frame2cms.py Command Help

Command: $SCHRODINGER/run frame2cms.py

usage: frame2cms.py [-h] [-s START:END:STEP] [-keep-inactive-atoms]
                    [-i FRAME_INDEX]
                    cms trj out

Convert Desmond trajectory into a series of .cms files.

Examples:
  - Converts a single frame into a .cms file:

      $SCHRODINGER/run frame2cms.py -i <frame#> <cms> <trj> <output-basename>

  - Converts the whole trajectory into a series of .cms files:

      $SCHRODINGER/run frame2cms.py <cms> <trj> <output-basename>

  - Converts frame# 1, 2, and 3 into three .cms files:

      $SCHRODINGER/run frame2cms.py -s 1:4 <cms> <trj> <output-basename>

    The first frame is frame# 0.

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.
  -keep-inactive-atoms  Keep inactive atoms.
  -i FRAME_INDEX        Specify the index of the frame to convert. If
                        unspecified, the -s option will effect.