trajectory_bfactors.py Command Help

Command: $SCHRODINGER/run trajectory_bfactors.py

usage: trajectory_bfactors.py [-v] [-h] [-asl ASL] [-csv] [-byatom]
                              [-s START:END:STEP]
                              cms outfile

This script takes in a trajectory, and writes out a structure file with the
B-factor atom-level properties added in. In addition, the RMSF and B-factor
values can be written to a CSV file. The script will only work on protein
residues.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  cms                Trajectory CMS file. The script will only calculate
                     B-factors for protein residues.
  outfile            Output structure file (Maestro or PDB).

options:
  -v, -version       Show the program's version and exit.
  -h, -help          Show this help message and exit.
  -asl ASL           ASL for the substructure to analyze (subset of the solute
                     only).
  -csv               Write per-residue RMSF and B-factors to a CSV file.
  -byatom            Store per-atom B-factors in the output structure file
                     instead of per-residue B-factors.
  -s START:END:STEP  Use the sliced trajectory. We use Python's slice
                     notation. START, END, and STEP should be integer numbers.