New Features in CYANA 2.0

This is an (incomplete) list of the new features of Cyana 2.0 compared to Cyana 1.x. Please see also the hints for a smooth migration from earlier Cyana versions.

• Examples and Demos: An updated and expanded collection of example files and demos are provided in the 'demo' subdirectory of the cyana-2.0 distribution.

• Automated NOE assignment algorithm: A new algorithm for automated NOE assignment replaces the former Candid method. All criteria for assignment are consistently formulated as probabilities. The new algorithm can in general tolerate larger uncertaincies in chemical shift values and peak positions, and is faster. In general, a higher number of NOEs can be assigned with the new algorithm. The 'cyanatable' script provides a quick overview over a running or completed automated structure calculation.

• Violation confinement: Violation confinement offers a new alternative to constraint combination in order to reduce the impact of erroneous restraints on the resulting structure in the initial cycles of structure calculations using automated NOE assignment. With violation confinement each assigned NOE yields a corresponding distance restraint for which the maximal contribution to the target function is limited to that of that of a given, maximal violation. The latter can be set globally with the variable 'viocut', or for individual distance restraints.

• Calibration elasticity: The standard calibration method for automated structure calculations is simplified in that the upper distance limits are dependent only on the peak volume or peak height (not also on the initially unknown assignment). To account for small errors in the peak intensity NOE upper distance bounds that are consistently violated to a limited extent can automatically and individually be treated in a more conservative manner by "elastically" increasing the distance limit.

• Chemical shift assignment during NOE assignment: The NOE assignment algorithm can handle a significant number of unassigned chemical shifts. These can be entered into the calculation with the random coil value and a large uncertainty, letting the program find the chemical shift if sufficient NOESY data is available. In this way, structures can also be obtained with auotmated NOE assignment from less complete chemical shift lists.

• NMRView peak lists: Cyana 2.0 can handle NMRView peak lists with the new 'read xpk' and 'write xpk' commands.

• Standard amino acid residue library: The amino acid library has been completely revised. It is now based on the geometric parameters of Engh and Huber (Acta Crystallogr. A47, 392-400, 1991) instead of the ECEPP/2 force field. The atom nomenclature follows strictly the IUPAC recommendations. Van der Waals radii for the repulsive term of the target function have been increased significantly in order to produce structures with better packing.

• Residue library handling:
  • The library file has "free" format.
  • Residue definitions can be read from several different library files.
  • The command group 'library' has been added (see below).

• Standard simulated annealing schedule: The standard simulated annealing schedule has been improved in order to achieve better convergence of the structure calculations, especially when larger van der Waals radii are used.

• PDB and BMRB submission: The preparation of coordinate files for submission to the Protein Data Bank (PDB) and of chemical shift lists for submission to the BioMagResBank (BMRB) is straightforward with the 'deposit' macro. Conformers in a file for PDB submission are superimposed and sorted such that the first conformer is closest to the average coordinates.

• New commands (incomplete list):
  • library check - check library for inconsistencies (e.g. duplicate atoms)
  • library mirror - create the mirror image of residue library entries (e.g. to handle D-amino acids)
  • library new - create a new residue library entry based on an existing one
  • library remove - remove selected residues, atoms, angles, atom types from a residue library
  • library rename - rename selected residues, atoms, angles
  • library replace - replace selected coordinates in the library with those of the current structure
  • read xpk - read NMRView peak list file
  • read bmrb - read chemical shift list in BMRB format
  • shifts - commands related to chemical shifts (formerly 'atom shifts')
  • write bmrb - write chemical shift list in BMRB format
  • write lib - write residue library
  • write seq - write sequence file
  • write xpk - write NMRView peak list file

• New standard macros:
  • calibration - NOE calibration with automatically determined or user-defined parameters
  • coco - invoke the external Coco program for covalent geometry checking
  • deposit - prepare coordinate and chemical shift lists for PDB and BMRB deposition
  • garant - invoke the external Garant program for automated assignment
  • karplus - Karplus curve definitions (that were previously in the residue library file)
  • noeassign - automated NOESY assignment (replaces the former 'candid' macro)
  • prolinebond - create restraints to close flexible proline rings
  • ramaaco - create angle restraints to favor allowed Ramachandran plot regions
  • renumber - consistently renumber a group of chemical shift and peak lists
  • rmsd - convenient RMSD calculations
  • rotameraco - create angle restraints to favor staggered side-chain rotamers
  • structcalc - perform structure calculation

• Short read/write commands: The file type specification is now optional if the file name has the default extension for the given type of file. For instance, 'write demo.seq' can be used as a short-hand form of 'write seq demo.seq'.

