structure_factor_driver.py Command Help

Command: $SCHRODINGER/run structure_factor_gui_dir/structure_factor_driver.py

usage: $SCHRODINGER/run structure_factor_gui_dir/structure_factor_driver.py
       [-h] -cms_file CMS_FILE -trj TRJ [-trj_min TRJ_MIN] [-trj_max TRJ_MAX]
       [-trj_step TRJ_STEP] -asl ASL [-pos_type {atom,com,coc,centroid}]
       [-sq_method {pos,rdf,poj}] [-deltar DELTAR] [-rmax RMAX]
       [-num_waves NUM_WAVES] [-HOST <hostname>] [-D] [-VIEWNAME <viewname>]
       [-JOBNAME JOBNAME]

Script to calculate structure factor from trajectory Copyright Schrodinger,
LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -cms_file CMS_FILE    Input cms file (default: None)
  -trj TRJ              Directory of the trajectory (default: None)
  -trj_min TRJ_MIN      Minimum of trajectory frame to be analysed. (default:
                        None)
  -trj_max TRJ_MAX      Maximum of trajectory frame to be analysed. (default:
                        None)
  -trj_step TRJ_STEP    Use every n-th frame in the trajectory range. The
                        first and last frames in the range will always be
                        included. (default: None)
  -asl ASL              Selection of atoms used for the calculations of
                        structure factor (default: None)
  -pos_type {atom,com,coc,centroid}
                        Position type for group of atoms. atom = atomic
                        position; com = molecular center of mass; coc =
                        molecular center of charge (for charged species;
                        centroid = molecular centroid. (default: atom)
  -sq_method {pos,rdf,poj}
                        Method used for calculating structure factor. pos =
                        Positions; rdf = Radial distribution function; poj =
                        Projections. (default: pos)
  -deltar DELTAR        The resolution of position (in Angstroms) used for
                        calculation. (default: 1)
  -rmax RMAX            The maximum distance (in Angstroms). The Radial
                        distribution function will be evaluated from 0 to this
                        value. (default: 10)
  -num_waves NUM_WAVES  Number of waves in each dimension, increasing number
                        of waves gives better resolution and range of
                        structure factor. (default: 20)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)