CYANA Wiki - User contributions [en]

CYANA Macro: write all

2010-01-12T11:00:48Z

Masayo: /* Parameters */

== Parameters ==

; name=''string''
:(required)
; ang
; cor
; pdb
; connect

== Description ==

Writes all selected structures to angle (ang), DG coordinate (cor), or PDB coordinate (pdb) files with names "namennn.ang", "namennn.cor", or "namennn.pdb", respectively. nnn denotes the structure number.

CYANA Command: write peaks

2010-01-12T10:43:16Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.peaks
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;format=''string''
:(default: ''blank'')
;reference
;append

== Description ==

Writes a peak list in Xeasy format (Eccles et al., 1991; Bartels et al., 1995). Optionally, the output may be appended to an existing file. By default all peaks are written. Optionally, only the selected peaks are written.

CYANA Macro: write all

2010-01-12T10:41:16Z

Masayo: /* Description */

== Parameters ==

; name=''string'' (required)
; ang
; cor
; pdb
; connect

== Description ==

Writes all selected structures to angle (ang), DG coordinate (cor), or PDB coordinate (pdb) files with names "namennn.ang", "namennn.cor", or "namennn.pdb", respectively. nnn denotes the structure number.

CYANA Command: write ang

2010-01-12T10:33:05Z

Masayo: /* Description */

== Parameters ==

;file=''filename''.ang
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;fixed
;all
;append

== Description ==

Writes an angle file. Optionally, the output may be appended to an
existing file. By default, the values of all rotatable dihedral
angles of the current structure conformation are written. The values of the fixed dihedral angles (e.g. peptide bond angles) may be written, too. Optionally, the angles of all selected structures may be written.

CYANA Command: write ang

2010-01-12T10:32:17Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.ang
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;fixed
;all
;append

== Description ==

Writes an angle file. Optionally, the output may be appended to an
existing file. By default, the values of all rotatable dihedral
angles of the current structure conformation are written. The values
of the fixed dihedral angles (e.g. peptide bond angles) may be written,
too. Optionally, the angles of all selected structures may be written.

CYANA Command: write cco

2010-01-12T10:31:05Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.cco
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;karpluscurves
;append

CYANA Command: write cor

2010-01-12T10:29:51Z

Masayo: /* Description */

== Parameters ==

;file=''filename''.cor
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;bfactor=''real''
:(default: 0.0)
;chains=''string''
:(default: *)
;details
;all
;oldall
;connect
;append

== Description ==

Writes a coordinate file in DG (Distance Geometry) format. Optionally, the output may be appended to an existing file. By default, the Cartesian coordinates of the current structure are written. The covalent connectivities may be included, too. Optionally, the Cartesian coordinates of all selected structures may be written.

CYANA Command: write cor

2010-01-12T10:29:13Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.cor
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;bfactor=''real''
:(default: 0.0)
;chains=''string''
:(default: *)
;details
;all
;oldall
;connect
;append

== Description ==

Writes a coordinate file in DG (Distance Geometry) format. Optionally,
the output may be appended to an existing file. By default, the
Cartesian coordinates of the current structure are written. The
covalent connectivities may be included, too. Optionally, the Cartesian
coordinates of all selected structures may be written.

CYANA Command: write lib

2010-01-12T10:27:37Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.lib
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;names
;append

CYANA Command: write lol

2010-01-12T10:26:24Z

Masayo: /* Parameters */

''Write lower distance limit file''

== Parameters ==

;file=''filename''.lol
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;sorted
;swapped
;xplor
;nocomments
;append

== Description ==

Writes a file with the currently selected lower distance limits in the standard [[distance restraint file]] format of the program CYANA, or optionally in XPLOR format.

Instead of the command

write lol ''filename''.lol

the shorthand version

write ''filename''.lol

can be used if the filename extension is ".lol".

CYANA Command: write pcs

2010-01-12T10:24:26Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.pcs
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;calculated
;append

CYANA Command: write pdb

2010-01-12T10:22:22Z

Masayo: /* Description */

== Parameters ==

;file=''filename''.pdb
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;bfactor=''real''
:(default: 0.0)
;chains=''string''
:(default: *)
;details
;all
;oldall
;connect
;append

== Description ==

Writes a coordinate file in PDB (Protein Data Bank; Bernstein et al.,1977) format. Optionally, the output may be appended to an existing file. By default, the Cartesian coordinates of the current structure are written. Optionally, the Cartesian coordinates of all selected structures may be written.

CYANA Command: write pdb

2010-01-12T10:21:49Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.pdb
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;bfactor=''real''
:(default: 0.0)
;chains=''string''
:(default: *)
;details
;all
;oldall
;connect
;append

== Description ==

Writes a coordinate file in PDB (Protein Data Bank; Bernstein et al.,
1977) format. Optionally, the output may be appended to an existing
file. By default, the Cartesian coordinates of the current structure
are written. Optionally, the Cartesian coordinates of all selected
structures may be written.

CYANA Command: write peaks

2010-01-12T10:19:11Z

Masayo: /* Description */

== Parameters ==

;file=''filename''.peaks
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;format=''string''
:(default: <blank>)
;reference
;append

== Description ==

Writes a peak list in Xeasy format (Eccles et al., 1991; Bartels et al., 1995). Optionally, the output may be appended to an existing file. By default all peaks are written. Optionally, only the selected peaks are written.

CYANA Command: write peaks

2010-01-12T10:18:33Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.peaks
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;format=''string''
:(default: <blank>)
;reference
;append

== Description ==

Writes a peak list in Xeasy format (Eccles et al., 1991; Bartels et
al., 1995). Optionally, the output may be appended to an existing file.
By default all peaks are written. Optionally, only the selected peaks
are written.

CYANA Command: write rdc

2010-01-12T10:16:56Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.rdc
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;calculated
;append

CYANA Command: write seq

2010-01-12T10:15:29Z

Masayo: /* Parameters */

''Write sequence file''

== Parameters ==

;file=''filename''.seq
:(required)
;list=''intege''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;pure
;append

== Description ==

Writes a file with the residue sequence in the standard [[sequence file]] format of the program CYANA.

Instead of the command

write seq ''filename''.seq

the shorthand version

write ''filename''.seq

can be used if the filename extension is ".seq".

CYANA Command: write sparky

2010-01-12T10:13:50Z

Masayo: /* Parameters */

== Parameters ==

;file=''filename''.sparky
:(required)
;list=''integer''
:(default: 1)
;nmrstar=''integer''
:(default: 2)
;details
;multiple
;format=''string''
:(default: ''blank'')
;reference
;append

CYANA Command: write upl

2010-01-12T10:11:43Z

Masayo: /* Description */

''Write upper distance limit file''

== Parameters ==

; file=''filename''.upl:(required)
;list=''integer'':(default: 1)
;nmrstar=''integer'':(default: 2)
;details
;multiple
;sorted
;swapped
;xplor
;nocomments
;append

== Description ==

Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file.

