New Features in CYANA 2.1 - Revision history

Admin at 16:08, 5 December 2008

2008-12-05T16:08:50Z

Admin at 16:06, 5 December 2008

2008-12-05T16:06:33Z

← Older revision		Revision as of 18:06, 5 December 2008
Line 57:		Line 57:

	* New or modified system functions:		* New or modified system functions:
	atomlong - long atom descriptor (replacement of the former function 'Atom')		** atomlong - long atom descriptor (replacement of the former function 'Atom')
	ipel - order number of nucleus detected in a given dimension of a peak list		** ipel - order number of nucleus detected in a given dimension of a peak list
	narmsd - number of atoms superimposed for RMSD		** narmsd - number of atoms superimposed for RMSD
	ndim - This function gives now an error message if no peak list(s) have been read yet.		** ndim - This function gives now an error message if no peak list(s) have been read yet.

	* New system variables:		* New system variables:
	weight_ide - weight for identity restraints		** weight_ide - weight for identity restraints
	weight_sym - weight for symmetry restraints		** weight_sym - weight for symmetry restraints

	* cyanafilter: The new '-S' option of the 'cyanafilter' shell script allows to select peaks from a given input peak list.		* cyanafilter: The new '-S' option of the 'cyanafilter' shell script allows to select peaks from a given input peak list.

Admin: New page: Cyana 2.1 is an update of Cyana 2.0 that provides a number of enhancements and bug fixes. It is recommended to upgrade to Cyana 2.1. * CYANA under Windows XP: CYANA is now fully supported...

2008-12-05T16:05:24Z

New page: Cyana 2.1 is an update of Cyana 2.0 that provides a number of enhancements and bug fixes. It is recommended to upgrade to Cyana 2.1. * CYANA under Windows XP: CYANA is now fully supported...

New page

Cyana 2.1 is an update of Cyana 2.0 that provides a number of enhancements and bug fixes. It is recommended to upgrade to Cyana 2.1.

* CYANA under Windows XP: CYANA is now fully supported on Windows XP systems with Cygwin, using the free g95 Fortran compiler.

* Output of restraints in X-PLOR/CNS format: Distance restraints and torsion angle restraints (with unambiguous assignment) can be saved in files in the format used by the programs X-PLOR and CNS. The new value 'pseudo=3' of the system variable 'pseudo' produces output for a pseudoatom QX in the form HX* used by X-PLOR and CNS.

* Automated NOESY assignment:
** Offsets between different chemical shift lists are taken into account when matching peaks from different spectra. This improves the power of network-anchoring when NOESY spectra recorded under slightly different conditions are used simultaneously.
** The new option 'changevol' of the 'noeassign' command allows to correct peak volumes based on the changes of upper distance limits by "elasticity".
** Non-intraresidual distances are only used for network anchoring if they are restricted to less than 5 A by the covalent structure.

* Assignment statistics for individual peak lists: The new option '-l' of the 'cyanafilter' shell script provides detailed assignment statistics for each peak list used for automated NOESY assignment.

* RMSDs to a reference structure in overview files: The new 'reference=...' option of the 'overview' command allows to include RMSDs to a reference structure in overview (.ovw) files.

* Residue library: To conform with IUPAC recommendations, the Arg sidechain amide protons HH11 and HH12, and HH21 and HH22 have been exchanged in the standard residue library file, 'cyana.lib', and 'cyanasmall.lib'. The standard CYANA 2.1 atom names follow exactly the IUPAC recommendations. - Likewise, the atom names HB1/HB2 in HIST and HIS+ have been changed to HB2/HB3 in the residue library file 'special.lib' to be consistent with IUPAC nomenclature.
** Lines in a residue library (.lib) file that are indented by 8 or more characters are treated as comments. This allows reading of previous libraries that containt comment blocks.
** The correction of van der Waals radii that is applied to 1-4 interactions is written on the 'ATOMTYPES' line of the residue library file.
** A 'README' file in the 'cyana-2.1/lib' directory describes the various residue libraries that come with Cyana 2.1.

