trj_occupancy.py Command Help

Command: $SCHRODINGER/run trj_occupancy.py

usage: trj_occupancy.py [-h] [-s START:END:STEP] [-ref-mae <file>]
                        [-ref-frame frame-number] [-fit-asl ASL]
                        [-map-asl ASL] [-grid-spacing VAL] [-grid-length VAL]
                        cms trj out

This script calculates the occupancy histogram of selected atoms in 3D space.
The trajectory is first aligned to the reference structure on the atoms
selected by the -fit-asl option, then it calculates the histogram on the atoms
selected by the -map-asl option. The result is written into a file in the
common map format (CNS/X-PLOR) for visualization on Maestro::

    (Maestro -> Workspace Menu -> Surfaces -> Import)

Note the occupancy histogram is only calculated for a limited cubic subspace,
whose size is specified by the -grid-length option. The subspace is centered
at the center-of-mass of the selected atoms by the -fit-asl option.

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
  -fit-asl ASL          ASL expression to specify the part of system to be
                        aligned. It should NOT be a dynamic ASL expression
                        (e.g., 'within 5 (m.n 1)'). Default: 'solute'.
  -map-asl ASL          ASL expression to specify the part of system used for
                        occupancy histogram calculation. It should NOT be a
                        dynamic ASL expression (e.g., 'within 5 (m.n 1)').
                        Default: 'solute'.
  -grid-spacing VAL     Grid spacing in Angstroms. Default: 1.0
  -grid-length VAL      Grid length in Angstroms. Default: 15.0