==== Ambiguous distance restraints ====

Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''1,''β''1),...,(''αn'',''βn'') and an upper distance bound ''b'' imposes on the structure the condition

:<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.

''d''(''α''i,''β''i) is the distance between the atoms ''α''i and ''β''i.

Note that the "effective distance" ''d''eff cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

==== Shorthand form ====

Instead of the command

write upl ''filename''.upl

the shorthand version

write ''filename''.upl

can be used if the filename extension is ".upl".

CYANA Command: write upl

2010-01-12T10:09:29Z

Masayo: /* Parameters */

''Write upper distance limit file''

== Parameters ==

; file=''filename''.upl:(required)
;list=''integer'':(default: 1)
;nmrstar=''integer'':(default: 2)
;details
;multiple
;sorted
;swapped
;xplor
;nocomments
;append

== Description ==

Writes a file with the currently selected upper distance limits in the standard [[distance restraint file]] format of the program CYANA, or optionally in XPLOR format.

==== Ambiguous distance restraints ====

Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''1,''β''1),...,(''αn'',''βn'') and an upper distance bound ''b'' imposes on the structure the condition

:<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.

''d''(''α''i,''β''i) is the distance between the atoms ''α''i and ''β''i.

Note that the "effective distance" ''d''eff cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

==== Shorthand form ====

Instead of the command

write upl ''filename''.upl

the shorthand version

write ''filename''.upl

can be used if the filename extension is ".upl".

CYANA Command: write xpk

2010-01-12T10:07:51Z

Masayo: /* Parameters */

== Parameters ==

; file=''filename''.xpk :(required)
; list=''integer'' :(default: 1)
; nmrstar=''integer'' :(default: 2)
; details
; multiple
; format=''string'' :(default: ''blank'')
; reference
; append

CYANA Command: write xpk

2010-01-12T10:05:59Z

Masayo: /* Parameters */

== Parameters ==

; file=''filename''.xpk (required)
; list=''integer'' : (default: 1)
; nmrstar=''integer'' : (default: 2)
; details
; multiple
; format=''string'' : (default: ''blank'')
; reference
; append

INCLAN Reference Manual

2009-09-09T16:22:33Z

Masayo: /* INCLAN Graphics */

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.

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.

The current version of INCLAN is implemented in Fortran-95, 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].

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.

* [[INCLAN: Special characters|Special characters]]

== INCLAN Commands ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: Commands|Introduction]]
</div>
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: abort|abort]]
* [[INCLAN: alias|alias]]
* [[INCLAN: ask|ask]]
* [[INCLAN: break|break]]
* [[INCLAN: cd, chdir|cd, chdir]]
* [[INCLAN: command|command]]
* [[INCLAN: do|do]]
* [[INCLAN: else|else]]
* [[INCLAN: else if|else if]]
* [[INCLAN: end|end]]
* [[INCLAN: end do|end do]]
* [[INCLAN: end if|end if]]
* [[INCLAN: error|error]]
* [[INCLAN: eval|eval]]
* [[INCLAN: external|external]]
* [[INCLAN: eval, show, set, unset, external|eval, show, set, unset, external]]
* [[INCLAN: exit|exit]]
* [[INCLAN: goto, go to|goto, go to]]
* [[INCLAN: help|help]]
* [[INCLAN: if|if]]
* [[INCLAN: label|label]]
* [[INCLAN: parameter|parameter]]
* [[INCLAN: plot|plot]]
* [[INCLAN: print|print]]
* [[INCLAN: print, error|print, error]]
* [[INCLAN: quit|quit]]
* [[INCLAN: readline|readline]]
* [[INCLAN: remove|remove]]
* [[INCLAN: return|return]]
* [[INCLAN: safe|safe]]
* [[INCLAN: set|set]]
* [[INCLAN: show|show]]
* [[INCLAN: sleep|sleep]]
* [[INCLAN: special characters|special characters]]
* [[INCLAN: subroutine|subroutine]]
* [[INCLAN: subroutine, command|subroutine, command]]
* [[INCLAN: synchronize|synchronize]]
* [[INCLAN: syntax|syntax]]
* [[INCLAN: system|system]]
* [[INCLAN: type|type]]
* [[INCLAN: unset|unset]]
* [[INCLAN: var|var]]
</div>

== INCLAN Variables==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: Variables|Introduction]]
* [[INCLAN: Variable substitutions|Variable substitutions]]
</div>
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: echo|echo]]
* [[INCLAN: erract|erract]]
* [[INCLAN: info|info]]
* [[INCLAN: label|label]]
* [[INCLAN: nparam|nparam]]
* [[INCLAN: nproc|nproc]]
* [[INCLAN: p1, p2,...|p1, p2,...]]
* [[INCLAN: path|path]]
* [[INCLAN: prompt|prompt]]
* [[INCLAN: protocol|protocol]]
* [[INCLAN: timing|timing]]
</div>

== Expressions and functions ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: Expressions|Expressions]]
* [[INCLAN: intrinsics|Intrinsic functions]]
</div>

== INCLAN Graphics ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: Graphics|Introduction]]
</div>
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN Graphics: plot arc|plot arc]]
* [[INCLAN Graphics: plot caro|plot caro]]
* [[INCLAN Graphics: plot clip|plot clip]]
* [[INCLAN Graphics: plot close|plot close]]
* [[INCLAN Graphics: plot comment|plot comment]]
* [[INCLAN Graphics: plot cross|plot cross]]
* [[INCLAN Graphics: plot curve|plot curve]]
* [[INCLAN Graphics: plot dot|plot dot]]
* [[INCLAN Graphics: plot errorbar|plot errorbar]]
* [[INCLAN Graphics: plot file|plot file]]
* [[INCLAN Graphics: plot fit|plot fit]]
* [[INCLAN Graphics: plot frame|plot frame]]
* [[INCLAN Graphics: plot function|plot function]]
* [[INCLAN Graphics: plot label|plot label]]
* [[INCLAN Graphics: plot layout|plot layout]]
* [[INCLAN Graphics: plot line|plot line]]
* [[INCLAN Graphics: plot plus|plot plus]]
* [[INCLAN Graphics: plot polygon|plot polygon]]
* [[INCLAN Graphics: plot ps|plot ps]]
* [[INCLAN Graphics: plot rectangle|plot rectangle]]
* [[INCLAN Graphics: plot scale|plot scale]]
* [[INCLAN Graphics: plot set|plot set]]
* [[INCLAN Graphics: plot shape|plot shape]]
* [[INCLAN Graphics: plot spline|plot spline]]
* [[INCLAN Graphics: plot square|plot square]]
* [[INCLAN Graphics: plot text|plot text]]
* [[INCLAN Graphics: plot triangle|plot triangle]]
* [[INCLAN Graphics: plot write|plot write]]
</div>

