<br />
<br />
'''Hint:''' The formats of other CYANA files are described in the [[CYANA 3.0 Reference Manual|CYANA Reference Manual]].<br />
<br />
<!--<br />
== FLYA initialization script ==<br />
<br />
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". <br />
<br />
One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any time one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence: <br />
<br />
cyanalib<br />
read demo.seq<br />
<br />
The command 'cyanalib' reads the standard CYANA library. The second command reads the protein sequence.<br />
--><br />
<br />
== Experiment definitions in the CYANA library ==<br />
<br />
When you start CYANA, the program reads the library and displays the full path name of the library file. You can open the standard library file to inspect, for example, the NMR experiment definitions that define how expected peaks are generated by FLYA. For instance, the definition for the HNCA spectrum (search for 'HNCA' in the library file 'cyana.lib') is<br />
<br />
SPECTRUM HNCA HN N C<br />
0.980 HN:H_AMI N:N_AM* C:C_ALI C_BYL<br />
0.800 HN:H_AMI N:N_AMI (C_ALI) C_BYL C:C_ALI <br />
<br />
The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and a label for the atoms that are detected in each dimension of the spectrum. The number of labels defines the dimensionality of the experiment (3 in case of HNCA).<br />
<br />
Each line below defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of HNCA there are two lines, corresponding to the intraresidual and sequential peak. For instance, the definition for the intraresidual peak starts with the probability to observe the peak (0.980), followed by a series of atom types, e.g. H_AMI for amide proton etc. An expected peak is generated for each molecular fragment in which these atom types occur connected by single covalent bonds. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for HNCA 'HN:', 'N:', and 'C:'. The additional atom types refer to atoms that are not detected but must be present in a matching molecular fragment. An atom type in parenthesis indicates a branch in the molecular fragment. For instance, in the second magnetization transfer pathway that specifies the sequential HNCA peak, '(C_ALI)' indicates that the atom 'N:N_ALI' must be connected by a covalent bond to both a C_ALI (i.e. CA) and a C_BYL (i.e. C' of the preceding residue.<br />
<br />
== FLYA execution scripts ==<br />
<br />
The CYANA scripts ("macros") 'CALC*.cya' contain the commands to perform various automated chemical shift assignment calculations.<br />
<br />
For instance, 'CALCbackbone.cya' performs automated backbone resonance assignment. It starts with the specification of the names of the input peak lists:<br />
<br />
peaks:=N15HSQC,HNCA,HNcaCO,HNCO,HNcoCA,CBCANH,CBCAcoNH<br />
<br />
The peak list names are separated by commas (without blanks!). The files on disk have the file name extension .peaks, e.g. HNCA.peaks.<br />
<br />
The commands above will use all available peak lists. You can choose any subset of them by modifying the 'peaks:=...' statement. <br />
<br />
These are followed by tolerances for chemical shift matching:<br />
<br />
assigncs_accH=0.03<br />
assigncs_accC=0.4<br />
assigncs_accN=assigncs_accC<br />
tolerance:=$assigncs_accH,$assigncs_accH,$assigncs_accC<br />
<br />
In this case, a tolerance of 0.03 ppm will be used for protons, and 0.4 ppm for carbon and nitrogen.<br />
<br />
The next parameter specifies the seed value for the random number generator (an arbitrary positive integer is ok). <br />
<br />
randomseed=101<br />
<br />
Groups of atoms for which assignment statistics will be calculated and reported in the 'flya.txt' output file can be defined like this:<br />
<br />
analyzeassign_group := BB: N H CA CB C <br />
<br />
The next commands restrict the generation of expected peaks to a subset of atoms, here the backbone atoms:<br />
<br />
command select_atoms<br />
atom select "N H CA CB C"<br />
end<br />
<br />
In this case, the command defines a group called BB (a name that can be chosen freely) comprising the atoms N, H, CA, CB, C.<br />
<br />
Specific labeling can be handled in the same way. Peak list-specific atom selections can be applied as follows (not used in 'CALCbackbone.cya' but in 'CALClabeling.cya'):<br />
<br />
command ''XXX''_select<br />
atoms select "..."<br />
end<br />
<br />
If desired, a "quick" optimization schedule can be used in the FLYA examples in order to speed up the calculation by inserting the following line above the 'flya ...' command:<br />
<br />
shiftassign_quick=1<br />
<br />
In production runs, better results can be expected (at the expense of longer computation times) if this variable is not set. <br />
Finally, there is the command to start the FLYA algorithm:<br />
<br />
flya runs=10 assignpeaks=$peaks structure= shiftreference=ref.prot<br />
<br />
Here, the given parameters of the 'flya' command specify that<br />
<br />
* The number of independent runs of the algorithm, from which the consolidated shift will be calculated (chosen smaller than in normal production runs in order to speed up the calculation).<br />
* The input peak lists that will be used (as defined above).<br />
* No ensemble of random structures will be calculated for generating expected peaks (is only necessary for NOESY-type experiments).<br />
* The results will be compared with the reference chemical shifts in the file 'ref.prot' (which have been determined independently by conventional methods). The reference chemical shifts will not be used by the algorithm but only for a subsequent analysis of its results.<br />
<br />
== Run a FLYA calculation ==<br />
<br />
To run a FLYA calculation, you start CYANA and execute the corresponding 'CALC*.cya' script. For instance:<br />
<br />
cyana "nproc=10; CALCbackbone"<br />
<br />
By specifying 'nproc=10', 10 independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes. For FLYA, the value of 'nproc' should correspond to the number of independent FLYA runs, i.e. the 'runs=10' parameter of the above 'flya' command.<br />
<br />
== FLYA output files ==<br />
<br />
The FLYA algorithm will produce the following output files:<br />
<br />
* '''flya.prot:''' Consensus assigned chemical shifts. This file contains a chemical shift for every atom that has been assigned to least one peak.<br />
* '''flya.tab:''' Table with details about the chemical shift assignment of each atom (comparison with reference shifts). In this file you can see for each atom whether the assignment is "strong" (self-consistent) or "weak" (only tentative).<br />
* '''flya.txt:''' Assignment statistics<br />
* '''flya.pdf:''' Graphical representation of the assignment results<br />
* '''''XXX''_exp.peaks:''' List of expected peaks, corresponding to input peak list ''XXX''.peaks<br />
* '''''XXX''_asn.peaks:''' Assigned peak list, corresponding to input peak list ''XXX''.peaks<br />
<br />
=== The flya.txt file ===<br />
<br />
This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in CALCbackbone.cya':<br />
<br />
____________________________________________________________<br />
<br />
CHEMICAL SHIFT ASSIGNMENT<br />
____________________________________________________________<br />
<br />
SEED: 1<br />
chemical shifts for 542 atoms found<br />
Peaks assigned from frequencies<br />
<br />
BB: REFERENCES(2):512 CHEMICALSHIFTS(1):542 (1)and(2):512 MATCH:507(99.0% of (2))<br />
<br />
* REFERENCES(2) is the number of reference assignments (in the selected group)<br />
* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA<br />
* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference. <br />
* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.<br />
<br />
Further below comes a table with information about each peak list:<br />
<br />
PEAKLISTS<br />
#Expected: Total number of expected peaks<br />
noRef: Number of expected peaks with missing reference shifts<br />
noPeak: Number of expected peaks for wich no peak can be measured<br />
Assigned: Number of expected peaks that could be assigned<br />
Match: Number of assigned peaks that fit reference shifts<br />
#Measured: Total number of peaks in peak list<br />
Assigned: Number of measured peaks that could be assigned to expected peaks<br />
exp/meas: Ratio of assigned expected and measured peaks<br />
<br />
Lists #Expected noRef noPeak Assigned Match #Measured Assigned exp/meas Assigned<br />
N15HSQC 106 8 1 104( 98.11%) 97( 91.51%) 131 96( 73.28%) 1.1<br />
HNCA 211 15 11 194( 91.94%) 186( 88.15%) 329 179( 54.41%) 1.1<br />
HNcaCO 211 15 11 197( 93.36%) 183( 86.73%) 246 176( 71.54%) 1.1<br />
HNCO 105 7 1 101( 96.19%) 97( 92.38%) 158 97( 61.39%) 1.0<br />
HNcoCA 105 7 0 101( 96.19%) 97( 92.38%) 158 99( 62.66%) 1.0<br />
CBCANH 399 26 25 361( 90.48%) 350( 87.72%) 623 339( 54.41%) 1.1<br />
CBCAcoNH 200 13 2 196( 98.00%) 185( 92.50%) 324 192( 59.26%) 1.0<br />
ALL 1337 91 51 1254( 93.79%) 1195( 89.38%) 1969 1178( 59.83%) 1.1<br />
<br />
It contains the following data:<br />
<br />
* '''#Expected:''' Total number of expected peaks<br />
* '''noRef:''' Number of expected peaks with missing reference shifts<br />
* '''noPeak:''' Number of expected peaks for which no peak can be measured<br />
* '''Assigned:''' Number of expected peaks that could be assigned based on the reference chemical shift assignments. The theoretical maximum of 100% corresponds to the situation that the spectra “explain” all expected peaks. Each expected peak can be mapped to at most one measured peak. Remaining expected peaks correspond to missing peaks in the measured peak list.<br />