* Symmetric dimers: Two new types of restraints have been introduced that improve the treatment of symmetric dimer structures. Identity restraints are harmonic potentials on the difference between corresponding torsion angles in the two molecules. They help to ensure identical structures of the two monomers. Symmetry restraints are harmonic potentials on the difference symmetry-related interatomic distances and can help to maintain the symmetry of the homodimeric structure. Various other problems relating to symmetric dimers have been resolved.

* Large molecules: The output of files for molecules with residue numbers > 999 (or < -99) is now possible. Bugs related to very large molecules have been fixed.

* Calibration: The new option 'iterative' of the 'calibration.cya' macro can improve automated calibration results when a large number of weak (predominantly artifact) peaks are present. This option can be particularly useful in conjunction with automated peak picking.

* RMSD calculation: A serious bug has been resolved in the 'rmsd' command. RMSD values to a reference structure were often not calculated correctly in Cyana 2.0.

* Peak lists:
** Problems with the automatic recognition of peak list dimensions have been resolved.
** Peak list specific chemical shift matching tolerances, as given by a '#TOLERANCE...' statement are written into output peak lists, if necessary.
** The command 'peaks volumecal' has been replaced by 'peaks set ... volume=upl'.
** The command 'peaks filter' to filter 3D peak lists based on a 2D peak list has been added.
** The command 'peaks set ... w1=...' has been replaced by 'peaks set ... ppm1=...' etc.
** The command 'peaks exclude' has been removed.

* Chemical shift lists:
** Unreadable lines in an input chemical shift list can be skipped rather than triggering an error if the option 'unknown=warning' is set.
** The 'read_all' command has been extended to allow for the reading of several chemical shift lists. This possibility is useful for chemical shift consolidation.
** Minor bugs when working with a reference chemical shift list, and when working with peak list specific chemical shift tolerances have been corrected.

* Consensus chemical shifts:
** When comparing results of chemical shift consolidation with a reference chemical shift list, differences within the same or nearby residues can be distinguished from "serious" errors by which no nearby chemical shift value matches. A new parameter 'nearby=...' has been added to the 'shift consolidate' and 'shift assign' commands.
** If an assignment is different from the reference assignment, the atom with the closest matching reference assignment is indicated.
** A statistics of the assigned, identical, different, non-neighboring, incompatible and additional assignments is made.
** Bugs when transferring consolidation results into the chemical shift list have been resolved.

* Selections:
** A bug with long (> 40 character) selections has been eliminated.
** The new keyword 'WITHCOORD' selects atoms for which coordinates are available
** Distance restraints can also be selected by peak number (option 'numbers=...').
** Peaks can be selected by ppm values (options 'ppm1=...' etc.).
** Peaks can be selected based on their deviation from the diagonal (options 'diagonal=...').
** Minor bugs with random selections of peaks and distance constraints have been corrected.

* Stereopair swapping: In Cyana 2.0 chemical shift values but not their errors were exchanged when swapping a stereopair. This bug has been eliminated.

* New or modified system functions:
atomlong - long atom descriptor (replacement of the former function 'Atom')
ipel - order number of nucleus detected in a given dimension of a peak list
narmsd - number of atoms superimposed for RMSD
ndim - This function gives now an error message if no peak list(s) have been read yet.

* New system variables:
weight_ide - weight for identity restraints
weight_sym - weight for symmetry restraints

* cyanafilter: The new '-S' option of the 'cyanafilter' shell script allows to select peaks from a given input peak list.

* Incomplete structures: Various bugs related to structures with missing atoms, i.e. coordinate files that do not provide coordinates for all atoms that are expected based on the residue library, have been fixed.

* Gradient check: The command 'gradient' to numerically check the accuracy of the gradient calculation now shows an error message when applied to a "rigid" structure that cannot be modified by the program because it does not adhere to the standard geometry in the library.

* Macro files that self-invoke Cyana: Lines in a macro (.cya) file that start with 'exec' are ignored by Cyana. This allows macro files to be started from the command line by invoking Cyana from within the macro file.

* g95 Fortran compiler: Compilation with the g95 Fortran compiler is supported on Linux, Windows XP with Cygwin, and on MacOSX systems. Please note that the program runs significantly slower when compiled with 'g95' than with the Intel Fortran compiler.

* Crash on SGI systems: A bug, specifically on SGI systems, that was related to the "flushing" of files has been resolved.