== INCLAN Plot Parameters ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN: align|align]]
* [[INCLAN: angle|angle]]
* [[INCLAN: autoscale|autoscale]]
* [[INCLAN: border|border]]
* [[INCLAN: color|color]]
* [[INCLAN: dash|dash]]
* [[INCLAN: fill|fill]]
* [[INCLAN: font|font]]
* [[INCLAN: linewidth|linewidth]]
* [[INCLAN: marksize|marksize]]
* [[INCLAN: mode|mode]]
* [[INCLAN: rotate|rotate]]
* [[INCLAN: textsize|textsize]]
* [[INCLAN: weight|weight]]
* [[INCLAN: x0, y0, x1, y1|x0, y0, x1, y1]]
* [[INCLAN: X0, Y0, X1, Y1|X0, Y0, X1, Y1]]

</div>

INCLAN Graphics: plot plus

2009-09-09T16:21:36Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot plus''' ''x'' ''y'' (normal mode)

'''plot plus''' [''x'' ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot line

2009-09-09T16:21:12Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot line''' ''x''1 ''y''1 ''x''2 ''y''2 ... (normal mode)

'''plot line''' [[''x''] ''y''1...] (list mode)

== Description ==

Normal mode:
Draws a line that connects the points (''x''1, ''y''1), (''x''2, ''y''2),... by straight line segments.

List mode:
Draws straight lines through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, straight lines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot line

2009-09-09T16:20:28Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot line''' ''x''1 ''y''1 ''x''2 ''y''2 ... (normal mode)

'''plot line''' [['''''x''''']''' ''y''1'''...] (list mode)

== Description ==

Normal mode:
Draws a line that connects the points (''x''1, ''y''1), (''x''2, ''y''2),... by straight line segments.

List mode:
Draws straight lines through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, straight lines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot errorbar

2009-09-09T16:18:54Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot errorbar''' ''x'' ''y''1 ''y''2

== Description ==

Draws an errorbar defined by the given ''x''- and ''y''-coordinates. This command can also be used in list mode, where ''x'', ''y''1 and ''y''2 are three vector expressions.

INCLAN Graphics: plot dot

2009-09-09T16:16:56Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot dot''' ''x'' ''y'' (normal mode)

'''plot dot''' [''x'' ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot curve

2009-09-09T16:16:32Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot curve''' ''x''1 ''y''1 ''x''2 ''y''2 ''x''3 ''y''3 ''x''4 ''y''4 ... (normal mode)

'''plot curve''' [[''x''] ''y''1...](list mode)

== Description ==

Normal mode: 
The command draws a Bézier spline curve defined by the points ('''x''i,''y''i). The total number of points must be 3''n'' + 1, with integer ''n'' ≥ 1. The resulting curve passes through the points 1, 4, 7,...; the other points guide the curve. Four points define the shape of each segment of the curve: The curve segment leaves (''x''1,''y''1) along the direction of the straight line connecting (''x''1,''y''1) with (''x''2,''y''2) and reaches (''x''4,''y''4) along the direction of the straight line connecting (''x''3,''y''3) with (x4,y4). The lengths of the lines connecting (''x''1,''y''1) with (''x''2,''y''2) and (''x''3,''y''3) with (''x''4,''y''4) represent, in a sense, the “velocity” of the path at the endpoints. The curve segment is always enclosed by the convex quadrilateral defined by the four points.

[[Image:plot curve.jpg]]

List mode: 
The command draws Bézier spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, splines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list. The number of list points must be 3''n'' + 1, with integer ''n''.

INCLAN Graphics: plot cross

2009-09-09T16:15:59Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot cross''' ''x'' ''y'' (normal mode)

'''plot cross''' [''x'' ''y''1...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot clip

2009-09-09T13:02:00Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot clip''' ''x''1 ''y''1 ''x''2 ''y''2

'''plot clip off'''

== Description ==

The '''plot clip''' command draws draws a rectangle with corners (''x''1,''y''1), (''x''1,''y''2), (''x''2,''y''1) and (''x''2,''y''2) sets the current clipping path to its border. Subsequent drawing commands will only draw within this rectangular area.

The '''plot clip off''' command resets the clipping path. After this command, graphics will no longer be confined to the rectangular area specified in a previous '''plot clip''' command.

INCLAN Graphics: plot caro

2009-09-09T13:01:03Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot caro''' ''x'' ''y'' (normal mode)

'''plot caro''' [''x'' ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot polygon

2009-09-09T13:00:24Z

Masayo: /* Synopsis */

== Synopsis ==

'''plot polygon''' ''x''1 ''y''1 ''x''2 ''y''2 ''x''3 ''y''3 ... (normal mode)

'''plot polygon''' [[''x''] ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

CYANA 3.0 Reference Manual

2009-09-02T13:38:12Z

Masayo: /* CYANA Commands */

__NOTOC__
== INCLAN (INteractive Command LANguage) ==

* [[INCLAN Reference Manual]]

== CYANA Scripts ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA script: cyanaclean|cyanaclean]]
* [[CYANA script: cyana|cyana]]
* [[CYANA script: cyanafilter|cyanafilter]]
* [[CYANA script: cyanajob|cyanajob]]
* [[CYANA script: cyanatable|cyanatable]]
</div>

== CYANA Commands ==

* [[CYANA Commands]] (complete list)

== CYANA Functions ==

* [[CYANA functions]] (complete list)

== CYANA Variables ==

* [[CYANA variables]] (complete list)

== Selections ==

<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Selection rules]]
</div>

<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Atom selection]]
* [[Angle selection]]
* [[Peak selection]]
* [[Distance restraint selection]]
* [[Scalar coupling selection]]
* [[Residual dipolar coupling selection]]
* [[Pseudocontact shift selection]]
* [[Structure selection]]
</div>

== Input files ==

<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Residue library file]] (.lib)
* [[Sequence file]] (.seq)
* [[Distance restraint file]] (.upl, .lol)
* [[Torsion angle restraint file]] (.aco)
* [[Residual dipolar coupling restraint file]] (.rdc)
* [[Pseudocontact shift restraint file]] (.pcs)
* [[DG Cartesian coordinate file]] (.cor)
* [[PDB coordinate file]] (.pdb)
* [[Torsion angle file]] (.ang)
* [[XEASY chemical shift list file]] (.prot)
* [[BMRB chemical shift list file]] (.bmrb)
* [[XEASY peak list file]] (.peaks)
* [[NMRView peak list file]] (.xpk)
</div>

== Algorithms ==

<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Coordinate generation]]
* [[Target function]]
* [[Torsion angle dynamics]]
* [[Momenta compensation]]
* [[Simulated annealing]]
</div>

