trajectory_binding_site_id.py Command Help

Command: $SCHRODINGER/run trajectory_binding_site_id.py

usage: trajectory_binding_site_id.py [-h] [-s STRIDE]
                                     [-sitemap-options SITEMAP_OPTIONS [SITEMAP_OPTIONS ...]]
                                     [-rank-sites-by {SiteScore,Dscore}]
                                     [-site-overlap-cutoff SITE_OVERLAP_CUTOFF]
                                     [-no_cleanup] [-HOST <hostname>]
                                     input [input ...] output

Script for identifying binding sites from trajectories of MxMD or MD simulations.

This script takes one or more trajectories of a MxMD or MD simulation, extract
frame structures with a (optional) slice step, run SiteMap on each frame
structure, and consolidate the SiteMap output sites. It is used to capture
transient/cryptic binding sites that may not exist in the static structure.

Copyright Schrödinger, LLC. All rights reserved.

positional arguments:
  input                 Desmond output cms file(s) for reading trajectory, a
                        trajectory .xtc file or directory should be present in
                        the same directory as the input cms file, the cms file
                        should point to a valid trajectory and the frames
                        should be aligned
  output                Output file basename

options:
  -h, --help            show this help message and exit
  -s STRIDE             Stride for trajectory extraction, default is 1
  -sitemap-options SITEMAP_OPTIONS [SITEMAP_OPTIONS ...]
                        Option to override default SiteMap Settings. Use a
                        list of 'option:value' pairs. For example: -sitemap-
                        options sitebox:6 maxsites:5
  -rank-sites-by {SiteScore,Dscore}
                        Site ranking method. (Default: SiteScore).
  -site-overlap-cutoff SITE_OVERLAP_CUTOFF
                        Site residue similarity cutoff for consolidating two
                        sites, site with higher score will be kept. Default is
                        0.3.
  -no_cleanup           Do not cleanup SiteMap output files.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.