* '''Match:''' Number of assigned peaks that fit (within tolerance) reference shifts. The theoretical maximum of 100% corresponds to having all measured peaks assigned. Note that several expected peaks can be mapped to the same measured peak, i.e. the assignments of measured peaks can be unambiguous or ambiguous. Remaining unassigned measured peaks are likely to be artifacts.<br />
* '''#Measured:''' Total number of peaks in peak list<br />
* '''Assigned:''' Number of measured peaks that could be assigned to expected peaks<br />
* '''exp/meas:''' Ratio of assigned expected and measured peaks<br />
<br />
There is more information on the results of the assignment calculation in the 'flya.txt' file (not described here).<br />
<br />
=== The flya.tab file ===<br />
<br />
This file provides information about the chemical shift assignment of each individual atom:<br />
<br />
Atom Residue Ref Shift Dev Extent inside inref<br />
...<br />
N GLY 57 102.109 102.043 0.066 10.0 100.0 100.0 strong=<br />
H GLY 57 8.571 8.570 0.001 10.0 100.0 100.0 strong=<br />
CA GLY 57 45.415 45.433 -0.018 10.0 100.0 100.0 strong=<br />
HA2 GLY 57 4.042<br />
HA3 GLY 57 3.436<br />
C GLY 57 173.621 173.662 -0.041 10.0 89.4 90.0 strong=<br />
N LEU 58 120.640 120.649 -0.009 10.0 80.0 80.0 =<br />
H LEU 58 7.488 7.492 -0.004 10.0 79.8 80.0 =<br />
CA LEU 58 51.943 51.940 0.003 10.0 70.0 70.0 =<br />
HA LEU 58 4.995<br />
CB LEU 58 45.602 45.568 0.034 10.0 82.7 80.0 strong=<br />
CG LEU 58 26.528<br />
HG LEU 58 1.515<br />
CD1 LEU 58 24.745<br />
C LEU 58 173.619 174.576 -0.957 10.0 40.1 10.0 ! (C 59)<br />
...<br />
<br />
* '''Ref:''' Chemical shift value in the reference chemical shift list (ref.prot). It was not used in the calculation.<br />
* '''Shift:''' Consensus chemical shift value from FLYA<br />
* '''Dev''' = Ref - Shift<br />
* '''Extent:''' Number of runs in which the atom was assigned by FLYA.<br />
* '''Inside:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the consensus value.<br />
* '''inref:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the reference value.<br />
* Outcome of the assignment:<br />
** '''strong:''' "strong" assignment, i.e. Inside > 80%.<br />
** '''=:''' Assignment that agrees with reference, i.e. Dev < tolerance.<br />
** '''!:''' Assignment that does not agree with the reference, i.e. Dev > tolerance.<br />
** '''('''''atom name'''''):''' Correct assignment, if within the same residue (no residue number given), or the neighboring residues.<br />
<br />
=== The flya.pdf file ===<br />
<br />
This PDF file provides a graphical representation of the 'flya.tab' file. Each assignment for an atom is represented by a colored rectangle. <br />
[[Image:flyabackbone.png|thumb|600px|'''flya.pdf generated by CALCbackbone.cya''']]<br />
<br />
* '''Green:''' Assignment by FLYA agrees with the manually determined reference assignment (within tolerance) <br />
* '''Red:''' Assignment by FLYA does not agree with the manually determined reference assignment<br />
* '''Blue:''' Assigned by FLYA but no reference available<br />
* '''Black:''' With reference assignment but not assigned by FLYA. <br />
<br />
Respective light colors indicate assignments not classified as strong by the chemical shift consolidation. The row labeled HN/Hα shows for each residue HN on the left and Hα in the center. The N/Cα/C’ row shows for each residue the N, Cα, and C’ assignments from left to right. The rows β-η show the side-chain assignments for the heavy atoms in the center and hydrogen atoms to the left and right. In the case of branched side-chains, the corresponding row is split into an upper part for one branch and a lower part for the other branch.<br />
<br />
== FLYA applications ==<br />
<br />
CYANA macros 'CALC*.cya' are provided for the following FLYA tasks:<br />
<br />
=== CALC.cya: standard automated chemical shift assignment ===<br />
<br />
* specify list of input peak lists in variable 'peaks' without intervening blanks<br />
* specify tolerances for 1H, 13C, 15N with variables assigncs_assH, assigncs_assC assigncs_assN<br />
* command 'select_atoms' excludes some nuclei that are difficult to detect<br />
* optional parameter 'shiftreference=ref.prot' specifies reference chemical shift list, used only for comparison in flya.tab, flya.txt, flya.pdf<br />
<!--<br />
'''Note that the input data for this calculation contains two mistakes. Try to identify the problem by inpecting the 'flya.txt' file and the input files. Correct the mistakes and rerun the calculation before proceeding with other calculations!<br />
'''--><br />
<br />
=== CALCbackbone.cya: standard backbone chemical shift assignment ===<br />
* parameter 'structure=' to avoid generation of random structures, which are not needed if using only through-bond spectra<br />
<br />
=== CALCexperiments.cya: using modified/new experiment definitions in library ===<br />
* modified HCCHTOCSY only for aromatics (library HCCHTOCSY.lib, peak list HCCHTOCSYaro.peaks)<br />
* new experiment N15NOESY2D (library peak list N15NOESY2D.lib, peak list N15NOESY2D.peaks)<br />
<br />
=== CALCexpfromlist.cya: read expected peaks from a peak list ===<br />
* command N15NOESY_expect, reading input peak list N15NOESY_in.peaks<br />
<br />
=== CALCfixedpeaks.cya: keep input peak assignments in user peak assignments ===<br />
* (partially) assigned input peak list N15HSQCassigned.peaks<br />
* parameter 'keepassigned' for loadspectra.cya<br />
<br />
=== CALCfixedshifts.cya: fix input chemical shift assignments ===<br />
* input chemical shift list 'fix.prot'<br />
* shift error in chemical shift list specifies range for assignment<br />
<br />
=== CALClabeling.cya: use of experiment-specific isotope labeling ===<br />
* command 'select_atoms' for general selection of assignable nuclei CcoNH + HSQCLEULYS<br />
* command '<peak list name>_select' with atom selection for a specific peak list (e.g. C13HSQC_LK.peaks) <br />
* command '<peak list name>_expect' for non-standard generation of expected peaks for a given peak list (e.g. CcoNH_LK.peaks with dimension-specific atom selection)<br />
<br />
=== CALCnoesyonly.cya: chemical shift assignment using exclusively NOESY ===<br />
*increased population size with 'shiftassign_population=200'<br />
* see Schmidt et al. J. Biomol. NMR 57, 193-204 (2013)<br />
<br />
<!--=== CALCquick.cya: fast automated chemical shift assignment ===<br />
* fixed number of generations in evolutionary optimization<br />
--><br />
=== CALCstatistics.cya: user-defined chemical shift statistics instead of standard BMRB statistics from library ===<br />
* average value and stddev from input chemical shift list 'shiftx.prot'<br />
* 'assigncs_sd:=bmrb' to use stddev from BMRB (cyana.lib) instead of input chemical shift list<br />
* 'assigncs_sdfactor:=0.5' to scale BMRB stddev by given factor<br />
<br />
=== CALCstructcalc.cya: follow automated shift assignment by automated NOESY assignment and structure calculation ===<br />
* peak lists for distance restraint generation specified by parameter 'structurepeaks='<br />
<br />
=== CALCstructure.cya: use input structure to generate expected peaks for through-space experiments ===<br />
* specify with parameter 'structure' of command 'flya'<br />
* if parameter 'structure' is absent, a set of random structures is generated automatically<br />
* if set to blank ('structure='), no random structures are generated (if not needed because only through-bond spectra are used)<br />
<br />
== Results ==<br />
<br />
You can download the [http://www.cyana.org/demo-results.tgz results of all CYANA demo calculations] (92 MB).</div>Guenterthttps://cyana.org/w/index.php?title=Automated_resonance_assignment_with_FLYA_(Gothenburg_2021)&diff=9869Automated resonance assignment with FLYA (Gothenburg 2021)2021-09-28T08:47:58Z<p>Guentert: /* Results */</p>
<hr />
<div>In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA. <br />
<br />
== Installation of CYANA demo version ==<br />
<br />
If not done yet, please install the [[Tutorials#Downloads|demo version of CYANA]].<br />
<br />
== Experimental input data ==<br />
<br />
Example data for FLYA is in the 'demo/flya' directory of the CYANA package. <br />
<br />
The protein sequence is stored in three-letter code in the file 'demo.seq'. <br />
<br />
Experimental peak lists are available for the following spectra:<br />
* [<sup>1</sup>H,<sup>13</sup>C]-HSQC (called 'C13HSQC' in FLYA)<br />
* [<sup>1</sup>H,<sup>15</sup>N]-HSQC (called 'N15HSQC' in FLYA)<br />
* 3D [<sup>13</sup>C]-resolved NOESY (called 'C13NOESY' in FLYA)<br />
* 3D [<sup>15</sup>N]-resolved NOESY (called 'N15NOESY' in FLYA)<br />
* HNCA<br />
* HN(CO)CA (called 'HNcoCA' in FLYA)<br />
* HNCO<br />
* HN(CA)CO (called 'HNcaCO' in FLYA)<br />
* CBCANH<br />
* CBCACONH (called 'CBCAcoNH' in FLYA)<br />
* HBHACONH (called 'HBHAcoNH' in FLYA)<br />
* HCCH-TOCSY (called 'HCCHTOCSY' in FLYA)<br />
* HCCH-COSY (called 'HCCHCOSY' in FLYA)<br />
* C(CO)NH (called 'CcoNH' in FLYA)<br />
* HC(CO)NH (called 'HCcoNH' in FLYA)<br />
<br />
Peak lists in XEASY format that have been prepared by automatic peak picking with the program NMRView are stored in files ''XXX''.peaks, where ''XXX'' denotes the FLYA spectrum type.<br />
<br />
Each peak list starts with a header that defines the experiment type and the order of dimensions. For instance, for HNCA.peaks:<br />
<br />
# Number of dimensions 3<br />
#FORMAT xeasy3D<br />
#INAME 1 HN<br />
#INAME 2 C<br />
#INAME 3 N<br />
#SPECTRUM HNCA HN C N<br />
5 6.475 58.033 98.548 1 U 2.769E+02 0.000E+00 e 0 0 0 0<br />
6 6.476 62.123 98.126 1 U 2.571E+01 0.000E+00 e 0 0 0 0<br />
7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0<br />