CYANA Commands

2009-09-02T13:37:32Z

Masayo: /* CYANA Macros */

__NOTOC__
== CYANA Commands ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
=== A ===
* [[CYANA Command: angles count|angles count]]
* [[CYANA Command: angles delete|angles delete]]
* [[CYANA Command: angles flip|angles flip]]
* [[CYANA Command: angles ramachandran|angles ramachandran]]
* [[CYANA Command: angles select|angles select]]
* [[CYANA Command: angles set|angles set]]
* [[CYANA Command: angles split|angles split]]
* [[CYANA Command: angstat clear|angstat clear]]
* [[CYANA Command: angstat list|angstat list]]
* [[CYANA Command: angstat make|angstat make]]
* [[CYANA Macro: anneal|anneal]] (macro)
* [[CYANA Command: assign|assign]]
* [[CYANA Command: atoms attach|atoms attach]]
* [[CYANA Command: atoms calibrate|atoms calibrate]]
* [[CYANA Command: atoms count|atoms count]]
* [[CYANA Command: atoms glomsa|atoms glomsa]]
* [[CYANA Command: atoms list|atoms list]]
* [[CYANA Command: atoms observable|atoms observable]]
* [[CYANA Command: atoms select|atoms select]]
* [[CYANA Command: atoms set|atoms set]]
* [[CYANA Command: atoms shifts|atoms shifts]]
* [[CYANA Command: atoms stereo|atoms stereo]]
* [[CYANA Command: atoms swap|atoms swap]]
=== C ===
* [[CYANA Macro: calc_all|calc_all]] (macro)
* [[CYANA Macro: caliba|caliba]] (macro)
* [[CYANA Command: calibrate|calibrate]]
* [[CYANA Macro: calibration|calibration]] (macro)
* [[CYANA Macro: cashiftaco|cashiftaco]] (macro)
* [[CYANA Macro: cashiftplot|cashiftplot]] (macro)
* [[CYANA Macro: cisprocheck|cisprocheck]] (macro)
* [[CYANA Macro: coco|coco]] (macro)
* [[CYANA Command: couplings count|couplings count]]
* [[CYANA Command: couplings delete|couplings delete]]
* [[CYANA Command: couplings make|couplings make]]
* [[CYANA Command: couplings select|couplings select]]
* [[CYANA Command: couplings set|couplings set]]
* [[CYANA Macro: cyscheck|cyscheck]] (macro)
=== D ===
* [[CYANA Macro: dcostat|dcostat]] (macro)
* [[CYANA Macro: dcotab|dcotab]] (macro)
* [[CYANA Macro: deposit|deposit]] (macro)
* [[CYANA Macro: dinucleotide|dinucleotide]] (macro)
* [[CYANA Command: distances calculate|distances calculate]]
* [[CYANA Command: distances check|distances check]]
* [[CYANA Command: distances combine|distances combine]]
* [[CYANA Command: distances compare|distances compare]]
* [[CYANA Command: distances correct|distances correct]]
* [[CYANA Command: distances count|distances count]]
* [[CYANA Command: distances delete|distances delete]]
* [[CYANA Command: distances expand|distances expand]]
* [[CYANA Command: distances falsify|distances falsify]]
* [[CYANA Command: distances hbond|distances hbond]]
* [[CYANA Command: distances make|distances make]]
* [[CYANA Command: distances modify|distances modify]]
* [[CYANA Command: distances multiple|distances multiple]]
* [[CYANA Command: distances select|distances select]]
* [[CYANA Command: distances set|distances set]]
* [[CYANA Command: distances short|distances short]]
* [[CYANA Command: distances split|distances split]]
* [[CYANA Command: distances stat|distances stat]]
* [[CYANA Command: distances stereoexpand|distances stereoexpand]]
* [[CYANA Command: distances unique|distances unique]]
* [[CYANA Command: distances vdw|distances vdw]]
=== F ===
* [[CYANA Macro: flip|flip]] (macro)
* [[CYANA Macro: forall|forall]] (macro)
=== G ===
* [[CYANA Macro: garant|garant]] (macro)
* [[CYANA Command: gradient|gradient]]
* [[CYANA Macro: graf|graf]] (macro)
* [[CYANA Command: grid aco|grid aco]]
* [[CYANA Command: grid correlate|grid correlate]]
* [[CYANA Command: grid fragment|grid fragment]]
* [[CYANA Command: grid memory|grid memory]]
* [[CYANA Macro: gridplot|gridplot]] (macro)
* [[CYANA Command: grid search|grid search]]
* [[CYANA Command: grid swap|grid swap]]
=== H ===
* [[CYANA Macro: habas|habas]] (macro)
* [[CYANA Macro: hbond|hbond]] (macro)
=== I ===
* [[CYANA Macro: init|init]] (macro)
* [[CYANA Macro: initsafe|initsafe]] (macro)
=== K ===
* [[CYANA Macro: karplus|karplus]] (macro)
* [[CYANA Macro: kringle|kringle]] (macro)
=== L ===
* [[CYANA Command: library check|library check]]
* [[CYANA Command: library mirror|library mirror]]
* [[CYANA Command: library new|library new]]
* [[CYANA Command: library remove|library remove]]
* [[CYANA Command: library rename|library rename]]
* [[CYANA Command: library replace|library replace]]
* [[CYANA Macro: longrangeplot|longrangeplot]] (macro)
* [[CYANA Macro: loop|loop]] (macro)
=== M ===
* [[CYANA Macro: makeaco|makeaco]] (macro)
* [[CYANA Command: md|md]]
* [[CYANA Command: minimize|minimize]]
* [[CYANA Command: molecules define|molecules define]]
* [[CYANA Command: molecules identity|molecules identity]]
* [[CYANA Command: molecules symdist|molecules symdist]]
=== N ===
* [[CYANA Macro: noeassign|noeassign]] (macro)
=== O ===
* [[CYANA Macro: onelettercode|onelettercode]] (macro)
* [[CYANA Macro: opalprefine|opalprefine]] (macro)
* [[CYANA Macro: overlay|overlay]] (macro)
* [[CYANA Macro: overview|overview]] (macro)
=== P ===
* [[CYANA Command: pcs axial|pcs axial]]
* [[CYANA Command: pcs count|pcs count]]
* [[CYANA Command: pcs delete|pcs delete]]
* [[CYANA Command: pcs list|pcs list]]
* [[CYANA Command: pcs make|pcs make]]
* [[CYANA Command: pcs rhombic|pcs rhombic]]
