trj_extract_subsystem.py Command Help

Command: $SCHRODINGER/run trj_extract_subsystem.py

usage: trj_extract_subsystem.py [-h] [-t TRJ] [-s START:END:STEP] [-asl ASL]
                                [-whole]
                                cms out

Extract subsystem and create a new file: <out>-out.cms. If the associated
trajectory directory for the original system is specified, a new trajectory
will be created for the subsystem, and the directory name of the new trajectory
will be <out>_trj.

Note that the ffio_ff blocks in the <cms>.cms file will be preserved for the
selected atoms in order to generate a valid output CMS file. For this reason,
atom selections may be automatically expanded so that the resultant molecular
structures will match the corresponding ffio_ff blocks. For example, say the
ffio_ff block is for the whole protein, if the atom selection is only part of
the protein (e.g., one residue), it will be automatically expanded to the whole
protein to match the ffio_ff block.

positional arguments:
  cms                   Input .cms file name
  out                   Output file basename

options:
  -h, --help            show this help message and exit
  -t TRJ, -trj 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
  -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.
  -asl ASL              ASL expression to specify the subsystem, default is
                        "not water".
  -whole                Fix molecules broken by the periodic boundary to make
                        them whole again.