YasaraRefine

This module refines structures of conformers by calling YASARA structure. YASARA structure requires a paid license. The MMMx wrapper automates refinement of conformers in ensembles and cleans up YASARA output PDB files. The feature emulates the Minimization Server of YASARA.

YasaraRefine can have an input argument:

!yasara [maxtime]
Arguments

  • maxtime - maximum computation time for a single model in hours, defaults to 1

Remarks

  • since the Yasara jobs cannot be killed from within Matlab, too short maximum times can result in too many parallel processes, which may slow down the computer

addpdb

Input of template conformers from PDB files.

addpdb file identifier
Arguments

  • file - file name, can contain wildcards

  • identifier - module-internal identifier for the ensemble, e.g. ‘ensemble_1’

Remarks

  • use wildcard ‘*’ for part of the filename to process all conformers from a previous step in the pipeline

  • individual PDB files can contain a single model or several models; this can be freely mixed

  • use this if you want to refine raw conformers after Flex or FlexRNA calls

console

Requests that Yasara is run in console mode.

console
Remarks

  • by default, Yasara is run with full display

  • for long production runs and for running on a server, console mode saves resources

getens

Input of template conformers from PDB files.

getens file identifier
Arguments

  • file - name of an MMMx ensemble file list (extension ‘.ens’ or ‘.zip’)

  • identifier - module-internal identifier for the ensemble, e.g. ‘ensemble_2’

Remarks

  • use this for refining conformers in an ensemble generated by the EnsembleFit module

  • if it is affordbale, it is better to refine the raw ensemble before calling the the EnsembleFit module

  • getens can also read zipped ensemble archives, as generated by the archive keyword in EnsembleAnalysis

getpdb

Input of a template by reading a single local PDB file or retrieving a PDB structure from a server.

getpdb file
Arguments

  • file - file name or PDB identifier, must have extension ‘.pdb’ if it specifies a file

Remarks

  • if the template has several conformers, the first one is used

repack

Requests sidechain repacking by SCWRL4 before calling Yasara.

repack
Remarks

  • use this if SCWRL4 is available and quality of input conformers might be poor

  • this is much faster than Yasara, if SCWRL4 is available, it is never wrong to specify this option

save

Specifies name for saving an output ensemble list

save file
Arguments

  • file - file name four output ensemble list

Remarks

  • extension ‘.ens’ is appended

  • this has only an effect, if input is an ensemble (key getens was used)