* [[CYANA Command: pcs select|pcs select]]
* [[CYANA Command: pcs set|pcs set]]
* [[CYANA Macro: peakcheck|peakcheck]] (macro)
* [[CYANA Command: peaks backcal|peaks backcal]]
* [[CYANA Command: peaks calibrate|peaks calibrate]]
* [[CYANA Command: peaks count|peaks count]]
* [[CYANA Command: peaks create|peaks create]]
* [[CYANA Command: peaks delete|peaks delete]]
* [[CYANA Command: peaks deviations|peaks deviations]]
* [[CYANA Command: peaks distance|peaks distance]]
* [[CYANA Command: peaks filter|peaks filter]]
* [[CYANA Command: peaks fit|peaks fit]]
* [[CYANA Command: peaks protonize|peaks protonize]]
* [[CYANA Command: peaks select|peaks select]]
* [[CYANA Command: peaks set|peaks set]]
* [[CYANA Command: peaks simplecal|peaks simplecal]]
* [[CYANA Command: peaks split|peaks split]]
* [[CYANA Command: peaks unassign|peaks unassign]]
* [[CYANA Command: peaks unique|peaks unique]]
* [[CYANA Macro: prolinebond|prolinebond]] (macro)
=== R ===
* [[CYANA Macro: ramaaco|ramaaco]] (macro)
* [[CYANA Macro: ramaplot|ramaplot]] (macro)
* [[CYANA Macro: random_all|random_all]] (macro)
* [[CYANA Command: randomize|randomize]]
* [[CYANA Command: rdc count|rdc count]]
* [[CYANA Command: rdc delete|rdc delete]]
* [[CYANA Command: rdc distance|rdc distance]]
* [[CYANA Macro: rdcdistances|rdcdistances]] (macro)
* [[CYANA Command: rdc fittensor|rdc fittensor]]
* [[CYANA Command: rdc list|rdc list]]
* [[CYANA Command: rdc make|rdc make]]
* [[CYANA Command: rdc select|rdc select]]
* [[CYANA Command: rdc set|rdc set]]
* [[CYANA Command: rdc tensor|rdc tensor]]
* [[CYANA Command: read aco|read aco]]
* [[CYANA Macro: read_all|read_all]] (macro)
* [[CYANA Command: read ang|read ang]]
* [[CYANA Command: read bmrb|read bmrb]]
* [[CYANA Command: read cco|read cco]]
* [[CYANA Command: read cor|read cor]]
* [[CYANA Macro: readdata|readdata]] (macro)
* [[CYANA Command: read lib|read lib]]
* [[CYANA Command: read lol|read lol]]
* [[CYANA Command: read nmrview|read nmrview]]
* [[CYANA Command: read pcs|read pcs]]
* [[CYANA Command: read pdb|read pdb]]
* [[CYANA Command: read peaks|read peaks]]
* [[CYANA Command: read prot|read prot]]
* [[CYANA Command: read rdc|read rdc]]
* [[CYANA Command: read upl|read upl]]
* [[CYANA Command: read xpk|read xpk]]
* [[CYANA Command: read xplor|read xplor]]
* [[CYANA Macro: redac|redac]] (macro)
* [[CYANA Macro: renumber|renumber]] (macro)
* [[CYANA Macro: rmsd|rmsd]] (macro)
* [[CYANA Macro: rotameraco|rotameraco]] (macro)
=== S ===
* [[CYANA Macro: savestereo|savestereo]] (macro)
* [[CYANA Macro: seqplot|seqplot]] (macro)
* [[CYANA Command: shifts adapt|shifts adapt]]
* [[CYANA Command: shifts assign|shifts assign]]
* [[CYANA Command: shifts check|shifts check]]
* [[CYANA Command: shifts collapse|shifts collapse]]
* [[CYANA Command: shifts consolidate|shifts consolidate]]
* [[CYANA Command: shifts converge|shifts converge]]
* [[CYANA Command: shifts d2o|shifts d2o]]
* [[CYANA Command: shifts incomplete|shifts incomplete]]
* [[CYANA Command: shifts initialize|shifts initialize]]
* [[CYANA Command: shifts missing|shifts missing]]
* [[CYANA Command: shifts randomcoil|shifts randomcoil]]
* [[CYANA Command: shifts renumber|shifts renumber]]
* [[CYANA Command: shifts unusual|shifts unusual]]
* [[CYANA Macro: ssbond|ssbond]] (macro)
* [[CYANA Macro: stereoassign|stereoassign]] (macro)
* [[CYANA Macro: structcalc|structcalc]] (macro)
* [[CYANA Command: structures clear|structures clear]]
* [[CYANA Command: structures copy|structures copy]]
* [[CYANA Command: structures hbonds|structures hbonds]]
* [[CYANA Command: structures insert|structures insert]]
* [[CYANA Command: structures list|structures list]]
* [[CYANA Command: structures mean|structures mean]]
* [[CYANA Command: structures overlay|structures overlay]]
* [[CYANA Command: structures secondary|structures secondary]]
* [[CYANA Command: structures select|structures select]]
* [[CYANA Command: structures sort|structures sort]]
* [[CYANA Command: structures swap|structures swap]]
* [[CYANA Command: structures violate|structures violate]]
* [[CYANA Macro: sugarbond|sugarbond]] (macro)
* [[CYANA Macro: sugarring|sugarring]] (macro)
* [[CYANA Macro: syscheck|syscheck]] (macro)
=== T ===
* [[CYANA Macro: talosaco|talosaco]] (macro)
* [[CYANA Macro: taloslist|taloslist]] (macro)
* [[CYANA Macro: threelettercode|threelettercode]] (macro)
* [[CYANA Macro: translate|translate]] (macro)
=== V ===
* [[CYANA Macro: vtfmin|vtfmin]] (macro)
=== W ===
* [[CYANA Macro: watsoncrick|watsoncrick]] (macro)
* [[CYANA Command: write aco|write aco]]
* [[CYANA Macro: write_all|write_all]] (macro)
* [[CYANA Command: write ang|write ang]]
* [[CYANA Command: write assign|write assign]]
* [[CYANA Command: write bmrb|write bmrb]]
* [[CYANA Command: write cco|write cco]]
* [[CYANA Command: write cor|write cor]]
* [[CYANA Command: write lib|write lib]]
* [[CYANA Command: write lol|write lol]]
* [[CYANA Command: write pcs|write pcs]]
* [[CYANA Command: write pdb|write pdb]]
* [[CYANA Command: write peaks|write peaks]]
* [[CYANA Command: write prot|write prot]]
* [[CYANA Command: write rdc|write rdc]]
* [[CYANA Command: write seq|write seq]]
* [[CYANA Command: write sparky|write sparky]]
* [[CYANA Command: write upl|write upl]]
* [[CYANA Command: write xpk|write xpk]]
</div>

