trj_rescue.py Command Help

Command: $SCHRODINGER/run trj_rescue.py

usage: trj_rescue.py [-h] [-transpose-box] [-o OUT] cms trj

Attempt to rescue a Desmond trajectory in case some frames are not saved
correctly. Example:

  $SCHRODINGER/run trj_rescue.py corrupt-out.cms corrupt_trj -o fixed

It saves the rescued trajectory in the same file format and creates a
corresponding new .cms file.

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

options:
  -h, --help      show this help message and exit
  -transpose-box  Transpose the simulation-box matrix. This only affects the
                  triclinic-box simulation system. The box matrix in GPU
                  trajectories before 2018-4 was incorrectly transposed. This
                  option will correct that.
  -o OUT          Output file base name. Default: "out"