trj2mae.py Command Help

Command: $SCHRODINGER/run trj2mae.py

usage: trj2mae.py [-h] [-s START:END:STEP] [-trj-frame-cutting FRAME-CUTTING]
                  -extract-asl EXTRACT_ASL [-align-asl ALIGN_ASL]
                  [-protocol PROTOCOL] [-separate] [-out-format {MAE,PDB}]
                  cms trj out

Convert a Desmond trajectory into a series of Maestro files. You can select part
of the original system to save into the Maestro files using the -extract-asl
option, and the ASL expression can be dynamic, meaning that the total number of
selected atoms doesn't have to be the same from frame to frame. Before the
extraction, you can optionally align the geometry from the trajectory frames
to that from the input <cms> file. The atoms for the alignment can be specified
via the -align-asl option. If you wish to not align the geometry, you can set
-align-asl to an empty string: -align-asl "".

Predefined atom extraction protocols:

* water-close-to-ligand
  This protocol is equivalent to the options::

    -align-asl "(fillres within 5 ligand) and backbone"
    -extract-asl "((fillres within 7 (ligand)) and (not water)) or
                   ((water and (fillres within 3.5 (((fillres within 7 (ligand))
                   and (not water))))) and (water and (fillres within 3.5
                   ligand))) or (water and (fillres within 2.5 ligand))"

Here the complicated EXTRACT_ASL is to select the ligand, some residues within
the binding pocket, and water molecules near those atoms.

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.
  -trj-frame-cutting FRAME-CUTTING
                        Compose a new trajectory where the original trajectory
                        frames are selected and/or reordered using frame
                        indices and ranges. Note that frame indices are
                        0-based, and that frame ranges are inclusive. For
                        example: '0,0,1,3:5' will give a new trajectory
                        containing the following frames (in that order) from
                        the original trajectory: 0, 0, 1, 3, 4, 5. If the
                        '-slice-trj' option is also specified, -trj-frame-
                        cutting will work on the sliced trajectory; in other
                        words, the frame indices here are those of the sliced
                        trajectory.
  -extract-asl EXTRACT_ASL
                        Specify atoms to extract.
  -align-asl ALIGN_ASL  Specify atoms to align to the geometry as in the input
                        CMS file. Default value: EXTRACT_ASL. If no alignment
                        is intended,set it as empty string ''.
  -protocol PROTOCOL    Specify a predefined protocol for alignment and
                        extraction. This will overwrite the -extract-asl and
                        -align-asl options. Valid values: water-close-to-
                        ligand.
  -separate             Write out separate .maegz file for each frame.
  -out-format {MAE,PDB}
                        Specify output file format. Default is MAE (case
                        insensitive).