← Older revision		Revision as of 18:08, 5 December 2008
Line 1:		Line 1:
	Cyana 2.1 is an update of Cyana 2.0 that provides a number of enhancements and bug fixes. It is recommended to upgrade to Cyana 2.1.		Cyana 2.1 is an update of Cyana 2.0 that provides a number of enhancements and bug fixes. It is recommended to upgrade to Cyana 2.1.

	* CYANA under Windows XP: CYANA is now fully supported on Windows XP systems with Cygwin, using the free g95 Fortran compiler.		* '''CYANA under Windows XP:''' CYANA is now fully supported on Windows XP systems with Cygwin, using the free g95 Fortran compiler.

	* Output of restraints in X-PLOR/CNS format: Distance restraints and torsion angle restraints (with unambiguous assignment) can be saved in files in the format used by the programs X-PLOR and CNS. The new value 'pseudo=3' of the system variable 'pseudo' produces output for a pseudoatom QX in the form HX* used by X-PLOR and CNS.		* '''Output of restraints in X-PLOR/CNS format:''' Distance restraints and torsion angle restraints (with unambiguous assignment) can be saved in files in the format used by the programs X-PLOR and CNS. The new value 'pseudo=3' of the system variable 'pseudo' produces output for a pseudoatom QX in the form HX* used by X-PLOR and CNS.

	* Automated NOESY assignment:		* '''Automated NOESY assignment:'''
	** Offsets between different chemical shift lists are taken into account when matching peaks from different spectra. This improves the power of network-anchoring when NOESY spectra recorded under slightly different conditions are used simultaneously.		** Offsets between different chemical shift lists are taken into account when matching peaks from different spectra. This improves the power of network-anchoring when NOESY spectra recorded under slightly different conditions are used simultaneously.
	** The new option 'changevol' of the 'noeassign' command allows to correct peak volumes based on the changes of upper distance limits by "elasticity".		** The new option 'changevol' of the 'noeassign' command allows to correct peak volumes based on the changes of upper distance limits by "elasticity".
	** Non-intraresidual distances are only used for network anchoring if they are restricted to less than 5 A by the covalent structure.		** Non-intraresidual distances are only used for network anchoring if they are restricted to less than 5 A by the covalent structure.

	* Assignment statistics for individual peak lists: The new option '-l' of the 'cyanafilter' shell script provides detailed assignment statistics for each peak list used for automated NOESY assignment.		* '''Assignment statistics for individual peak lists:''' The new option '-l' of the 'cyanafilter' shell script provides detailed assignment statistics for each peak list used for automated NOESY assignment.

	* RMSDs to a reference structure in overview files: The new 'reference=...' option of the 'overview' command allows to include RMSDs to a reference structure in overview (.ovw) files.		* '''RMSDs to a reference structure in overview files:''' The new 'reference=...' option of the 'overview' command allows to include RMSDs to a reference structure in overview (.ovw) files.

	* Residue library: To conform with IUPAC recommendations, the Arg sidechain amide protons HH11 and HH12, and HH21 and HH22 have been exchanged in the standard residue library file, 'cyana.lib', and 'cyanasmall.lib'. The standard CYANA 2.1 atom names follow exactly the IUPAC recommendations. - Likewise, the atom names HB1/HB2 in HIST and HIS+ have been changed to HB2/HB3 in the residue library file 'special.lib' to be consistent with IUPAC nomenclature.		* '''Residue library:''' To conform with IUPAC recommendations, the Arg sidechain amide protons HH11 and HH12, and HH21 and HH22 have been exchanged in the standard residue library file, 'cyana.lib', and 'cyanasmall.lib'. The standard CYANA 2.1 atom names follow exactly the IUPAC recommendations. - Likewise, the atom names HB1/HB2 in HIST and HIS+ have been changed to HB2/HB3 in the residue library file 'special.lib' to be consistent with IUPAC nomenclature.
	** Lines in a residue library (.lib) file that are indented by 8 or more characters are treated as comments. This allows reading of previous libraries that containt comment blocks.		** Lines in a residue library (.lib) file that are indented by 8 or more characters are treated as comments. This allows reading of previous libraries that containt comment blocks.
	** The correction of van der Waals radii that is applied to 1-4 interactions is written on the 'ATOMTYPES' line of the residue library file.		** The correction of van der Waals radii that is applied to 1-4 interactions is written on the 'ATOMTYPES' line of the residue library file.
	** A 'README' file in the 'cyana-2.1/lib' directory describes the various residue libraries that come with Cyana 2.1.		** A 'README' file in the 'cyana-2.1/lib' directory describes the various residue libraries that come with Cyana 2.1.

