trj_essential_dynamics.py Command Help

Command: $SCHRODINGER/run trj_essential_dynamics.py

usage: trj_essential_dynamics.py [-h] [-s START:END:STEP] [-nmodes <int>]
                                 [-asl <ASL>] [-projection]
                                 [-cross-correlation] [-pca-nframes <int>]
                                 [-pca-scale <float>]
                                 cms trj out

This script runs protein essential dynamics analysis, which includes calculating
the principal components of the protein C-alpha atoms.
The resulting mode vectors are stored as atom level properties in the output
Maestro structure, and the resulting motion for the selected modes
is written out in XTC format.
Optionally, cross-correlation plots and per-frame conformational deviations
projected onto the modes can also be generated.

Reference:
   Amadei A, Linssen AB, Berendsen HJ, "Essential Dynamics of Proteins.",
   Proteins, 17(4):412-25, 1993. DOI: 10.1002/prot.340170408

The output trajectories contains artificial motions for each mode where the
scaled collective displacement is added to the initial frame. Time in such
trajectories corresponds to the displacement scaling.

Example:
  $SCHRODINGER/run trj_essential_dynamics.py jobname-out.cms jobname_trj out

positional arguments:
  cms                   Input .cms file name
  trj                   Input trajectory file or dir name, which typically
                        ends with an extension name of '.xtc' (XTC format) or
                        '_trj' (DTR format), e.g., jobname.xtc, jobname_trj
  out                   Output file basename

options:
  -h, --help            show this help message and exit
  -s START:END:STEP, -slice-trj START:END:STEP
                        Use the sliced trajectory. We use Python's slice
                        notation. START, END, and STEP should be integer
                        numbers.
  -nmodes <int>         Number of modes to calculate. Default: 10
  -asl <ASL>            ASL expression to select protein C-alpha atoms. The
                        non-C-alpha atoms are automatically excluded. Default:
                        protein or nucleic_acids
  -projection           Write to CSV file the projection of per-frame
                        conformational deviations onto calculated modes
                        (principal component space). Default: False
  -cross-correlation    Write cross-correlation matrix plot and data. Default:
                        False
  -pca-nframes <int>    Specify the number of frames in the to-be-generated
                        PCA trajectory. This parameter controls the number of
                        frames between the initial conformation and the
                        conformation with maximum normal modes displacement.
                        Default: 20
  -pca-scale <float>    This scaling value is used to amplify the PCA mode
                        displacement for visualization purposes. Default: 10.0