trj_align.py Command Help

Command: $SCHRODINGER/run trj_align.py

usage: trj_align.py [-h] [-s START:END:STEP] [-ref-mae <file>]
                    [-ref-frame frame-number] [-asl ASL]
                    cms trj out

This script aligns the structure in the trajectory to the reference
structure as specified by the user. By default, the reference is the first
frame of the trajectory.

Copyright Schrodinger, LLC. All rights reserved.

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.
  -ref-mae <file>       Reference structure file in either .cms or .mae format
  -ref-frame frame-number
                        Specify the frame to use as the reference geometry.
                        Frame indices are 0-based indices. Number 0 is the
                        first frame. Negative numbers means counting from the
                        end of the trajectory, e.g., -1 means the last frame.
                        Default: 0
  -asl ASL              ASL expression to specify the part of system to be
                        aligned. The expression will be applied to the
                        structure from the input <cms> file to get the atoms
                        indices, which will then be used to get the geometries
                        in both the reference structure and the trajectory.
                        Default: solute