• PDB coordinate files: The standard format for coordinate files is now that of the PDB (.pdb) rather than the (still supported) DG (.cor) format. A (compatible) variant that makes uses of the B-factor column to store an additional digit for each of the three Cartesian coordinates provides a higher accuracy than default PDB files.

• Nomenclature conversion: Transparent name translation includes now residue, atom and angle names, and applies to all kinds of input and output files. It is, for instance, straightforward to use the nomenclature of the PDB throughout a calcluation without explicitly changing names in the residue library. The 'translate' macro provides prefined translation tables for IUPAC, Cyana 1.x/Dyana Xplor/CNS, PDB, BMRB and NMRView. Importing/exporting data from other programs is much simplified in this way.

• Pseudoatom handling:
  • Coordinate files do by default no longer include pseudo atoms. The positions of pseudoatoms are calculated internally by the program if the variable 'pseudo' is set to 0, its default value. Traditional behavior can be restored with 'pseudo=1'.
  • As an alternative, a simplified naming scheme can be used interchangeably with the traditional 'Q...' names for pseudo atoms. In the simplified system the name of a pseudoatom is obtained from the names of the hydrogen atoms that it represents by removing the last (or the two last) digits. For instance, in the case of Val methyl protons HG11, HG12, HG13, HG21, HG22, HG23 the pseudo atoms are called QG1 --> HG1, QG2 --> HG2, and QQG --> HG. To use the simplified pseudo atom naming scheme on output, set 'pseudo=2'.
  • Multiple angle restraints: A new type of multiple angle restraint is available that simultaneously involves several torsion angles and yields a violation only if all its individual torsion angle restraints are violated. Multiple angle restraints are useful, for example, to implement a Ramachandran plot potential that puts a penalty on "forbidden regions of the Ramachandran plot.

• Temporary angle restraints: It is now possible to apply angle restraints only temporarily during certain phases of the simulated annealing schedule.

• Ramachandran and rotamer angle restraints: Angle restraints that favor allowed regions of the Ramachandran plot and staggered rotamer positions for side-chain torsion angles can be used automatically during the initial phases of simulated annealing.

• Symmetric dimers: The automated NOE assignment algorithm has been extended to make explicit use of the dimer symmetry, if necessary, and the new command group 'molecules' has been added to treat symmetric dimers.

• Fortran 90 implementation: The program has been rewritten in Fortran 90 making use of the dynamic memory allocation features of Fortran 90. There are no longer any hard-coded limitations on the numbers of atoms, peaks, restraints etc.

• INCLAN command language improvements:
  • Fortran 90 implementation without memory limitations.
  • Possibility for Inclan macros (.cya files) to be started as shell scripts at the Unix prompt that automatically invoke Cyana.
  • Macro names given as a parameter on the command line that starts Cyana can, optionally, contain the .cya extension. E.g. the command 'cyana CALC.cya' given at the Unix prompt will start Cyana and execute the CALC.cya macro.
  • New command 'cd' or 'chdir' to change the current working directory.
  • New intrinsic character function 'getcwd' to obtain the name of the current working directory.
  • New intrinsic logical function 'master' that is true for the master process in parallel execution, and false otherwise.

• Additionally supported systems:
  • Full support for the Mac OS X operating system.
  • Experimental support for Windows XP using Cygwin and the Intel Fortran compiler.
  • Experimental support for the free 'g95' Fortran compiler.
  • File systems that do not distinguish upper from lower case letters are supported.

• Parallelization: Setting up parallel structure calculations on Linux cluster systems with MPI is straightforward with the 'cyanajob' script.

• New system functions:
  • anamlib(i) - original name of atom i in the residue library
  • dnamlib(i) - original name of angle i in the residue library
  • rnamlib(i) - original name of residue i in the residue library
  • cyanadir - directory in which cyana is installed (=libdir)
  • nmol - number of molecules (e.g. 2 for a symmetric dimer)
  • nlol - number of lower distance limits
  • rmsd - calculate RMSD value to the average coordinates
  • rmsdcurr - calculate average RMSD value of selected structure with respect to current structure
  • rmsdpair - calculate average pairwise RMSD value
  • rmsdstd - standard deviation of RMSD values
  • rmsdmin - maximal individual RMSD value
  • rmsdmax - maximal individual RMSD value
  • iccoa(j,i) - j-th atom of scalar coupling constant i (j=1,2)
  • dcosel(i) - is distance restraint i selected?