trajectory_dihedral.py Command Help

Command: $SCHRODINGER/run trajectory_dihedral.py

usage: $SCHRODINGER/run trajectory_dihedral.py -c input_cmsfile
    -r residue_numbers (required) -output_csv output_csvfile -chain chain_name
     -dihedrals dihedral_types (default backbone) -f frame_frequency (default 1)
    

Measures 'phi', 'psi', 'omega', 'chi1', 'chi2', 'chi3', 'chi4', 'chi5' for
selected residues over a Desmond trajectory.

Prints out the value of one or more dihedral angles over the course of a
simulation.  The residues to monitor can be specified, and the dihedral angle
can be chosen from 'phi', 'psi', 'omega', 'chi1', 'chi2', 'chi3', 'chi4', 'chi5'
'backbone', or 'all'

backbone = Phi and Psi
all = All choices except backbone

For each evaluated frame, a comma-separated list of dihedral values is output to
a specified csv file, one value for each monitored residue.

Copyright Schrodinger, LLC. All rights reserved.

options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -c INPUT_CMSFILE      Input cms file.
  -chain CHAIN          Chain identifier of the input structure corresponding
                        to the residue numbers. If no chain is specified the
                        input should haveonly a single chain in it.
  -r RESIDUE_NUMBERS    Comma-separated residue numbers to monitor. Colons can
                        be used to specify a range of residue numbers. Any
                        insertion codes should be specied with individual
                        residue numbers. If no residue numbers are specified
                        all residue numbers will be reported. For example:
                        1,3A,75 or 4A,12:20,172.
  -output_csv OUTPUT_CSV
                        Output csv file. Outputting to CSV will also hide
                        terminal output
  -d {phi,psi,omega,chi1,chi2,chi3,chi4,chi5,backbone,all} [{phi,psi,omega,chi1,chi2,chi3,chi4,chi5,backbone,all} ...], -dihedrals {phi,psi,omega,chi1,chi2,chi3,chi4,chi5,backbone,all} [{phi,psi,omega,chi1,chi2,chi3,chi4,chi5,backbone,all} ...]
                        Dihedral type to monitor. Must be one or more of the
                        following: phi, psi, omega, chi1, chi2, chi3, chi4,
                        chi5, backbone, all. The default is 'backbone'.
  -f FREQUENCY, -frequency FREQUENCY
                        Evaluate frames starting at frame 0, and every Nth
                        frame after that.