<br />
The first line specifies the number of dimensions (3 in this case). The next 4 lines ('#FORMAT' and '#INAME') are ignored by CYANA. The '#SPECTRUM' line is crucial and gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. These labels must match those in the corresponding experiment definition in the general CYANA library (see below). After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has<br />
<br />
* Peak number 5<br />
* HN chemical shift 6.475 ppm<br />
* C (i.e. CA) chemical shift 58.033 ppm<br />
* N chemical shift 98.548 ppm<br />
<br />
The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm.<br />
<br />
'''Hint:''' The formats of other CYANA files are described in the [[CYANA 3.0 Reference Manual|CYANA Reference Manual]].<br />
<br />
<!--<br />
== FLYA initialization script ==<br />
<br />
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". <br />
<br />
One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any time one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence: <br />
<br />
cyanalib<br />
read demo.seq<br />
<br />
The command 'cyanalib' reads the standard CYANA library. The second command reads the protein sequence.<br />
--><br />
<br />
== Experiment definitions in the CYANA library ==<br />
<br />
When you start CYANA, the program reads the library and displays the full path name of the library file. You can open the standard library file to inspect, for example, the NMR experiment definitions that define how expected peaks are generated by FLYA. For instance, the definition for the HNCA spectrum (search for 'HNCA' in the library file 'cyana.lib') is<br />
<br />
SPECTRUM HNCA HN N C<br />
0.980 HN:H_AMI N:N_AM* C:C_ALI C_BYL<br />
0.800 HN:H_AMI N:N_AMI (C_ALI) C_BYL C:C_ALI <br />
<br />
The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and a label for the atoms that are detected in each dimension of the spectrum. The number of labels defines the dimensionality of the experiment (3 in case of HNCA).<br />
<br />
Each line below defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of HNCA there are two lines, corresponding to the intraresidual and sequential peak. For instance, the definition for the intraresidual peak starts with the probability to observe the peak (0.980), followed by a series of atom types, e.g. H_AMI for amide proton etc. An expected peak is generated for each molecular fragment in which these atom types occur connected by single covalent bonds. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for HNCA 'HN:', 'N:', and 'C:'. The additional atom types refer to atoms that are not detected but must be present in a matching molecular fragment. An atom type in parenthesis indicates a branch in the molecular fragment. For instance, in the second magnetization transfer pathway that specifies the sequential HNCA peak, '(C_ALI)' indicates that the atom 'N:N_ALI' must be connected by a covalent bond to both a C_ALI (i.e. CA) and a C_BYL (i.e. C' of the preceding residue.<br />
<br />
== FLYA execution scripts ==<br />
<br />
The CYANA scripts ("macros") 'CALC*.cya' contain the commands to perform various automated chemical shift assignment calculations.<br />
<br />
For instance, 'CALCbackbone.cya' performs automated backbone resonance assignment. It starts with the specification of the names of the input peak lists:<br />
<br />
peaks:=N15HSQC,HNCA,HNcaCO,HNCO,HNcoCA,CBCANH,CBCAcoNH<br />
<br />
The peak list names are separated by commas (without blanks!). The files on disk have the file name extension .peaks, e.g. HNCA.peaks.<br />
<br />
The commands above will use all available peak lists. You can choose any subset of them by modifying the 'peaks:=...' statement. <br />
<br />
These are followed by tolerances for chemical shift matching:<br />
<br />
assigncs_accH=0.03<br />
assigncs_accC=0.4<br />
assigncs_accN=assigncs_accC<br />
tolerance:=$assigncs_accH,$assigncs_accH,$assigncs_accC<br />
<br />
In this case, a tolerance of 0.03 ppm will be used for protons, and 0.4 ppm for carbon and nitrogen.<br />
<br />
The next parameter specifies the seed value for the random number generator (an arbitrary positive integer is ok). <br />
<br />
randomseed=101<br />
<br />
Groups of atoms for which assignment statistics will be calculated and reported in the 'flya.txt' output file can be defined like this:<br />
<br />
analyzeassign_group := BB: N H CA CB C <br />
<br />
The next commands restrict the generation of expected peaks to a subset of atoms, here the backbone atoms:<br />
<br />
command select_atoms<br />
atom select "N H CA CB C"<br />
end<br />
<br />
In this case, the command defines a group called BB (a name that can be chosen freely) comprising the atoms N, H, CA, CB, C.<br />
<br />
Specific labeling can be handled in the same way. Peak list-specific atom selections can be applied as follows (not used in 'CALCbackbone.cya' but in 'CALClabeling.cya'):<br />
<br />
command ''XXX''_select<br />
atoms select "..."<br />
end<br />
<br />
If desired, a "quick" optimization schedule can be used in the FLYA examples in order to speed up the calculation by inserting the following line above the 'flya ...' command:<br />
<br />
shiftassign_quick=1<br />
<br />
In production runs, better results can be expected (at the expense of longer computation times) if this variable is not set. <br />
Finally, there is the command to start the FLYA algorithm:<br />
<br />
flya runs=10 assignpeaks=$peaks structure= shiftreference=ref.prot<br />
<br />
Here, the given parameters of the 'flya' command specify that<br />
<br />
* The number of independent runs of the algorithm, from which the consolidated shift will be calculated (chosen smaller than in normal production runs in order to speed up the calculation).<br />
* The input peak lists that will be used (as defined above).<br />
* No ensemble of random structures will be calculated for generating expected peaks (is only necessary for NOESY-type experiments).<br />
* The results will be compared with the reference chemical shifts in the file 'ref.prot' (which have been determined independently by conventional methods). The reference chemical shifts will not be used by the algorithm but only for a subsequent analysis of its results.<br />
<br />
== Run a FLYA calculation ==<br />
<br />
To run a FLYA calculation, you start CYANA and execute the corresponding 'CALC*.cya' script. For instance:<br />
<br />
cyana "nproc=10; CALCbackbone"<br />
<br />
By specifying 'nproc=10', 10 independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes. For FLYA, the value of 'nproc' should correspond to the number of independent FLYA runs, i.e. the 'runs=10' parameter of the above 'flya' command.<br />
<br />
== FLYA output files ==<br />
<br />
The FLYA algorithm will produce the following output files:<br />
<br />
* '''flya.prot:''' Consensus assigned chemical shifts. This file contains a chemical shift for every atom that has been assigned to least one peak.<br />
* '''flya.tab:''' Table with details about the chemical shift assignment of each atom (comparison with reference shifts). In this file you can see for each atom whether the assignment is "strong" (self-consistent) or "weak" (only tentative).<br />
* '''flya.txt:''' Assignment statistics<br />
* '''flya.pdf:''' Graphical representation of the assignment results<br />
* '''''XXX''_exp.peaks:''' List of expected peaks, corresponding to input peak list ''XXX''.peaks<br />
* '''''XXX''_asn.peaks:''' Assigned peak list, corresponding to input peak list ''XXX''.peaks<br />
<br />
=== The flya.txt file ===<br />
<br />
This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in CALCbackbone.cya':<br />
<br />
____________________________________________________________<br />
<br />
CHEMICAL SHIFT ASSIGNMENT<br />
____________________________________________________________<br />
<br />
SEED: 1<br />
chemical shifts for 542 atoms found<br />
Peaks assigned from frequencies<br />
<br />
BB: REFERENCES(2):512 CHEMICALSHIFTS(1):542 (1)and(2):512 MATCH:507(99.0% of (2))<br />
<br />
* REFERENCES(2) is the number of reference assignments (in the selected group)<br />
* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA<br />
* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference. <br />
* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.<br />
<br />
Further below comes a table with information about each peak list:<br />
<br />
PEAKLISTS<br />
#Expected: Total number of expected peaks<br />
noRef: Number of expected peaks with missing reference shifts<br />
noPeak: Number of expected peaks for wich no peak can be measured<br />
Assigned: Number of expected peaks that could be assigned<br />
Match: Number of assigned peaks that fit reference shifts<br />
#Measured: Total number of peaks in peak list<br />
Assigned: Number of measured peaks that could be assigned to expected peaks<br />
exp/meas: Ratio of assigned expected and measured peaks<br />
<br />
Lists #Expected noRef noPeak Assigned Match #Measured Assigned exp/meas Assigned<br />
N15HSQC 106 8 1 104( 98.11%) 97( 91.51%) 131 96( 73.28%) 1.1<br />
HNCA 211 15 11 194( 91.94%) 186( 88.15%) 329 179( 54.41%) 1.1<br />
HNcaCO 211 15 11 197( 93.36%) 183( 86.73%) 246 176( 71.54%) 1.1<br />
HNCO 105 7 1 101( 96.19%) 97( 92.38%) 158 97( 61.39%) 1.0<br />
HNcoCA 105 7 0 101( 96.19%) 97( 92.38%) 158 99( 62.66%) 1.0<br />
CBCANH 399 26 25 361( 90.48%) 350( 87.72%) 623 339( 54.41%) 1.1<br />
CBCAcoNH 200 13 2 196( 98.00%) 185( 92.50%) 324 192( 59.26%) 1.0<br />
ALL 1337 91 51 1254( 93.79%) 1195( 89.38%) 1969 1178( 59.83%) 1.1<br />
<br />
It contains the following data:<br />
