cross_link_proteins_backend.py Command Help

Command: $SCHRODINGER/run cross_link_proteins_backend.py

usage: cross_link_proteins_backend.py [-h] -input_structure INFILE
                                      [-linker_sequences LINKER_SEQUENCES]
                                      [-energy_method {prime_solvent,macromodel_solvent,macromodel_gas}]
                                      [-prediction_method {interdomain_linker_library,intradomain_loop_library,de_novo}]
                                      [-configfile CONFIGFILE]
                                      [-loopdb_path LOOPDB_PATH] [-host HOST]
                                      [-ncpus NCPUS]

Build linkers into protein structures. New-style usage:
cross_link_proteins_backend.py -infile input.mae -linker_sequences seqs.fasta
Legacy usage (for GUI compatibility): cross_link_proteins_backend.py -infile
input.mae -configfile config.yaml

options:
  -h, --help            show this help message and exit
  -input_structure INFILE, -infile INFILE
                        Input structure to build linkers into.
  -linker_sequences LINKER_SEQUENCES
                        Path to a FASTA file containing linker sequences in
                        1-letter amino acid codes.
  -energy_method {prime_solvent,macromodel_solvent,macromodel_gas}
                        Energy method. Default: prime_solvent
  -prediction_method {interdomain_linker_library,intradomain_loop_library,de_novo}
                        Linker structure prediction method. Default:
                        interdomain_linker_library
  -configfile CONFIGFILE
                        (Legacy) Config (yaml) file holding options and
                        sequences to be linked.
  -loopdb_path LOOPDB_PATH
                        Path for loop database used to build linkers.
  -host HOST            The host to run on.
  -ncpus NCPUS          Number of cpus on host.