CYANA Commands

2009-09-02T13:36:39Z

Masayo:

CYANA Commands

2009-09-02T13:23:58Z

Masayo: /* CYANA Macros */

__NOTOC__
== CYANA Commands ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
=== A ===
* [[CYANA Command: angles count|angles count]]
* [[CYANA Command: angles delete|angles delete]]
* [[CYANA Command: angles flip|angles flip]]
* [[CYANA Command: angles ramachandran|angles ramachandran]]
* [[CYANA Command: angles select|angles select]]
* [[CYANA Command: angles set|angles set]]
* [[CYANA Command: angles split|angles split]]
* [[CYANA Command: angstat clear|angstat clear]]
* [[CYANA Command: angstat list|angstat list]]
* [[CYANA Command: angstat make|angstat make]]
* [[CYANA Command: assign|assign]]
* [[CYANA Command: atoms attach|atoms attach]]
* [[CYANA Command: atoms calibrate|atoms calibrate]]
* [[CYANA Command: atoms count|atoms count]]
* [[CYANA Command: atoms glomsa|atoms glomsa]]
* [[CYANA Command: atoms list|atoms list]]
* [[CYANA Command: atoms observable|atoms observable]]
* [[CYANA Command: atoms select|atoms select]]
* [[CYANA Command: atoms set|atoms set]]
* [[CYANA Command: atoms shifts|atoms shifts]]
* [[CYANA Command: atoms stereo|atoms stereo]]
* [[CYANA Command: atoms swap|atoms swap]]
=== C ===
* [[CYANA Command: calibrate|calibrate]]
* [[CYANA Command: couplings count|couplings count]]
* [[CYANA Command: couplings delete|couplings delete]]
* [[CYANA Command: couplings make|couplings make]]
* [[CYANA Command: couplings select|couplings select]]
* [[CYANA Command: couplings set|couplings set]]
=== D ===
* [[CYANA Command: distances calculate|distances calculate]]
* [[CYANA Command: distances check|distances check]]
* [[CYANA Command: distances combine|distances combine]]
* [[CYANA Command: distances compare|distances compare]]
* [[CYANA Command: distances correct|distances correct]]
* [[CYANA Command: distances count|distances count]]
* [[CYANA Command: distances delete|distances delete]]
* [[CYANA Command: distances expand|distances expand]]
* [[CYANA Command: distances falsify|distances falsify]]
* [[CYANA Command: distances hbond|distances hbond]]
* [[CYANA Command: distances make|distances make]]
* [[CYANA Command: distances modify|distances modify]]
* [[CYANA Command: distances multiple|distances multiple]]
* [[CYANA Command: distances select|distances select]]
* [[CYANA Command: distances set|distances set]]
* [[CYANA Command: distances short|distances short]]
* [[CYANA Command: distances split|distances split]]
* [[CYANA Command: distances stat|distances stat]]
* [[CYANA Command: distances stereoexpand|distances stereoexpand]]
* [[CYANA Command: distances unique|distances unique]]
* [[CYANA Command: distances vdw|distances vdw]]
=== G ===
* [[CYANA Command: gradient|gradient]]
* [[CYANA Command: grid aco|grid aco]]
* [[CYANA Command: grid correlate|grid correlate]]
* [[CYANA Command: grid fragment|grid fragment]]
* [[CYANA Command: grid memory|grid memory]]
* [[CYANA Command: grid search|grid search]]
* [[CYANA Command: grid swap|grid swap]]
=== L ===
* [[CYANA Command: library check|library check]]
* [[CYANA Command: library mirror|library mirror]]
* [[CYANA Command: library new|library new]]
* [[CYANA Command: library remove|library remove]]
* [[CYANA Command: library rename|library rename]]
* [[CYANA Command: library replace|library replace]]
=== M ===
* [[CYANA Command: md|md]]
* [[CYANA Command: minimize|minimize]]
* [[CYANA Command: molecules define|molecules define]]
* [[CYANA Command: molecules identity|molecules identity]]
* [[CYANA Command: molecules symdist|molecules symdist]]
=== P ===
* [[CYANA Command: pcs axial|pcs axial]]
* [[CYANA Command: pcs count|pcs count]]
* [[CYANA Command: pcs delete|pcs delete]]
* [[CYANA Command: pcs list|pcs list]]
* [[CYANA Command: pcs make|pcs make]]
* [[CYANA Command: pcs rhombic|pcs rhombic]]
* [[CYANA Command: pcs select|pcs select]]
* [[CYANA Command: pcs set|pcs set]]
* [[CYANA Command: peaks backcal|peaks backcal]]
* [[CYANA Command: peaks calibrate|peaks calibrate]]
* [[CYANA Command: peaks count|peaks count]]
* [[CYANA Command: peaks create|peaks create]]
* [[CYANA Command: peaks delete|peaks delete]]
* [[CYANA Command: peaks deviations|peaks deviations]]
* [[CYANA Command: peaks distance|peaks distance]]
* [[CYANA Command: peaks filter|peaks filter]]
* [[CYANA Command: peaks fit|peaks fit]]
* [[CYANA Command: peaks protonize|peaks protonize]]
* [[CYANA Command: peaks select|peaks select]]
* [[CYANA Command: peaks set|peaks set]]
* [[CYANA Command: peaks simplecal|peaks simplecal]]
* [[CYANA Command: peaks split|peaks split]]
* [[CYANA Command: peaks unassign|peaks unassign]]
* [[CYANA Command: peaks unique|peaks unique]]
* [[CYANA Command: randomize|randomize]]
=== R ===
* [[CYANA Command: rdc count|rdc count]]
* [[CYANA Command: rdc delete|rdc delete]]
* [[CYANA Command: rdc distance|rdc distance]]
* [[CYANA Command: rdc fittensor|rdc fittensor]]
* [[CYANA Command: rdc list|rdc list]]
* [[CYANA Command: rdc make|rdc make]]
* [[CYANA Command: rdc select|rdc select]]
* [[CYANA Command: rdc set|rdc set]]
* [[CYANA Command: rdc tensor|rdc tensor]]
* [[CYANA Command: read aco|read aco]]
* [[CYANA Command: read ang|read ang]]
* [[CYANA Command: read bmrb|read bmrb]]
* [[CYANA Command: read cco|read cco]]
* [[CYANA Command: read cor|read cor]]
* [[CYANA Command: read lib|read lib]]
* [[CYANA Command: read lol|read lol]]
* [[CYANA Command: read nmrview|read nmrview]]
* [[CYANA Command: read pcs|read pcs]]
* [[CYANA Command: read pdb|read pdb]]
* [[CYANA Command: read peaks|read peaks]]
* [[CYANA Command: read prot|read prot]]
* [[CYANA Command: read rdc|read rdc]]
* [[CYANA Command: read upl|read upl]]
* [[CYANA Command: read xpk|read xpk]]
* [[CYANA Command: read xplor|read xplor]]
=== S ===
* [[CYANA Command: shifts adapt|shifts adapt]]
* [[CYANA Command: shifts assign|shifts assign]]
* [[CYANA Command: shifts check|shifts check]]
* [[CYANA Command: shifts collapse|shifts collapse]]
* [[CYANA Command: shifts consolidate|shifts consolidate]]
* [[CYANA Command: shifts converge|shifts converge]]
* [[CYANA Command: shifts d2o|shifts d2o]]
* [[CYANA Command: shifts incomplete|shifts incomplete]]
* [[CYANA Command: shifts initialize|shifts initialize]]
* [[CYANA Command: shifts missing|shifts missing]]
* [[CYANA Command: shifts randomcoil|shifts randomcoil]]
* [[CYANA Command: shifts renumber|shifts renumber]]
* [[CYANA Command: shifts unusual|shifts unusual]]
* [[CYANA Command: structures clear|structures clear]]
* [[CYANA Command: structures copy|structures copy]]
* [[CYANA Command: structures hbonds|structures hbonds]]
* [[CYANA Command: structures insert|structures insert]]
* [[CYANA Command: structures list|structures list]]
* [[CYANA Command: structures mean|structures mean]]
* [[CYANA Command: structures overlay|structures overlay]]
* [[CYANA Command: structures secondary|structures secondary]]
* [[CYANA Command: structures select|structures select]]
* [[CYANA Command: structures sort|structures sort]]
* [[CYANA Command: structures swap|structures swap]]
* [[CYANA Command: structures violate|structures violate]]
=== W ===
* [[CYANA Command: write aco|write aco]]
* [[CYANA Command: write ang|write ang]]
* [[CYANA Command: write assign|write assign]]
* [[CYANA Command: write bmrb|write bmrb]]
* [[CYANA Command: write cco|write cco]]
* [[CYANA Command: write cor|write cor]]
* [[CYANA Command: write lib|write lib]]
* [[CYANA Command: write lol|write lol]]
* [[CYANA Command: write pcs|write pcs]]
* [[CYANA Command: write pdb|write pdb]]
* [[CYANA Command: write peaks|write peaks]]
* [[CYANA Command: write prot|write prot]]
* [[CYANA Command: write rdc|write rdc]]
* [[CYANA Command: write seq|write seq]]
* [[CYANA Command: write sparky|write sparky]]
* [[CYANA Command: write upl|write upl]]
* [[CYANA Command: write xpk|write xpk]]
</div>