	* Symmetric dimers: Two new types of restraints have been introduced that improve the treatment of symmetric dimer structures. Identity restraints are harmonic potentials on the difference between corresponding torsion angles in the two molecules. They help to ensure identical structures of the two monomers. Symmetry restraints are harmonic potentials on the difference symmetry-related interatomic distances and can help to maintain the symmetry of the homodimeric structure. Various other problems relating to symmetric dimers have been resolved.		* '''Symmetric dimers:''' Two new types of restraints have been introduced that improve the treatment of symmetric dimer structures. Identity restraints are harmonic potentials on the difference between corresponding torsion angles in the two molecules. They help to ensure identical structures of the two monomers. Symmetry restraints are harmonic potentials on the difference symmetry-related interatomic distances and can help to maintain the symmetry of the homodimeric structure. Various other problems relating to symmetric dimers have been resolved.

	* Large molecules: The output of files for molecules with residue numbers > 999 (or < -99) is now possible. Bugs related to very large molecules have been fixed.		* '''Large molecules:''' The output of files for molecules with residue numbers > 999 (or < -99) is now possible. Bugs related to very large molecules have been fixed.

	* Calibration: The new option 'iterative' of the 'calibration.cya' macro can improve automated calibration results when a large number of weak (predominantly artifact) peaks are present. This option can be particularly useful in conjunction with automated peak picking.		* '''Calibration:''' The new option 'iterative' of the 'calibration.cya' macro can improve automated calibration results when a large number of weak (predominantly artifact) peaks are present. This option can be particularly useful in conjunction with automated peak picking.

	* RMSD calculation: A serious bug has been resolved in the 'rmsd' command. RMSD values to a reference structure were often not calculated correctly in Cyana 2.0.		* '''RMSD calculation:''' A serious bug has been resolved in the 'rmsd' command. RMSD values to a reference structure were often not calculated correctly in Cyana 2.0.

	* Peak lists:		* '''Peak lists:'''
	** Problems with the automatic recognition of peak list dimensions have been resolved.		** Problems with the automatic recognition of peak list dimensions have been resolved.
	** Peak list specific chemical shift matching tolerances, as given by a '#TOLERANCE...' statement are written into output peak lists, if necessary.		** Peak list specific chemical shift matching tolerances, as given by a '#TOLERANCE...' statement are written into output peak lists, if necessary.
Line 35:		Line 35:
	** The command 'peaks exclude' has been removed.		** The command 'peaks exclude' has been removed.

	* Chemical shift lists:		* '''Chemical shift lists:'''
	** Unreadable lines in an input chemical shift list can be skipped rather than triggering an error if the option 'unknown=warning' is set.		** Unreadable lines in an input chemical shift list can be skipped rather than triggering an error if the option 'unknown=warning' is set.
	** The 'read_all' command has been extended to allow for the reading of several chemical shift lists. This possibility is useful for chemical shift consolidation.		** The 'read_all' command has been extended to allow for the reading of several chemical shift lists. This possibility is useful for chemical shift consolidation.
	** Minor bugs when working with a reference chemical shift list, and when working with peak list specific chemical shift tolerances have been corrected.		** Minor bugs when working with a reference chemical shift list, and when working with peak list specific chemical shift tolerances have been corrected.