<br />
* '''#Expected:''' Total number of expected peaks<br />
* '''noRef:''' Number of expected peaks with missing reference shifts<br />
* '''noPeak:''' Number of expected peaks for which no peak can be measured<br />
* '''Assigned:''' Number of expected peaks that could be assigned based on the reference chemical shift assignments. The theoretical maximum of 100% corresponds to the situation that the spectra “explain” all expected peaks. Each expected peak can be mapped to at most one measured peak. Remaining expected peaks correspond to missing peaks in the measured peak list.<br />
* '''Match:''' Number of assigned peaks that fit (within tolerance) reference shifts. The theoretical maximum of 100% corresponds to having all measured peaks assigned. Note that several expected peaks can be mapped to the same measured peak, i.e. the assignments of measured peaks can be unambiguous or ambiguous. Remaining unassigned measured peaks are likely to be artifacts.<br />
* '''#Measured:''' Total number of peaks in peak list<br />
* '''Assigned:''' Number of measured peaks that could be assigned to expected peaks<br />
* '''exp/meas:''' Ratio of assigned expected and measured peaks<br />
<br />
There is more information on the results of the assignment calculation in the 'flya.txt' file (not described here).<br />
<br />
=== The flya.tab file ===<br />
<br />
This file provides information about the chemical shift assignment of each individual atom:<br />
<br />
Atom Residue Ref Shift Dev Extent inside inref<br />
...<br />
N GLY 57 102.109 102.043 0.066 10.0 100.0 100.0 strong=<br />
H GLY 57 8.571 8.570 0.001 10.0 100.0 100.0 strong=<br />
CA GLY 57 45.415 45.433 -0.018 10.0 100.0 100.0 strong=<br />
HA2 GLY 57 4.042<br />
HA3 GLY 57 3.436<br />
C GLY 57 173.621 173.662 -0.041 10.0 89.4 90.0 strong=<br />
N LEU 58 120.640 120.649 -0.009 10.0 80.0 80.0 =<br />
H LEU 58 7.488 7.492 -0.004 10.0 79.8 80.0 =<br />
CA LEU 58 51.943 51.940 0.003 10.0 70.0 70.0 =<br />
HA LEU 58 4.995<br />
CB LEU 58 45.602 45.568 0.034 10.0 82.7 80.0 strong=<br />
CG LEU 58 26.528<br />
HG LEU 58 1.515<br />
CD1 LEU 58 24.745<br />
C LEU 58 173.619 174.576 -0.957 10.0 40.1 10.0 ! (C 59)<br />
...<br />
<br />
* '''Ref:''' Chemical shift value in the reference chemical shift list (ref.prot). It was not used in the calculation.<br />
* '''Shift:''' Consensus chemical shift value from FLYA<br />
* '''Dev''' = Ref - Shift<br />
* '''Extent:''' Number of runs in which the atom was assigned by FLYA.<br />
* '''Inside:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the consensus value.<br />
* '''inref:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the reference value.<br />
* Outcome of the assignment:<br />
** '''strong:''' "strong" assignment, i.e. Inside > 80%.<br />
** '''=:''' Assignment that agrees with reference, i.e. Dev < tolerance.<br />
** '''!:''' Assignment that does not agree with the reference, i.e. Dev > tolerance.<br />
** '''('''''atom name'''''):''' Correct assignment, if within the same residue (no residue number given), or the neighboring residues.<br />
<br />
=== The flya.pdf file ===<br />
<br />
This PDF file provides a graphical representation of the 'flya.tab' file. Each assignment for an atom is represented by a colored rectangle. <br />
[[Image:flyabackbone.png|thumb|600px|'''flya.pdf generated by CALCbackbone.cya''']]<br />
<br />
* '''Green:''' Assignment by FLYA agrees with the manually determined reference assignment (within tolerance) <br />
* '''Red:''' Assignment by FLYA does not agree with the manually determined reference assignment<br />
* '''Blue:''' Assigned by FLYA but no reference available<br />
* '''Black:''' With reference assignment but not assigned by FLYA. <br />
<br />
Respective light colors indicate assignments not classified as strong by the chemical shift consolidation. The row labeled HN/Hα shows for each residue HN on the left and Hα in the center. The N/Cα/C’ row shows for each residue the N, Cα, and C’ assignments from left to right. The rows β-η show the side-chain assignments for the heavy atoms in the center and hydrogen atoms to the left and right. In the case of branched side-chains, the corresponding row is split into an upper part for one branch and a lower part for the other branch.<br />
<br />
== FLYA applications ==<br />
<br />
CYANA macros 'CALC*.cya' are provided for the following FLYA tasks:<br />
<br />
=== CALC.cya: standard automated chemical shift assignment ===<br />
<br />
* specify list of input peak lists in variable 'peaks' without intervening blanks<br />
* specify tolerances for 1H, 13C, 15N with variables assigncs_assH, assigncs_assC assigncs_assN<br />
* command 'select_atoms' excludes some nuclei that are difficult to detect<br />
* optional parameter 'shiftreference=ref.prot' specifies reference chemical shift list, used only for comparison in flya.tab, flya.txt, flya.pdf<br />
<!--<br />
'''Note that the input data for this calculation contains two mistakes. Try to identify the problem by inpecting the 'flya.txt' file and the input files. Correct the mistakes and rerun the calculation before proceeding with other calculations!<br />
'''--><br />
<br />
=== CALCbackbone.cya: standard backbone chemical shift assignment ===<br />
* parameter 'structure=' to avoid generation of random structures, which are not needed if using only through-bond spectra<br />
<br />
=== CALCexperiments.cya: using modified/new experiment definitions in library ===<br />
* modified HCCHTOCSY only for aromatics (library HCCHTOCSY.lib, peak list HCCHTOCSYaro.peaks)<br />
* new experiment N15NOESY2D (library peak list N15NOESY2D.lib, peak list N15NOESY2D.peaks)<br />
<br />
=== CALCexpfromlist.cya: read expected peaks from a peak list ===<br />
* command N15NOESY_expect, reading input peak list N15NOESY_in.peaks<br />
<br />
=== CALCfixedpeaks.cya: keep input peak assignments in user peak assignments ===<br />
* (partially) assigned input peak list N15HSQCassigned.peaks<br />
* parameter 'keepassigned' for loadspectra.cya<br />
<br />
=== CALCfixedshifts.cya: fix input chemical shift assignments ===<br />
* input chemical shift list 'fix.prot'<br />
* shift error in chemical shift list specifies range for assignment<br />
<br />
=== CALClabeling.cya: use of experiment-specific isotope labeling ===<br />
* command 'select_atoms' for general selection of assignable nuclei CcoNH + HSQCLEULYS<br />
* command '<peak list name>_select' with atom selection for a specific peak list (e.g. C13HSQC_LK.peaks) <br />
* command '<peak list name>_expect' for non-standard generation of expected peaks for a given peak list (e.g. CcoNH_LK.peaks with dimension-specific atom selection)<br />
<br />
=== CALCnoesyonly.cya: chemical shift assignment using exclusively NOESY ===<br />
*increased population size with 'shiftassign_population=200'<br />
* see Schmidt et al. J. Biomol. NMR 57, 193-204 (2013)<br />
<br />
<!--=== CALCquick.cya: fast automated chemical shift assignment ===<br />
* fixed number of generations in evolutionary optimization<br />
--><br />
=== CALCstatistics.cya: user-defined chemical shift statistics instead of standard BMRB statistics from library ===<br />
* average value and stddev from input chemical shift list 'shiftx.prot'<br />
* 'assigncs_sd:=bmrb' to use stddev from BMRB (cyana.lib) instead of input chemical shift list<br />
* 'assigncs_sdfactor:=0.5' to scale BMRB stddev by given factor<br />
<br />
=== CALCstructcalc.cya: follow automated shift assignment by automated NOESY assignment and structure calculation ===<br />
* peak lists for distance restraint generation specified by parameter 'structurepeaks='<br />
<br />
=== CALCstructure.cya: use input structure to generate expected peaks for through-space experiments ===<br />
* specify with parameter 'structure' of command 'flya'<br />
* if parameter 'structure' is absent, a set of random structures is generated automatically<br />
* if set to blank ('structure='), no random structures are generated (if not needed because only through-bond spectra are used)<br />
<br />
== Results ==<br />
<br />
You can download the [https://www.cyana.org/demo-results.tgz results of all CYANA demo calculations] (92 MB).</div>Guenterthttps://cyana.org/w/index.php?title=Automated_resonance_assignment_with_FLYA_(Gothenburg_2021)&diff=9868Automated resonance assignment with FLYA (Gothenburg 2021)2021-09-28T08:45:32Z<p>Guentert: /* FLYA applications */</p>
<hr />
<div>In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA. <br />
<br />
== Installation of CYANA demo version ==<br />
<br />
If not done yet, please install the [[Tutorials#Downloads|demo version of CYANA]].<br />
<br />
== Experimental input data ==<br />
<br />
Example data for FLYA is in the 'demo/flya' directory of the CYANA package. <br />
<br />
The protein sequence is stored in three-letter code in the file 'demo.seq'. <br />
<br />
Experimental peak lists are available for the following spectra:<br />
* [<sup>1</sup>H,<sup>13</sup>C]-HSQC (called 'C13HSQC' in FLYA)<br />
* [<sup>1</sup>H,<sup>15</sup>N]-HSQC (called 'N15HSQC' in FLYA)<br />
* 3D [<sup>13</sup>C]-resolved NOESY (called 'C13NOESY' in FLYA)<br />
* 3D [<sup>15</sup>N]-resolved NOESY (called 'N15NOESY' in FLYA)<br />
* HNCA<br />
* HN(CO)CA (called 'HNcoCA' in FLYA)<br />
* HNCO<br />
* HN(CA)CO (called 'HNcaCO' in FLYA)<br />
* CBCANH<br />
* CBCACONH (called 'CBCAcoNH' in FLYA)<br />
* HBHACONH (called 'HBHAcoNH' in FLYA)<br />
* HCCH-TOCSY (called 'HCCHTOCSY' in FLYA)<br />
* HCCH-COSY (called 'HCCHCOSY' in FLYA)<br />
* C(CO)NH (called 'CcoNH' in FLYA)<br />