== CYANA Macros ==

<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA Macro: anneal|anneal]] (macro)
* [[CYANA Macro: calc_all|calc_all]] (macro)
* [[CYANA Macro: caliba|caliba]] (macro)
* [[CYANA Macro: calibration|calibration]] (macro)
* [[CYANA Macro: cashiftaco|cashiftaco]] (macro)
* [[CYANA Macro: cashiftplot|cashiftplot]] (macro)
* [[CYANA Macro: cisprocheck|cisprocheck]] (macro)
* [[CYANA Macro: coco|coco]] (macro)
* [[CYANA Macro: cyscheck|cyscheck]] (macro)
* [[CYANA Macro: dcostat|dcostat]] (macro)
* [[CYANA Macro: dcotab|dcotab]] (macro)
* [[CYANA Macro: deposit|deposit]] (macro)
* [[CYANA Macro: dinucleotide|dinucleotide]] (macro)
* [[CYANA Macro: flip|flip]] (macro)
* [[CYANA Macro: forall|forall]] (macro)
* [[CYANA Macro: garant|garant]] (macro)
* [[CYANA Macro: graf|graf]] (macro)
* [[CYANA Macro: gridplot|gridplot]] (macro)
* [[CYANA Macro: habas|habas]] (macro)
* [[CYANA Macro: hbond|hbond]] (macro)
* [[CYANA Macro: init|init]] (macro)
* [[CYANA Macro: initsafe|initsafe]] (macro)
* [[CYANA Macro: karplus|karplus]] (macro)
* [[CYANA Macro: kringle|kringle]] (macro)
* [[CYANA Macro: longrangeplot|longrangeplot]] (macro)
* [[CYANA Macro: loop|loop]] (macro)
* [[CYANA Macro: makeaco|makeaco]] (macro)
* [[CYANA Macro: noeassign|noeassign]] (macro)
* [[CYANA Macro: onelettercode|onelettercode]] (macro)
* [[CYANA Macro: opalprefine|opalprefine]] (macro)
* [[CYANA Macro: overlay|overlay]] (macro)
* [[CYANA Macro: overview|overview]] (macro)
* [[CYANA Macro: peakcheck|peakcheck]] (macro)
* [[CYANA Macro: prolinebond|prolinebond]] (macro)
* [[CYANA Macro: ramaaco|ramaaco]] (macro)
* [[CYANA Macro: ramaplot|ramaplot]] (macro)
* [[CYANA Macro: random_all|random_all]] (macro)
* [[CYANA Macro: rdcdistances|rdcdistances]] (macro)
* [[CYANA Macro: read_all|read_all]] (macro)
* [[CYANA Macro: readdata|readdata]] (macro)
* [[CYANA Macro: redac|redac]] (macro)
* [[CYANA Macro: renumber|renumber]] (macro)
* [[CYANA Macro: rmsd|rmsd]] (macro)
* [[CYANA Macro: rotameraco|rotameraco]] (macro)
* [[CYANA Macro: savestereo|savestereo]] (macro)
* [[CYANA Macro: seqplot|seqplot]] (macro)
* [[CYANA Macro: ssbond|ssbond]] (macro)
* [[CYANA Macro: stereoassign|stereoassign]] (macro)
* [[CYANA Macro: structcalc|structcalc]] (macro)
* [[CYANA Macro: sugarbond|sugarbond]] (macro)
* [[CYANA Macro: sugarring|sugarring]] (macro)
* [[CYANA Macro: syscheck|syscheck]] (macro)
* [[CYANA Macro: talosaco|talosaco]] (macro)
* [[CYANA Macro: taloslist|taloslist]] (macro)
* [[CYANA Macro: threelettercode|threelettercode]] (macro)
* [[CYANA Macro: translate|translate]] (macro)
* [[CYANA Macro: vtfmin|vtfmin]] (macro)
* [[CYANA Macro: watsoncrick|watsoncrick]] (macro)
* [[CYANA Macro: write_all|write_all]] (macro)
</div>

INCLAN Graphics: plot shape

2009-08-19T08:51:24Z

Masayo: /* Description */

== Synopsis ==

'''plot shape''' ''x''1 ''y''1 ''x''2 ''y''2 ''x''3 ''y''3 ''x''4 ''y''4 ''x''5 ''y''5 ''x''6 ''y''6... (normal mode)

'''plot shape''' [[''x''] ''y''1...] (list mode)

== Description ==

Normal mode: 
Draws a shape enclosed by a closed Bézier spline curve that is defined by the points (''x''i,''y''i). The total number of points must be 3''n'', with integer ''n''.

