mut_pred.py Command Help
Command: $SCHRODINGER/run -FROM psp mut_pred.py
usage: mut_pred.py [-h] [-NJOBS NJOBS] [-HOST <hostname>] [-JOBNAME JOBNAME]
[-no_cleanup] [-res_file RES_FILE | -muts_file MUTS_FILE]
[-dna_res_file DNA_RES_FILE | -dna_muts_file DNA_MUTS_FILE]
[-rna_res_file RNA_RES_FILE | -rna_muts_file RNA_MUTS_FILE]
[-receptor_asl RECEPTOR_ASL | -ligand_asl LIGAND_ASL]
[-residue_structure RESIDUE_STRUCTURE] [-use_membrane]
[-dist Ang.] [-calc CALC] [-residues RESIDUES] [-mut MUT]
[-solvent {vsgb2.0,vsgb2.1,sgbnp,vac}] [-add_res_scan_wam]
[-forcefield {OPLS_2005,OPLS3e,OPLS4}]
[-refine_mut {prime_minimize,prime_residue,prime_sidechain,prime_sidechain_cbeta,prime_sidechain_bb,prime_loop_prediction}]
[-concurrent] [-mutate_only]
[-remove_waters WATER_FREE_RADIUS]
inpmae
positional arguments:
inpmae input Maestro structure file
options:
-h, --help show this help message and exit
-no_cleanup Do not clean up intermediate files.
-res_file RES_FILE A file containing residue mutations. Each line defines
the mutation targets for a single residue. The format
of a line is "<chain>:<resnum><inscode(optional)>
<comma-separated 3-letter mutations>", e.g. "A:24
ARG,GLU,ASN,GLN". This option overrides the "-mut" and
"-residues" flags. (This option is incompatible with
-muts_file.)
-muts_file MUTS_FILE A file containing multiple residue mutations to
perform. Each line defines ONE mutation, which may
involve multiple residues and cannot combine with
other mutations. Not compatible with the -concurrent
and -sequential. The format of each line is a list of
space-separated residue mutations:
"<chain>:<resnum><inscode(optional)>" followed by "->"
and then the 3-letter residue name or 1-letter code,
e.g. "A:24->SER A:25->R". (This option is incompatible
with -res_file.)
-dna_res_file DNA_RES_FILE
A file containing DNA residue mutations. Each line
defines the mutation targets for a single residue. The
format of a line is
"<chain>:<resnum><inscode(optional)> <comma-separated
1-letter mutations>", e.g. "A:24 A,T,C,G". This option
overrides the "-mut" and "-residues" flags. (This
option is incompatible with -muts_file.)
-dna_muts_file DNA_MUTS_FILE
A file containing multiple DNA residue mutations to
perform. Each line defines ONE mutation, which may
involve multiple residues and cannot combine with
other mutations. Not compatible with the -concurrent
and -sequential. The format of each line is a list of
space-separated residue mutations:
"<chain>:<resnum><inscode(optional)>" followed by "->"
and then the 1-letter code, e.g. "A:24->A". (This
option is incompatible with -res_file.)
-rna_res_file RNA_RES_FILE
A file containing RNA residue mutations. Each line
defines the mutation targets for a single residue. The
format of a line is
"<chain>:<resnum><inscode(optional)> <comma-separated
1-letter mutations>", e.g. "A:24 A,T,C,G". This option
overrides the "-mut" and "-residues" flags. (This
option is incompatible with -muts_file.)
-rna_muts_file RNA_MUTS_FILE
A file containing multiple RNA residue mutations to
perform. Each line defines ONE mutation, which may
involve multiple residues and cannot combine with
other mutations. Not compatible with the -concurrent
and -sequential. The format of each line is a list of
space-separated residue mutations:
"<chain>:<resnum><inscode(optional)>" followed by "->"
and then the 1-letter code, e.g. "A:24->A". (This
option is incompatible with -res_file.)
-receptor_asl RECEPTOR_ASL
asl for receptor
-ligand_asl LIGAND_ASL
asl for ligand
-residue_structure RESIDUE_STRUCTURE
nonstandard residues mae file
-use_membrane Use the implicit membrane, which has to be set up and
saved in the input structure already.
-dist Ang., -d Ang. Cutoff distance (angstroms) from the mutated
residues/ligand for which other residues should be
included in refinement. The distance is measured from
a reference arginine residue placed at the mutated
position. Any residue containing an atom within the
cutoff distance will be included in the refinement.
Default: 0.0.
-calc CALC A list of properties to calculate for reference
structure and mutant structure. Multiple calculations
are separated by commas, e.g: "-calc pka,rotatable".
NOTE: "prime_energy" will always be calculated when a
Prime refinement is used. Current valid properties:
e_pot, prime_energy, pka, sasa_polar, sasa_nonpolar,
sasa_total, hydropathy, rotatable, vdw_surf_comp
-residues RESIDUES List of residues to mutate. Each residue should be in
the form of comma-separated <chain>:<resnum>. For
blank chain name, use "_".Example: "-residues
A:122,_:12,A:18A".
-mut MUT List of residues to mutate reference residues to.
Residues should be a comma-separated list of 3-letter
residue names with no spaces.Example: "-mut
ARG,GLU,ASN,GLN".
-solvent {vsgb2.0,vsgb2.1,sgbnp,vac}
The sovlent model for Prime jobs. Available options
are vsgb2.0, vsgb2.1, sgbnp and vac. Defaults to
vsgb2.0.
-add_res_scan_wam Whether to add "RESIDUE SCANNING" wam to output file.
-forcefield {OPLS_2005,OPLS3e,OPLS4}
The sovlent model for Prime jobs. Available options
are OPLS_2005, OPLS3e, and OPLS4. Defaults to
OPLS_2005.
-refine_mut {prime_minimize,prime_residue,prime_sidechain,prime_sidechain_cbeta,prime_sidechain_bb,prime_loop_prediction}
Refinement method. Available options:"prime_residue"
(default) - Refine with Prime side-chain prediction
followed by residue minimization; "prime_minimize" -
Refine with just residue minimization;
"prime_sidechain" - Refine with Prime side-chain
prediction; "prime_sidechain_cbeta" - Refine with
Prime side-chain prediction with CA-CB vector
sampling; "prime_sidechain_bb" - Refine with Prime
side-chain prediction with backbone
sampling."prime_loop_prediction" - Refine with Prime
loop prediction.
-concurrent Maximum concurrent residue changes (default 1)
-mutate_only Perform naive mutation without sidechain repacking,
minimization, or property calculation (stability,
affinity, etc). Use this flag to quickly generate many
(potentially high-energy) structures that may have
unresolved steric clashes.
-remove_waters WATER_FREE_RADIUS
Removes all waters within specified radius of all
mutable residues during sidechain prediction and
structure refinment.
Standard Options:
-NJOBS NJOBS Divide the overall job into NJOBS subjobs.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-JOBNAME JOBNAME Provide an explicit name for the job.