* HC(CO)NH (called 'HCcoNH' in FLYA)<br />
<br />
Peak lists in XEASY format that have been prepared by automatic peak picking with the program NMRView are stored in files ''XXX''.peaks, where ''XXX'' denotes the FLYA spectrum type.<br />
<br />
Each peak list starts with a header that defines the experiment type and the order of dimensions. For instance, for HNCA.peaks:<br />
<br />
# Number of dimensions 3<br />
#FORMAT xeasy3D<br />
#INAME 1 HN<br />
#INAME 2 C<br />
#INAME 3 N<br />
#SPECTRUM HNCA HN C N<br />
5 6.475 58.033 98.548 1 U 2.769E+02 0.000E+00 e 0 0 0 0<br />
6 6.476 62.123 98.126 1 U 2.571E+01 0.000E+00 e 0 0 0 0<br />
7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0<br />
<br />
The first line specifies the number of dimensions (3 in this case). The next 4 lines ('#FORMAT' and '#INAME') are ignored by CYANA. The '#SPECTRUM' line is crucial and gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. These labels must match those in the corresponding experiment definition in the general CYANA library (see below). After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has<br />
<br />
* Peak number 5<br />
* HN chemical shift 6.475 ppm<br />
* C (i.e. CA) chemical shift 58.033 ppm<br />
* N chemical shift 98.548 ppm<br />
<br />
The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm.<br />
<br />
'''Hint:''' The formats of other CYANA files are described in the [[CYANA 3.0 Reference Manual|CYANA Reference Manual]].<br />
<br />
<!--<br />
== FLYA initialization script ==<br />
<br />
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". <br />
<br />
One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any time one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence: <br />
<br />
cyanalib<br />
read demo.seq<br />
<br />
The command 'cyanalib' reads the standard CYANA library. The second command reads the protein sequence.<br />
--><br />
<br />
== Experiment definitions in the CYANA library ==<br />
<br />
When you start CYANA, the program reads the library and displays the full path name of the library file. You can open the standard library file to inspect, for example, the NMR experiment definitions that define how expected peaks are generated by FLYA. For instance, the definition for the HNCA spectrum (search for 'HNCA' in the library file 'cyana.lib') is<br />
<br />
SPECTRUM HNCA HN N C<br />
0.980 HN:H_AMI N:N_AM* C:C_ALI C_BYL<br />
0.800 HN:H_AMI N:N_AMI (C_ALI) C_BYL C:C_ALI <br />
<br />
The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and a label for the atoms that are detected in each dimension of the spectrum. The number of labels defines the dimensionality of the experiment (3 in case of HNCA).<br />
<br />
Each line below defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of HNCA there are two lines, corresponding to the intraresidual and sequential peak. For instance, the definition for the intraresidual peak starts with the probability to observe the peak (0.980), followed by a series of atom types, e.g. H_AMI for amide proton etc. An expected peak is generated for each molecular fragment in which these atom types occur connected by single covalent bonds. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for HNCA 'HN:', 'N:', and 'C:'. The additional atom types refer to atoms that are not detected but must be present in a matching molecular fragment. An atom type in parenthesis indicates a branch in the molecular fragment. For instance, in the second magnetization transfer pathway that specifies the sequential HNCA peak, '(C_ALI)' indicates that the atom 'N:N_ALI' must be connected by a covalent bond to both a C_ALI (i.e. CA) and a C_BYL (i.e. C' of the preceding residue.<br />
<br />
== FLYA execution scripts ==<br />
<br />
The CYANA scripts ("macros") 'CALC*.cya' contain the commands to perform various automated chemical shift assignment calculations.<br />
<br />
For instance, 'CALCbackbone.cya' performs automated backbone resonance assignment. It starts with the specification of the names of the input peak lists:<br />
<br />
peaks:=N15HSQC,HNCA,HNcaCO,HNCO,HNcoCA,CBCANH,CBCAcoNH<br />
<br />
The peak list names are separated by commas (without blanks!). The files on disk have the file name extension .peaks, e.g. HNCA.peaks.<br />
<br />
The commands above will use all available peak lists. You can choose any subset of them by modifying the 'peaks:=...' statement. <br />
<br />
These are followed by tolerances for chemical shift matching:<br />
<br />
assigncs_accH=0.03<br />
assigncs_accC=0.4<br />
assigncs_accN=assigncs_accC<br />
tolerance:=$assigncs_accH,$assigncs_accH,$assigncs_accC<br />
<br />
In this case, a tolerance of 0.03 ppm will be used for protons, and 0.4 ppm for carbon and nitrogen.<br />
<br />
The next parameter specifies the seed value for the random number generator (an arbitrary positive integer is ok). <br />
<br />
randomseed=101<br />
<br />
Groups of atoms for which assignment statistics will be calculated and reported in the 'flya.txt' output file can be defined like this:<br />
<br />
analyzeassign_group := BB: N H CA CB C <br />
<br />
The next commands restrict the generation of expected peaks to a subset of atoms, here the backbone atoms:<br />
<br />
command select_atoms<br />
atom select "N H CA CB C"<br />
end<br />
<br />
In this case, the command defines a group called BB (a name that can be chosen freely) comprising the atoms N, H, CA, CB, C.<br />
<br />
Specific labeling can be handled in the same way. Peak list-specific atom selections can be applied as follows (not used in 'CALCbackbone.cya' but in 'CALClabeling.cya'):<br />
<br />
command ''XXX''_select<br />
atoms select "..."<br />
end<br />
<br />
If desired, a "quick" optimization schedule can be used in the FLYA examples in order to speed up the calculation by inserting the following line above the 'flya ...' command:<br />
<br />
shiftassign_quick=1<br />
<br />
In production runs, better results can be expected (at the expense of longer computation times) if this variable is not set. <br />
Finally, there is the command to start the FLYA algorithm:<br />
<br />
flya runs=10 assignpeaks=$peaks structure= shiftreference=ref.prot<br />
<br />
Here, the given parameters of the 'flya' command specify that<br />
<br />
* The number of independent runs of the algorithm, from which the consolidated shift will be calculated (chosen smaller than in normal production runs in order to speed up the calculation).<br />
* The input peak lists that will be used (as defined above).<br />
* No ensemble of random structures will be calculated for generating expected peaks (is only necessary for NOESY-type experiments).<br />
* The results will be compared with the reference chemical shifts in the file 'ref.prot' (which have been determined independently by conventional methods). The reference chemical shifts will not be used by the algorithm but only for a subsequent analysis of its results.<br />
<br />
== Run a FLYA calculation ==<br />
<br />
To run a FLYA calculation, you start CYANA and execute the corresponding 'CALC*.cya' script. For instance:<br />
<br />
cyana "nproc=10; CALCbackbone"<br />
<br />
By specifying 'nproc=10', 10 independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes. For FLYA, the value of 'nproc' should correspond to the number of independent FLYA runs, i.e. the 'runs=10' parameter of the above 'flya' command.<br />
<br />
== FLYA output files ==<br />
<br />
The FLYA algorithm will produce the following output files:<br />
<br />
* '''flya.prot:''' Consensus assigned chemical shifts. This file contains a chemical shift for every atom that has been assigned to least one peak.<br />
* '''flya.tab:''' Table with details about the chemical shift assignment of each atom (comparison with reference shifts). In this file you can see for each atom whether the assignment is "strong" (self-consistent) or "weak" (only tentative).<br />
* '''flya.txt:''' Assignment statistics<br />
* '''flya.pdf:''' Graphical representation of the assignment results<br />
* '''''XXX''_exp.peaks:''' List of expected peaks, corresponding to input peak list ''XXX''.peaks<br />
* '''''XXX''_asn.peaks:''' Assigned peak list, corresponding to input peak list ''XXX''.peaks<br />
<br />
=== The flya.txt file ===<br />
<br />
This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in CALCbackbone.cya':<br />
<br />
____________________________________________________________<br />
<br />
CHEMICAL SHIFT ASSIGNMENT<br />
____________________________________________________________<br />
<br />
SEED: 1<br />
chemical shifts for 542 atoms found<br />
Peaks assigned from frequencies<br />
<br />
BB: REFERENCES(2):512 CHEMICALSHIFTS(1):542 (1)and(2):512 MATCH:507(99.0% of (2))<br />
<br />
* REFERENCES(2) is the number of reference assignments (in the selected group)<br />
* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA<br />
* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference. <br />
* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.<br />
<br />
Further below comes a table with information about each peak list:<br />
<br />
PEAKLISTS<br />
#Expected: Total number of expected peaks<br />
noRef: Number of expected peaks with missing reference shifts<br />
noPeak: Number of expected peaks for wich no peak can be measured<br />
Assigned: Number of expected peaks that could be assigned<br />
Match: Number of assigned peaks that fit reference shifts<br />
#Measured: Total number of peaks in peak list<br />
Assigned: Number of measured peaks that could be assigned to expected peaks<br />
exp/meas: Ratio of assigned expected and measured peaks<br />
<br />