	* Consensus chemical shifts:		* '''Consensus chemical shifts:'''
	** When comparing results of chemical shift consolidation with a reference chemical shift list, differences within the same or nearby residues can be distinguished from "serious" errors by which no nearby chemical shift value matches. A new parameter 'nearby=...' has been added to the 'shift consolidate' and 'shift assign' commands.		** When comparing results of chemical shift consolidation with a reference chemical shift list, differences within the same or nearby residues can be distinguished from "serious" errors by which no nearby chemical shift value matches. A new parameter 'nearby=...' has been added to the 'shift consolidate' and 'shift assign' commands.
	** If an assignment is different from the reference assignment, the atom with the closest matching reference assignment is indicated.		** If an assignment is different from the reference assignment, the atom with the closest matching reference assignment is indicated.
Line 46:		Line 46:
	** Bugs when transferring consolidation results into the chemical shift list have been resolved.		** Bugs when transferring consolidation results into the chemical shift list have been resolved.

	* Selections:		* '''Selections:'''
	** A bug with long (> 40 character) selections has been eliminated.		** A bug with long (> 40 character) selections has been eliminated.
	** The new keyword 'WITHCOORD' selects atoms for which coordinates are available		** The new keyword 'WITHCOORD' selects atoms for which coordinates are available
Line 54:		Line 54:
	** Minor bugs with random selections of peaks and distance constraints have been corrected.		** Minor bugs with random selections of peaks and distance constraints have been corrected.

	* Stereopair swapping: In Cyana 2.0 chemical shift values but not their errors were exchanged when swapping a stereopair. This bug has been eliminated.		* '''Stereopair swapping:''' In Cyana 2.0 chemical shift values but not their errors were exchanged when swapping a stereopair. This bug has been eliminated.

	* New or modified system functions:		* '''New or modified system functions:'''
	** atomlong - long atom descriptor (replacement of the former function 'Atom')		** atomlong - long atom descriptor (replacement of the former function 'Atom')
	** ipel - order number of nucleus detected in a given dimension of a peak list		** ipel - order number of nucleus detected in a given dimension of a peak list
Line 62:		Line 62:
	** ndim - This function gives now an error message if no peak list(s) have been read yet.		** ndim - This function gives now an error message if no peak list(s) have been read yet.

	* New system variables:		* '''New system variables:'''
	** weight_ide - weight for identity restraints		** weight_ide - weight for identity restraints
	** weight_sym - weight for symmetry restraints		** weight_sym - weight for symmetry restraints

	* cyanafilter: The new '-S' option of the 'cyanafilter' shell script allows to select peaks from a given input peak list.		* '''cyanafilter:''' The new '-S' option of the 'cyanafilter' shell script allows to select peaks from a given input peak list.

	* Incomplete structures: Various bugs related to structures with missing atoms, i.e. coordinate files that do not provide coordinates for all atoms that are expected based on the residue library, have been fixed.		* '''Incomplete structures:''' Various bugs related to structures with missing atoms, i.e. coordinate files that do not provide coordinates for all atoms that are expected based on the residue library, have been fixed.

	* Gradient check: The command 'gradient' to numerically check the accuracy of the gradient calculation now shows an error message when applied to a "rigid" structure that cannot be modified by the program because it does not adhere to the standard geometry in the library.		* '''Gradient check:''' The command 'gradient' to numerically check the accuracy of the gradient calculation now shows an error message when applied to a "rigid" structure that cannot be modified by the program because it does not adhere to the standard geometry in the library.

	* Macro files that self-invoke Cyana: Lines in a macro (.cya) file that start with 'exec' are ignored by Cyana. This allows macro files to be started from the command line by invoking Cyana from within the macro file.		* '''Macro files that self-invoke Cyana:''' Lines in a macro (.cya) file that start with 'exec' are ignored by Cyana. This allows macro files to be started from the command line by invoking Cyana from within the macro file.

	* g95 Fortran compiler: Compilation with the g95 Fortran compiler is supported on Linux, Windows XP with Cygwin, and on MacOSX systems. Please note that the program runs significantly slower when compiled with 'g95' than with the Intel Fortran compiler.		* '''g95 Fortran compiler:''' Compilation with the g95 Fortran compiler is supported on Linux, Windows XP with Cygwin, and on MacOSX systems. Please note that the program runs significantly slower when compiled with 'g95' than with the Intel Fortran compiler.

	* Crash on SGI systems: A bug, specifically on SGI systems, that was related to the "flushing" of files has been resolved.		* '''Crash on SGI systems:''' A bug, specifically on SGI systems, that was related to the "flushing" of files has been resolved.