[[Image:plot_sharp.jpg]]

List mode: 
Draws shapes enclosed by Bézier spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, shapes are drawn for all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1 , is given), the ''x''-coordinates are taken from the ''x''-column of the list. The number of list points must be 3''n'', with integer ''n''.

File:Plot sharp.jpg

2009-08-19T08:51:04Z

Masayo:

INCLAN Graphics: plot curve

2009-08-19T08:50:10Z

Masayo: /* Description */

== Synopsis ==

'''plot curve ''x''1 ''y''1 ''x''2 ''y''2 ''x''3 ''y''3 ''x''4 ''y''4 ...''' (normal mode)

'''plot curve [[''x''] ''y''1...]'''(list mode)

== Description ==

Normal mode: 
The command draws a Bézier spline curve defined by the points ('''x''i,''y''i). The total number of points must be 3''n'' + 1, with integer ''n'' ≥ 1. The resulting curve passes through the points 1, 4, 7,...; the other points guide the curve. Four points define the shape of each segment of the curve: The curve segment leaves (''x''1,''y''1) along the direction of the straight line connecting (''x''1,''y''1) with (''x''2,''y''2) and reaches (''x''4,''y''4) along the direction of the straight line connecting (''x''3,''y''3) with (x4,y4). The lengths of the lines connecting (''x''1,''y''1) with (''x''2,''y''2) and (''x''3,''y''3) with (''x''4,''y''4) represent, in a sense, the “velocity” of the path at the endpoints. The curve segment is always enclosed by the convex quadrilateral defined by the four points.

[[Image:plot curve.jpg]]

List mode: 
The command draws Bézier spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, splines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list. The number of list points must be 3''n'' + 1, with integer ''n''.

File:Plot curve.jpg

2009-08-19T08:48:50Z

Masayo:

INCLAN Graphics: plot write

2009-08-19T08:36:31Z

Masayo:

== Synopsis ==

'''plot write''' ''text''

== Description ==

Writes ''text'' into the output plot file.

INCLAN Graphics: plot triangle

2009-08-19T08:35:35Z

Masayo:

== Synopsis ==

'''plot triangle''' ''x'' ''y'' (normal mode)

'''plot triangle''' [''x'' ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot text

2009-08-19T08:34:22Z

Masayo:

== Synopsis ==

'''plot text''' ''x'' ''y'' ''text''

== Description ==

Print ''text'' at position (''x'', ''y''). The alignment of the text with respect to the reference position depends on the current values of the plot parameters '''align''' and '''rotate'''. The current values of the plot parameters '''font''', '''textsize''', '''weight''' and '''angle''' define the font used to write the ''text''. In addition, the ''text'' may contain the following embedded text commands:

@T Change font type to Times.
@H Change font type to Helvetica.
@C Change font type to Courier.
@S Change font type to Symbol.
@b Change to '''boldface'''.
@i Change to ''italics''.
@^ Start a superscript.
@v Start a subscript.
@N Return to standard font, end sub- or superscript.

If the text contains multiple blanks, it must be enclosed in double quotes. Double quotes that are part of the text must be preceded by a backslash.

INCLAN Graphics: plot square

2009-08-19T08:29:49Z

Masayo:

== Synopsis ==

'''plot square''' ''x'' ''y'' (normal mode)

'''plot square''' [''x'' ''y1''...] (list mode)

== Description ==

Normal mode:
This command marks the position (''x'',''y'') with the corresponding symbol.The size of the symbol is determined by the current value of the plot
parameter '''marksize'''.

List mode:
This command marks the positions given by the vector expressions ''x'', ''y''1,... with the corresponding symbol. If no vector expressions are specified, all points of the list columns are marked. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot spline

2009-08-19T08:27:46Z

Masayo: /* Description */

== Synopsis ==

'''plot spline''' ''x''1 ''y''1 ''x''2 ''y''2 ... (normal mode)

'''plot spline''' [[''x''] ''y''1...] (list mode)

== Description ==

Normal mode: 
Draws a cubic spline through the points (''x''1, ''y''1), (''x''2, ''y''2), ... The spline starts at the first point and ends at the last point with vanishing second derivative. The ''x''-values must be increasing: ''x''''i''<''x''''i''+1, for all ''i''.

List mode: 
Draws cubic spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, splines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot spline

2009-08-19T08:27:36Z

Masayo:

== Synopsis ==

'''plot spline''' ''x''1 ''y''1 ''x''2 ''y''2 ... (normal mode)

'''plot spline''' [[''x''] ''y''1...] (list mode)

== Description ==

Normal mode: 
Draws a cubic spline through the points (''x''1, ''y''1), (''x''2, ''y''2), ... The spline starts at the first point and ends at the last point with vanishing second derivative. The ''x''-values must be increasing: ''x''''i''<''x''''i''+1, for all ''i''.

List mode:
Draws cubic spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, splines are drawn through the points of all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1, is given), the ''x''-coordinates are taken from the ''x''-column of the list.

INCLAN Graphics: plot shape

2009-08-19T08:19:01Z

Masayo:

== Synopsis ==

'''plot shape''' ''x''1 ''y''1 ''x''2 ''y''2 ''x''3 ''y''3 ''x''4 ''y''4 ''x''5 ''y''5 ''x''6 ''y''6... (normal mode)

'''plot shape''' [[''x''] ''y''1...] (list mode)

== Description ==

Normal mode: 
Draws a shape enclosed by a closed Bézier spline curve that is defined by the points (''x''i,''y''i). The total number of points must be 3''n'', with integer ''n''.

List mode: 
Draws shapes enclosed by Bézier spline curves through the points of the given vector expressions ''x'', ''y''1,... If no vector expressions are specified, shapes are drawn for all list columns. If the ''x''-expression is omitted (i.e. if only a single expression, ''y''1 , is given), the ''x''-coordinates are taken from the ''x''-column of the list. The number of list points must be 3''n'', with integer ''n''.

INCLAN Graphics: plot scale

2009-08-17T15:27:30Z

Masayo:

== Synopsis ==

'''plot scale''' ''axis'' ''f''1... [exact] (list mode)

== Description ==

Performs scaling of the given ''axis'' ('''x''' or '''y''') on the basis of the vector expressions ''f''1,... Scaling sets the coordinates of the reference points in the user coordinate system (''X''0 and ''X''1 for the ''x''-axis, ''Y''0 and ''Y''1 for the ''y''-axis) such that they include all values of the vector expressions ''f''1,... If the option '''exact''' is present, then the new coordinates of the reference points will correspond exactly to the minimum and maximum of the vector expressions ''f''1,...; otherwise a small margin will be added in order to avoid that points lie exactly on the boundary.

INCLAN Graphics: plot set

2009-08-17T15:21:53Z

Masayo:

== Synopsis ==

'''plot set''' ''parameter''=''value'' ...

== Description ==

Sets one or several plot ''parameters'' to the given ''values''. The keyword '''set''' is optional.