Lists #Expected noRef noPeak Assigned Match #Measured Assigned exp/meas Assigned<br />
N15HSQC 106 8 1 104( 98.11%) 97( 91.51%) 131 96( 73.28%) 1.1<br />
HNCA 211 15 11 194( 91.94%) 186( 88.15%) 329 179( 54.41%) 1.1<br />
HNcaCO 211 15 11 197( 93.36%) 183( 86.73%) 246 176( 71.54%) 1.1<br />
HNCO 105 7 1 101( 96.19%) 97( 92.38%) 158 97( 61.39%) 1.0<br />
HNcoCA 105 7 0 101( 96.19%) 97( 92.38%) 158 99( 62.66%) 1.0<br />
CBCANH 399 26 25 361( 90.48%) 350( 87.72%) 623 339( 54.41%) 1.1<br />
CBCAcoNH 200 13 2 196( 98.00%) 185( 92.50%) 324 192( 59.26%) 1.0<br />
ALL 1337 91 51 1254( 93.79%) 1195( 89.38%) 1969 1178( 59.83%) 1.1<br />
<br />
It contains the following data:<br />
<br />
* '''#Expected:''' Total number of expected peaks<br />
* '''noRef:''' Number of expected peaks with missing reference shifts<br />
* '''noPeak:''' Number of expected peaks for which no peak can be measured<br />
* '''Assigned:''' Number of expected peaks that could be assigned based on the reference chemical shift assignments. The theoretical maximum of 100% corresponds to the situation that the spectra “explain” all expected peaks. Each expected peak can be mapped to at most one measured peak. Remaining expected peaks correspond to missing peaks in the measured peak list.<br />
* '''Match:''' Number of assigned peaks that fit (within tolerance) reference shifts. The theoretical maximum of 100% corresponds to having all measured peaks assigned. Note that several expected peaks can be mapped to the same measured peak, i.e. the assignments of measured peaks can be unambiguous or ambiguous. Remaining unassigned measured peaks are likely to be artifacts.<br />
* '''#Measured:''' Total number of peaks in peak list<br />
* '''Assigned:''' Number of measured peaks that could be assigned to expected peaks<br />
* '''exp/meas:''' Ratio of assigned expected and measured peaks<br />
<br />
There is more information on the results of the assignment calculation in the 'flya.txt' file (not described here).<br />
<br />
=== The flya.tab file ===<br />
<br />
This file provides information about the chemical shift assignment of each individual atom:<br />
<br />
Atom Residue Ref Shift Dev Extent inside inref<br />
...<br />
N GLY 57 102.109 102.043 0.066 10.0 100.0 100.0 strong=<br />
H GLY 57 8.571 8.570 0.001 10.0 100.0 100.0 strong=<br />
CA GLY 57 45.415 45.433 -0.018 10.0 100.0 100.0 strong=<br />
HA2 GLY 57 4.042<br />
HA3 GLY 57 3.436<br />
C GLY 57 173.621 173.662 -0.041 10.0 89.4 90.0 strong=<br />
N LEU 58 120.640 120.649 -0.009 10.0 80.0 80.0 =<br />
H LEU 58 7.488 7.492 -0.004 10.0 79.8 80.0 =<br />
CA LEU 58 51.943 51.940 0.003 10.0 70.0 70.0 =<br />
HA LEU 58 4.995<br />
CB LEU 58 45.602 45.568 0.034 10.0 82.7 80.0 strong=<br />
CG LEU 58 26.528<br />
HG LEU 58 1.515<br />
CD1 LEU 58 24.745<br />
C LEU 58 173.619 174.576 -0.957 10.0 40.1 10.0 ! (C 59)<br />
...<br />
<br />
* '''Ref:''' Chemical shift value in the reference chemical shift list (ref.prot). It was not used in the calculation.<br />
* '''Shift:''' Consensus chemical shift value from FLYA<br />
* '''Dev''' = Ref - Shift<br />
* '''Extent:''' Number of runs in which the atom was assigned by FLYA.<br />
* '''Inside:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the consensus value.<br />
* '''inref:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the reference value.<br />
* Outcome of the assignment:<br />
** '''strong:''' "strong" assignment, i.e. Inside > 80%.<br />
** '''=:''' Assignment that agrees with reference, i.e. Dev < tolerance.<br />
** '''!:''' Assignment that does not agree with the reference, i.e. Dev > tolerance.<br />
** '''('''''atom name'''''):''' Correct assignment, if within the same residue (no residue number given), or the neighboring residues.<br />
<br />
=== The flya.pdf file ===<br />
<br />
This PDF file provides a graphical representation of the 'flya.tab' file. Each assignment for an atom is represented by a colored rectangle. <br />
[[Image:flyabackbone.png|thumb|600px|'''flya.pdf generated by CALCbackbone.cya''']]<br />
<br />
* '''Green:''' Assignment by FLYA agrees with the manually determined reference assignment (within tolerance) <br />
* '''Red:''' Assignment by FLYA does not agree with the manually determined reference assignment<br />
* '''Blue:''' Assigned by FLYA but no reference available<br />
* '''Black:''' With reference assignment but not assigned by FLYA. <br />
<br />
Respective light colors indicate assignments not classified as strong by the chemical shift consolidation. The row labeled HN/Hα shows for each residue HN on the left and Hα in the center. The N/Cα/C’ row shows for each residue the N, Cα, and C’ assignments from left to right. The rows β-η show the side-chain assignments for the heavy atoms in the center and hydrogen atoms to the left and right. In the case of branched side-chains, the corresponding row is split into an upper part for one branch and a lower part for the other branch.<br />
<br />
== FLYA applications ==<br />
<br />
CYANA macros 'CALC*.cya' are provided for the following FLYA tasks:<br />
<br />
=== CALC.cya: standard automated chemical shift assignment ===<br />
<br />
* specify list of input peak lists in variable 'peaks' without intervening blanks<br />
* specify tolerances for 1H, 13C, 15N with variables assigncs_assH, assigncs_assC assigncs_assN<br />
* command 'select_atoms' excludes some nuclei that are difficult to detect<br />
* optional parameter 'shiftreference=ref.prot' specifies reference chemical shift list, used only for comparison in flya.tab, flya.txt, flya.pdf<br />
<!--<br />
'''Note that the input data for this calculation contains two mistakes. Try to identify the problem by inpecting the 'flya.txt' file and the input files. Correct the mistakes and rerun the calculation before proceeding with other calculations!<br />
'''--><br />
<br />
=== CALCbackbone.cya: standard backbone chemical shift assignment ===<br />
* parameter 'structure=' to avoid generation of random structures, which are not needed if using only through-bond spectra<br />
<br />
=== CALCexperiments.cya: using modified/new experiment definitions in library ===<br />
* modified HCCHTOCSY only for aromatics (library HCCHTOCSY.lib, peak list HCCHTOCSYaro.peaks)<br />
* new experiment N15NOESY2D (library peak list N15NOESY2D.lib, peak list N15NOESY2D.peaks)<br />
<br />
=== CALCexpfromlist.cya: read expected peaks from a peak list ===<br />
* command N15NOESY_expect, reading input peak list N15NOESY_in.peaks<br />
<br />
=== CALCfixedpeaks.cya: keep input peak assignments in user peak assignments ===<br />
* (partially) assigned input peak list N15HSQCassigned.peaks<br />
* parameter 'keepassigned' for loadspectra.cya<br />
<br />
=== CALCfixedshifts.cya: fix input chemical shift assignments ===<br />
* input chemical shift list 'fix.prot'<br />
* shift error in chemical shift list specifies range for assignment<br />
<br />
=== CALClabeling.cya: use of experiment-specific isotope labeling ===<br />
* command 'select_atoms' for general selection of assignable nuclei CcoNH + HSQCLEULYS<br />
* command '<peak list name>_select' with atom selection for a specific peak list (e.g. C13HSQC_LK.peaks) <br />
* command '<peak list name>_expect' for non-standard generation of expected peaks for a given peak list (e.g. CcoNH_LK.peaks with dimension-specific atom selection)<br />
<br />
=== CALCnoesyonly.cya: chemical shift assignment using exclusively NOESY ===<br />
*increased population size with 'shiftassign_population=200'<br />
* see Schmidt et al. J. Biomol. NMR 57, 193-204 (2013)<br />
<br />
<!--=== CALCquick.cya: fast automated chemical shift assignment ===<br />
* fixed number of generations in evolutionary optimization<br />
--><br />
=== CALCstatistics.cya: user-defined chemical shift statistics instead of standard BMRB statistics from library ===<br />
* average value and stddev from input chemical shift list 'shiftx.prot'<br />
* 'assigncs_sd:=bmrb' to use stddev from BMRB (cyana.lib) instead of input chemical shift list<br />
* 'assigncs_sdfactor:=0.5' to scale BMRB stddev by given factor<br />
<br />
=== CALCstructcalc.cya: follow automated shift assignment by automated NOESY assignment and structure calculation ===<br />
* peak lists for distance restraint generation specified by parameter 'structurepeaks='<br />
<br />
=== CALCstructure.cya: use input structure to generate expected peaks for through-space experiments ===<br />
* specify with parameter 'structure' of command 'flya'<br />
* if parameter 'structure' is absent, a set of random structures is generated automatically<br />
* if set to blank ('structure='), no random structures are generated (if not needed because only through-bond spectra are used)<br />
<br />
== Results ==<br />
<br />
You can download the [http://www.cyana.org/demo-results.tgz|results of all CYANA demo calculations] (92 MB).</div>Guenterthttps://cyana.org/w/index.php?title=Automated_resonance_assignment_with_FLYA_(Gothenburg_2021)&diff=9867Automated resonance assignment with FLYA (Gothenburg 2021)2021-09-28T08:44:48Z<p>Guentert: </p>
<hr />
<div>In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA. <br />
<br />
== Installation of CYANA demo version ==<br />
<br />
If not done yet, please install the [[Tutorials#Downloads|demo version of CYANA]].<br />
<br />
== Experimental input data ==<br />
<br />
Example data for FLYA is in the 'demo/flya' directory of the CYANA package. <br />
<br />
The protein sequence is stored in three-letter code in the file 'demo.seq'. <br />
<br />
Experimental peak lists are available for the following spectra:<br />
