cysteine_mutation_backend.py Command Help

Command: $SCHRODINGER/run cysteine_mutation_backend.py

usage: cysteine_mutation_backend.py [-h] [-flex_dist FLEX_DIST]
                                    [-flex_adj_res FLEX_ADJ_RES]
                                    [-cys_to_x CYS_TO_X]
                                    [-refine_mut {python_minimize,prime_minimize,none}]
                                    [-res_pairs RES_PAIRS] [-j] [-NOJOBID]
                                    [-HOST <host_list>] [-LOCAL] [-OVERWRITE]
                                    [-RESTART] [-no_cleanup]
                                    [infile]

This script is used by cysteine_mutation_gui.py.

positional arguments:
  infile                Input structure file

options:
  -h, --help            show this help message and exit
  -flex_dist FLEX_DIST  Optimize atoms within this distance of the mutated
                        residues (by default, only mutated residues are
                        optimized)
  -flex_adj_res FLEX_ADJ_RES
                        Optimize residues that are within this distance, by
                        sequence (by default, only mutated residues are
                        optimized)
  -cys_to_x CYS_TO_X    Mutate each cysteine to each of these residue types
                        (comma-separated)
  -refine_mut {python_minimize,prime_minimize,none}
                        Refinement method. Available options:"python_minimize"
                        (default) - Minimize using the Python Minimizer
                        (ffld); "prime_minimize" - Refine with Prime
                        minimization; "none" - Do not minimize nor calculate
                        energies (for debugging).
  -res_pairs RES_PAIRS  Residues to mutate (comma-separated)
  -j , -jobname         The job name.
  -NOJOBID              Run the script without job control
  -HOST <host_list>     Run job remotely on the indicated host entry.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -OVERWRITE            Overwrite any existing job files.
  -RESTART              Attempt to restart the previous job. All arguments
                        other than the jobname are ignored when -RESTART is
                        specified. NOTE: For job to be restartable, it must
                        have been started with -LOCAL.
  -no_cleanup           Do not clean up intermediate Prime subjob files.