EnsembleAnalysis

This module analyzes ensembles in terms of intermediate order. In this module, ensembles have internal variable names (identifiers).

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

getens

Input of template conformers from PDB files specified by an MMMx ensemble list.

gentens file identifier
Arguments
  • file - name of an MMMx ensemble file list (extension ‘.ens’)

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

Remarks
  • best way of analyzing an ensemble generated by the EnsembleFit module

subsample

Subsample an ensemble to a smaller ensemble.

subsample ratio input output
Arguments
  • ratio - integer reduction factor for ensemble size

  • input - identifier of the input ensemble

  • output - identifier of the output (reduced) ensemble

Remarks
  • this is particularly useful for molecular dynamics trajectories

figures

Subsample an ensemble to a smaller ensemble.

figures format
Arguments
  • format - one of the formats in which Matlab can save figures, e.g. ‘pdf’, default is ‘pdf’

Remarks
  • figure saving is on by default in this module, use format ‘off’ to switch it off

sort

Iterative hierarchical clustering and sorting of an ensemble.

sort filename input [option]
Arguments
  • filename - name of the output ensemble list, extension should be ‘.ens’

  • input - identifier of the input ensemble

  • option - option ‘oriented’ assumes that the conformers are already in the same frame, otherwise they are optimally superimposed

  • option - option ‘drms’ uses orientation-independent distance root-mean square as a metric

Remarks
  • the algorithm attempts to group similar conformers and to start from the most typical conformers

measures

Compute various measures of the ensemble. This is a block key with n lines for n measures.

measures filename  input [range]
   subkey
   ...
.measures
Arguments
  • filename - basis name for the output files, abbreviated below as ‘%s’

  • input - identifier for the input ensemble

  • range - optional MMMx address that specifies only a range of a conformer for analysis, e.g. (A)187-320

  • measure - a subkey that specifies a measure from the following list

Available subkeys
  • matlab - save output data to Matlab files * csv - save output data to comma-separated value files

  • oriented - assume that conformers are already oriented, default is false (conformers are superimposed)

  • Rg - radius of gyration. including standard deviation (output to logfile)

  • width - ensemble width and density in Angstroem (output to logfile), also computes pair r.m.s.d. matrix and central conformer

  • correlation - correlation matrix, output as figure and to files ‘residue_pair_correlation_%s’ with extensions ‘.csv’and ‘.mat’

  • sort - sort for computation of correlation matrix * drms - uses distance root mean square deviation for correlation matrix and sorting

  • compactness - compactness matrix

Remarks
  • saving output to both Matlab (‘.mat’) and ‘.csv’ files is allowed * if neither the matlab nor the csv subkey is present, output is only to figures or logfile

  • oriented affects only computation of pair r.m.s.d. (correlation matrix)

flexibility

Computes local flexibility profiles of peptide or nucleotide chains

flexibility filename input
Arguments
  • filename - name of the output file

  • input - identifier of the input ensemble

Remarks
  • the algorithm analyzes variation of backbone dihedrals \psi and \phi

  • for RNA, pseudo-torsion angles are analyzed

  • local flexibility ranges between 0 (rigid) and 1 (random)

order

Computes local order profiles of peptide or nucleotide chains

order filename input
Arguments
  • filename - name of the output file

  • input - identifier of the input ensemble

Remarks
  • the algorithm is based on an adapttation of Flory’s characteristic ratio to polymers with secondary structure

  • the local order parameter ranges between 0 (random) and 1 (perfect order)

  • the local order parameter is somewhat longer ranged than the flexibility parameter mentioned above

density

Computes a 3D density map (pseudo-electron density) of an ensemble

density filename input [range [resolution]]
Arguments
  • filename - name of the output file, specify with extension ‘.mrc’

  • input - identifier of the input ensemble

  • range - optional MMMx address that specifies only a range of a conformer for analysis, e.g. (A)187-320

  • resolution - resolution in Angstroem (optional), defaults to 1

Remarks
  • output is as a ‘.mrc’ file, which can be visualized by most protein graphics programs

  • a larger value for resolution leads to faster computation and a smaller file and may still be adequate for strong disorder

superimpose

Superposition of conformers in an ensemble

superimpose output input [range [template [template_range [mode]]]]
Arguments
  • output - name of the output file, extension ‘.pdb’ is appended, if none

  • input - identifier of the input ensemble

  • range - optional MMMx address that specifies only a range of a conformer for analysis, e.g. (A)187-320

  • template - template ensemble or structure (optional)

  • template_range - optional MMMx address that specifies a template range of a conformer, e.g. (B)187-320

  • mode - optional string mode can be ‘central’ to request superposition onto the central conformer

Remarks
  • by default, superposition is to the first conformer of the input ensemble if no range is provided

  • if a template and central are specified, superposition is to central conformer of a superensemble consisting of input and template

  • the range argument ‘(*)’ selects the complete structure

save

Save ensemble to a single PDB file

save output ensemble_id
Arguments
  • output - name of the output file, extension ‘.pdb’ is appended, if none

  • ensemble_id - identifier of the ensemble to be save

Remarks
  • populations are stored in a REMARK 400 field

compare

Comparison of two ensembles

compare ensemble_1 ensemble_2 [range [mode]]
Arguments
  • ensemble_1 - identifier of the first ensemble

  • ensemble_2 - identifier of the second ensemble

  • range - optional MMMx address that specifies only a range of a conformer for comparison, e.g. (A)187-320

  • mode - optional string mode can be ‘resolved’ to request residue-wise comparison

Remarks
  • the algorithm computes overlap of pseudo-electron densities between ensembles

  • the range argument ‘(*)’ selects the complete structure

  • the two ensembles may have different numbers of conformers

  • residue-wise comparison of large ensembles can take very long