* [<sup>1</sup>H,<sup>13</sup>C]-HSQC (called 'C13HSQC' in FLYA)<br />
* [<sup>1</sup>H,<sup>15</sup>N]-HSQC (called 'N15HSQC' in FLYA)<br />
* 3D [<sup>13</sup>C]-resolved NOESY (called 'C13NOESY' in FLYA)<br />
* 3D [<sup>15</sup>N]-resolved NOESY (called 'N15NOESY' in FLYA)<br />
* HNCA<br />
* HN(CO)CA (called 'HNcoCA' in FLYA)<br />
* HNCO<br />
* HN(CA)CO (called 'HNcaCO' in FLYA)<br />
* CBCANH<br />
* CBCACONH (called 'CBCAcoNH' in FLYA)<br />
* HBHACONH (called 'HBHAcoNH' in FLYA)<br />
* HCCH-TOCSY (called 'HCCHTOCSY' in FLYA)<br />
* HCCH-COSY (called 'HCCHCOSY' in FLYA)<br />
* C(CO)NH (called 'CcoNH' in FLYA)<br />
* HC(CO)NH (called 'HCcoNH' in FLYA)<br />
<br />
Peak lists in XEASY format that have been prepared by automatic peak picking with the program NMRView are stored in files ''XXX''.peaks, where ''XXX'' denotes the FLYA spectrum type.<br />
<br />
Each peak list starts with a header that defines the experiment type and the order of dimensions. For instance, for HNCA.peaks:<br />
<br />
# Number of dimensions 3<br />
#FORMAT xeasy3D<br />
#INAME 1 HN<br />
#INAME 2 C<br />
#INAME 3 N<br />
#SPECTRUM HNCA HN C N<br />
5 6.475 58.033 98.548 1 U 2.769E+02 0.000E+00 e 0 0 0 0<br />
6 6.476 62.123 98.126 1 U 2.571E+01 0.000E+00 e 0 0 0 0<br />
7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0<br />
<br />
The first line specifies the number of dimensions (3 in this case). The next 4 lines ('#FORMAT' and '#INAME') are ignored by CYANA. The '#SPECTRUM' line is crucial and gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. These labels must match those in the corresponding experiment definition in the general CYANA library (see below). After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has<br />
<br />
* Peak number 5<br />
* HN chemical shift 6.475 ppm<br />
* C (i.e. CA) chemical shift 58.033 ppm<br />
* N chemical shift 98.548 ppm<br />
<br />
The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm.<br />
<br />
'''Hint:''' The formats of other CYANA files are described in the [[CYANA 3.0 Reference Manual|CYANA Reference Manual]].<br />
<br />
<!--<br />
== FLYA initialization script ==<br />
<br />
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". <br />
<br />
One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any time one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library and the protein sequence: <br />
<br />
cyanalib<br />
read demo.seq<br />
<br />
The command 'cyanalib' reads the standard CYANA library. The second command reads the protein sequence.<br />
--><br />
<br />
== Experiment definitions in the CYANA library ==<br />
<br />
When you start CYANA, the program reads the library and displays the full path name of the library file. You can open the standard library file to inspect, for example, the NMR experiment definitions that define how expected peaks are generated by FLYA. For instance, the definition for the HNCA spectrum (search for 'HNCA' in the library file 'cyana.lib') is<br />
<br />
SPECTRUM HNCA HN N C<br />
0.980 HN:H_AMI N:N_AM* C:C_ALI C_BYL<br />
0.800 HN:H_AMI N:N_AMI (C_ALI) C_BYL C:C_ALI <br />
<br />
The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and a label for the atoms that are detected in each dimension of the spectrum. The number of labels defines the dimensionality of the experiment (3 in case of HNCA).<br />
<br />
Each line below defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of HNCA there are two lines, corresponding to the intraresidual and sequential peak. For instance, the definition for the intraresidual peak starts with the probability to observe the peak (0.980), followed by a series of atom types, e.g. H_AMI for amide proton etc. An expected peak is generated for each molecular fragment in which these atom types occur connected by single covalent bonds. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for HNCA 'HN:', 'N:', and 'C:'. The additional atom types refer to atoms that are not detected but must be present in a matching molecular fragment. An atom type in parenthesis indicates a branch in the molecular fragment. For instance, in the second magnetization transfer pathway that specifies the sequential HNCA peak, '(C_ALI)' indicates that the atom 'N:N_ALI' must be connected by a covalent bond to both a C_ALI (i.e. CA) and a C_BYL (i.e. C' of the preceding residue.<br />
<br />
== FLYA execution scripts ==<br />
<br />
The CYANA scripts ("macros") 'CALC*.cya' contain the commands to perform various automated chemical shift assignment calculations.<br />
<br />
For instance, 'CALCbackbone.cya' performs automated backbone resonance assignment. It starts with the specification of the names of the input peak lists:<br />
<br />
peaks:=N15HSQC,HNCA,HNcaCO,HNCO,HNcoCA,CBCANH,CBCAcoNH<br />
<br />
The peak list names are separated by commas (without blanks!). The files on disk have the file name extension .peaks, e.g. HNCA.peaks.<br />
<br />
The commands above will use all available peak lists. You can choose any subset of them by modifying the 'peaks:=...' statement. <br />
<br />
These are followed by tolerances for chemical shift matching:<br />
<br />
assigncs_accH=0.03<br />
assigncs_accC=0.4<br />
assigncs_accN=assigncs_accC<br />
tolerance:=$assigncs_accH,$assigncs_accH,$assigncs_accC<br />
<br />
In this case, a tolerance of 0.03 ppm will be used for protons, and 0.4 ppm for carbon and nitrogen.<br />
<br />
The next parameter specifies the seed value for the random number generator (an arbitrary positive integer is ok). <br />
<br />
randomseed=101<br />
<br />
Groups of atoms for which assignment statistics will be calculated and reported in the 'flya.txt' output file can be defined like this:<br />
<br />
analyzeassign_group := BB: N H CA CB C <br />
<br />
The next commands restrict the generation of expected peaks to a subset of atoms, here the backbone atoms:<br />
<br />
command select_atoms<br />
atom select "N H CA CB C"<br />
end<br />
<br />
In this case, the command defines a group called BB (a name that can be chosen freely) comprising the atoms N, H, CA, CB, C.<br />
<br />
Specific labeling can be handled in the same way. Peak list-specific atom selections can be applied as follows (not used in 'CALCbackbone.cya' but in 'CALClabeling.cya'):<br />
<br />
command ''XXX''_select<br />
atoms select "..."<br />
end<br />
<br />
If desired, a "quick" optimization schedule can be used in the FLYA examples in order to speed up the calculation by inserting the following line above the 'flya ...' command:<br />
<br />
shiftassign_quick=1<br />
<br />
In production runs, better results can be expected (at the expense of longer computation times) if this variable is not set. <br />
Finally, there is the command to start the FLYA algorithm:<br />
<br />
flya runs=10 assignpeaks=$peaks structure= shiftreference=ref.prot<br />
<br />
Here, the given parameters of the 'flya' command specify that<br />
<br />
* The number of independent runs of the algorithm, from which the consolidated shift will be calculated (chosen smaller than in normal production runs in order to speed up the calculation).<br />
* The input peak lists that will be used (as defined above).<br />
* No ensemble of random structures will be calculated for generating expected peaks (is only necessary for NOESY-type experiments).<br />
* The results will be compared with the reference chemical shifts in the file 'ref.prot' (which have been determined independently by conventional methods). The reference chemical shifts will not be used by the algorithm but only for a subsequent analysis of its results.<br />
<br />
== Run a FLYA calculation ==<br />
<br />
To run a FLYA calculation, you start CYANA and execute the corresponding 'CALC*.cya' script. For instance:<br />
<br />
cyana "nproc=10; CALCbackbone"<br />
<br />
By specifying 'nproc=10', 10 independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes. For FLYA, the value of 'nproc' should correspond to the number of independent FLYA runs, i.e. the 'runs=10' parameter of the above 'flya' command.<br />
<br />
== FLYA output files ==<br />
<br />
The FLYA algorithm will produce the following output files:<br />
<br />
* '''flya.prot:''' Consensus assigned chemical shifts. This file contains a chemical shift for every atom that has been assigned to least one peak.<br />
* '''flya.tab:''' Table with details about the chemical shift assignment of each atom (comparison with reference shifts). In this file you can see for each atom whether the assignment is "strong" (self-consistent) or "weak" (only tentative).<br />
* '''flya.txt:''' Assignment statistics<br />
* '''flya.pdf:''' Graphical representation of the assignment results<br />
* '''''XXX''_exp.peaks:''' List of expected peaks, corresponding to input peak list ''XXX''.peaks<br />
* '''''XXX''_asn.peaks:''' Assigned peak list, corresponding to input peak list ''XXX''.peaks<br />
<br />
=== The flya.txt file ===<br />
<br />
This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in CALCbackbone.cya':<br />
<br />
____________________________________________________________<br />
<br />
CHEMICAL SHIFT ASSIGNMENT<br />
____________________________________________________________<br />
<br />
SEED: 1<br />
chemical shifts for 542 atoms found<br />
Peaks assigned from frequencies<br />
<br />
BB: REFERENCES(2):512 CHEMICALSHIFTS(1):542 (1)and(2):512 MATCH:507(99.0% of (2))<br />
<br />
* REFERENCES(2) is the number of reference assignments (in the selected group)<br />
* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA<br />
* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference. <br />
* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.<br />
<br />
Further below comes a table with information about each peak list:<br />
<br />
PEAKLISTS<br />
#Expected: Total number of expected peaks<br />
noRef: Number of expected peaks with missing reference shifts<br />
noPeak: Number of expected peaks for wich no peak can be measured<br />
Assigned: Number of expected peaks that could be assigned<br />
Match: Number of assigned peaks that fit reference shifts<br />
#Measured: Total number of peaks in peak list<br />
Assigned: Number of measured peaks that could be assigned to expected peaks<br />
exp/meas: Ratio of assigned expected and measured peaks<br />
<br />
Lists #Expected noRef noPeak Assigned Match #Measured Assigned exp/meas Assigned<br />
N15HSQC 106 8 1 104( 98.11%) 97( 91.51%) 131 96( 73.28%) 1.1<br />
HNCA 211 15 11 194( 91.94%) 186( 88.15%) 329 179( 54.41%) 1.1<br />
HNcaCO 211 15 11 197( 93.36%) 183( 86.73%) 246 176( 71.54%) 1.1<br />
HNCO 105 7 1 101( 96.19%) 97( 92.38%) 158 97( 61.39%) 1.0<br />
HNcoCA 105 7 0 101( 96.19%) 97( 92.38%) 158 99( 62.66%) 1.0<br />
CBCANH 399 26 25 361( 90.48%) 350( 87.72%) 623 339( 54.41%) 1.1<br />
CBCAcoNH 200 13 2 196( 98.00%) 185( 92.50%) 324 192( 59.26%) 1.0<br />
ALL 1337 91 51 1254( 93.79%) 1195( 89.38%) 1969 1178( 59.83%) 1.1<br />
<br />
It contains the following data:<br />
<br />
* '''#Expected:''' Total number of expected peaks<br />
* '''noRef:''' Number of expected peaks with missing reference shifts<br />
* '''noPeak:''' Number of expected peaks for which no peak can be measured<br />
* '''Assigned:''' Number of expected peaks that could be assigned based on the reference chemical shift assignments. The theoretical maximum of 100% corresponds to the situation that the spectra “explain” all expected peaks. Each expected peak can be mapped to at most one measured peak. Remaining expected peaks correspond to missing peaks in the measured peak list.<br />
* '''Match:''' Number of assigned peaks that fit (within tolerance) reference shifts. The theoretical maximum of 100% corresponds to having all measured peaks assigned. Note that several expected peaks can be mapped to the same measured peak, i.e. the assignments of measured peaks can be unambiguous or ambiguous. Remaining unassigned measured peaks are likely to be artifacts.<br />
* '''#Measured:''' Total number of peaks in peak list<br />
* '''Assigned:''' Number of measured peaks that could be assigned to expected peaks<br />
* '''exp/meas:''' Ratio of assigned expected and measured peaks<br />
<br />
There is more information on the results of the assignment calculation in the 'flya.txt' file (not described here).<br />
<br />
=== The flya.tab file ===<br />
<br />
This file provides information about the chemical shift assignment of each individual atom:<br />
<br />
Atom Residue Ref Shift Dev Extent inside inref<br />
...<br />
N GLY 57 102.109 102.043 0.066 10.0 100.0 100.0 strong=<br />
H GLY 57 8.571 8.570 0.001 10.0 100.0 100.0 strong=<br />
CA GLY 57 45.415 45.433 -0.018 10.0 100.0 100.0 strong=<br />
HA2 GLY 57 4.042<br />
HA3 GLY 57 3.436<br />
C GLY 57 173.621 173.662 -0.041 10.0 89.4 90.0 strong=<br />
N LEU 58 120.640 120.649 -0.009 10.0 80.0 80.0 =<br />
H LEU 58 7.488 7.492 -0.004 10.0 79.8 80.0 =<br />
CA LEU 58 51.943 51.940 0.003 10.0 70.0 70.0 =<br />
HA LEU 58 4.995<br />
CB LEU 58 45.602 45.568 0.034 10.0 82.7 80.0 strong=<br />
CG LEU 58 26.528<br />
HG LEU 58 1.515<br />
CD1 LEU 58 24.745<br />
C LEU 58 173.619 174.576 -0.957 10.0 40.1 10.0 ! (C 59)<br />
...<br />
<br />
* '''Ref:''' Chemical shift value in the reference chemical shift list (ref.prot). It was not used in the calculation.<br />
* '''Shift:''' Consensus chemical shift value from FLYA<br />
* '''Dev''' = Ref - Shift<br />
* '''Extent:''' Number of runs in which the atom was assigned by FLYA.<br />
* '''Inside:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the consensus value.<br />
* '''inref:''' Percentage of chemical shift values from the (10) independent runs of FLYA that agree (within the tolerance) with the reference value.<br />
* Outcome of the assignment:<br />
** '''strong:''' "strong" assignment, i.e. Inside > 80%.<br />
** '''=:''' Assignment that agrees with reference, i.e. Dev < tolerance.<br />
** '''!:''' Assignment that does not agree with the reference, i.e. Dev > tolerance.<br />
** '''('''''atom name'''''):''' Correct assignment, if within the same residue (no residue number given), or the neighboring residues.<br />
<br />
=== The flya.pdf file ===<br />
<br />
This PDF file provides a graphical representation of the 'flya.tab' file. Each assignment for an atom is represented by a colored rectangle. <br />
[[Image:flyabackbone.png|thumb|600px|'''flya.pdf generated by CALCbackbone.cya''']]<br />
<br />
* '''Green:''' Assignment by FLYA agrees with the manually determined reference assignment (within tolerance) <br />
* '''Red:''' Assignment by FLYA does not agree with the manually determined reference assignment<br />
* '''Blue:''' Assigned by FLYA but no reference available<br />
* '''Black:''' With reference assignment but not assigned by FLYA. <br />
<br />
Respective light colors indicate assignments not classified as strong by the chemical shift consolidation. The row labeled HN/Hα shows for each residue HN on the left and Hα in the center. The N/Cα/C’ row shows for each residue the N, Cα, and C’ assignments from left to right. The rows β-η show the side-chain assignments for the heavy atoms in the center and hydrogen atoms to the left and right. In the case of branched side-chains, the corresponding row is split into an upper part for one branch and a lower part for the other branch.<br />
<br />
== FLYA applications ==<br />
<br />
CYANA macros 'CALC*.cya' are provided for the following FLYA tasks:<br />
<br />
=== CALC.cya: standard automated chemical shift assignment ===<br />
<br />
* specify list of input peak lists in variable 'peaks' without intervening blanks<br />
* specify tolerances for 1H, 13C, 15N with variables assigncs_assH, assigncs_assC assigncs_assN<br />
* command 'select_atoms' excludes some nuclei that are difficult to detect<br />
* optional parameter 'shiftreference=ref.prot' specifies reference chemical shift list, used only for comparison in flya.tab, flya.txt, flya.pdf<br />
<!--<br />
'''Note that the input data for this calculation contains two mistakes. Try to identify the problem by inpecting the 'flya.txt' file and the input files. Correct the mistakes and rerun the calculation before proceeding with other calculations!<br />
'''--><br />
<br />
=== CALCbackbone.cya: standard backbone chemical shift assignment ===<br />
* parameter 'structure=' to avoid generation of random structures, which are not needed if using only through-bond spectra<br />
<br />
=== CALCexperiments.cya: using modified/new experiment definitions in library ===<br />
* modified HCCHTOCSY only for aromatics (library HCCHTOCSY.lib, peak list HCCHTOCSYaro.peaks)<br />
* new experiment N15NOESY2D (library peak list N15NOESY2D.lib, peak list N15NOESY2D.peaks)<br />
<br />
=== CALCexpfromlist.cya: read expected peaks from a peak list ===<br />
* command N15NOESY_expect, reading input peak list N15NOESY_in.peaks<br />
<br />
=== CALCfixedpeaks.cya: keep input peak assignments in user peak assignments ===<br />
* (partially) assigned input peak list N15HSQCassigned.peaks<br />
* parameter 'keepassigned' for loadspectra.cya<br />
<br />
=== CALCfixedshifts.cya: fix input chemical shift assignments ===<br />
* input chemical shift list 'fix.prot'<br />
* shift error in chemical shift list specifies range for assignment<br />
<br />
=== CALClabeling.cya: use of experiment-specific isotope labeling ===<br />
* command 'select_atoms' for general selection of assignable nuclei CcoNH + HSQCLEULYS<br />
* command '<peak list name>_select' with atom selection for a specific peak list (e.g. C13HSQC_LK.peaks) <br />
* command '<peak list name>_expect' for non-standard generation of expected peaks for a given peak list (e.g. CcoNH_LK.peaks with dimension-specific atom selection)<br />
<br />
=== CALCnoesyonly.cya: chemical shift assignment using exclusively NOESY ===<br />
*increased population size with 'shiftassign_population=200'<br />
* see Schmidt et al. J. Biomol. NMR 57, 193-204 (2013)<br />
<br />
<!--=== CALCquick.cya: fast automated chemical shift assignment ===<br />
* fixed number of generations in evolutionary optimization<br />
--><br />
=== CALCstatistics.cya: user-defined chemical shift statistics instead of standard BMRB statistics from library ===<br />
* average value and stddev from input chemical shift list 'shiftx.prot'<br />
* 'assigncs_sd:=bmrb' to use stddev from BMRB (cyana.lib) instead of input chemical shift list<br />
* 'assigncs_sdfactor:=0.5' to scale BMRB stddev by given factor<br />
<br />
=== CALCstructcalc.cya: follow automated shift assignment by automated NOESY assignment and structure calculation ===<br />
* peak lists for distance restraint generation specified by parameter 'structurepeaks='<br />
<br />
=== CALCstructure.cya: use input structure to generate expected peaks for through-space experiments ===<br />
* specify with parameter 'structure' of command 'flya'<br />
* if parameter 'structure' is absent, a set of random structures is generated automatically<br />
* if set to blank ('structure='), no random structures are generated (if not needed because only through-bond spectra are used)<br />
<br />
== FLYA applications ==<br />
<br />
You can download the [results of all CYANA demo calculations http://www.cyana.org/demo-results.tgz] (92 MB).</div>Guentert