residue_scanning_backend.py Command Help
Command: $SCHRODINGER/run residue_scanning_backend.py
usage: residue_scanning_backend.py [-h] [-jobname] [-subjob]
[-residues RESIDUES] [-mut MUT]
[-mut_by_type] [-res_file] [-muts_file]
[-residue_structure] [-calc CALC]
[-concurrent] [-sequential]
[-refine_mut {python_minimize,prime_minimize,prime_residue,prime_sidechain,prime_sidechain_cbeta,prime_sidechain_bb,prime_loop_prediction}]
[-dist Ang.] [-loop LOOP] [-loop2 LOOP2]
[-loop_options LOOP_OPTIONS] [-ligand_asl]
[-receptor_asl] [-not_idealized]
[-solvent {vsgb2.0,vsgb2.1,sgbnp,vac}]
[-use_membrane] [-fast] [-classic]
[-rigidmove] [-refine_mutable_only]
[-refine_all_mutable] [-refine_unbound]
[-MC] [-mc_nstep MC_NSTEP]
[-mc_noutput MC_NOUTPUT] [-mc_temp MC_TEMP]
[-mc_write_trj] [-mc_nterm MC_NTERM]
[-mc_stability_weight MC_STABILITY_WEIGHT]
[-mc_affinity_weight MC_AFFINITY_WEIGHT]
[-mc_stability_cutoff MC_STABILITY_CUTOFF]
[-mc_affinity_cutoff MC_AFFINITY_CUTOFF]
[-mc_random_seed MC_RANDOM_SEED]
[-mc_random_start] [-minimizer_nbcutoff]
[-no_cleanup] [-NOJOBID]
[-HOST <host_list>]
[-subhost <subhost_list>] [-NJOBS <#jobs>]
[-LOCAL] [-WAIT] [-SAVE]
[-add_res_scan_wam]
[-merge_mae PREVIOUS_OUTPUT_STRUCTURE]
structures
The driver script to mutate residues and compute various property changes such
as stability, binding affinity, surface area, etc. It can also search the best
mutations for affinity maturation with a Monte Carlo based approach. The
mutant structures and related properties are stored in the output file.
positional arguments:
structures The input structure file containing the receptor, the
receptor/ligand complex, or a Pose Viewer file (first
CT is the receptor, all remaining are docked ligands).
If multiple CTs are in the "struct_file" it is assumed
to be a PV file.
options:
-h, --help show this help message and exit
-jobname , -JOBNAME The base jobname.
-subjob The number of this subjob (for internal use only)
-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".
-mut_by_type Choose the residues to mutate by type. Available
options: polar, nonpolar, aromatic, neutral, basic,
acidic, charged.
-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.
-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".
-residue_structure A Mae file containing the non-standard residues that
are mutation targets. The Mae file can have multiple
structures. Each structure can be a free amino acid,
or a amino acid capped by ACE and NME, and the
structure must have the same 3-letter residue name as
in the mutation definition.
-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, and "e_pot" will always be
calculated when "python_minimize" refinement is used
-concurrent Maximum concurrent residue changes (default 1)
-sequential Make concurrent changes to only sequential (neighbor)
residues.
-refine_mut {python_minimize,prime_minimize,prime_residue,prime_sidechain,prime_sidechain_cbeta,prime_sidechain_bb,prime_loop_prediction}
Refinement method. Available options:"python_minimize"
- Minimize using the Python Minimizer (ffld);
"prime_residue" (default) - Refine with Prime side-
chain prediction followed by residue minimization;
"prime_minimize" (obsolete, same as prime_residue);
"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.
-dist Ang., -d Ang. Cutoff distance 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
-loop LOOP Two residues to define the loop. Each residue should
be in the form <chain>:<resnum>. If there is no chain
use "_". Example: "-loop A:6,A:10".
-loop2 LOOP2 Two residues to define the second loop in cooperative
loop sampling.Each residue should be in the form
<chain>:<resnum>. If there is no chain use "_".
Example: "-loop2 A:22,A:27".
-loop_options LOOP_OPTIONS
Options for loop refinement. Keyword/Value are
separated by comma,e.g.:MAX_CA_MOVEMENT/4.0,RES_SPHERE
/7.5,HOST/localhost:8,PROTOCOL/[LOOP_BLD][EXTENDED][LO
NG_LOOP_2]
-ligand_asl ASL used to split the receptor and ligand for bound
and unbound calculations. This is only needed if the
"struct_file" is a single CT, receptor/ligand complex.
If this argument is not supplied there will not be any
bound/unbound calculations. Note: The "-receptor_asl"
cannot be used with this flag.
-receptor_asl ASL used to split the receptor and ligand for bound
and unbound calculations. This also triggers a binding
affinity calculation, as with "-ligand_asl". Note: The
"-ligand_asl" cannot be used with this flag.
-not_idealized Turn off ideal reference mutations. Ideal reference
mutations take the same methods which idealize a
residue's bond length and angles in the mutant
residue, and apply it to the reference. Turning this
off will use the input bond length and angles in the
reference when calculating the deltas.
-solvent {vsgb2.0,vsgb2.1,sgbnp,vac}
The sovlent model for Prime jobs. Available options
are vsgb2.0 (default), vsgb2.1, sgbnp and vac.
-use_membrane Use the implicit membrane, which has to be set up and
saved in the input structure already.
-fast Use the fast Prime residue mutation backend (the
default).
-classic Use the Python driver based residue mutation backend.
-rigidmove Allow rigidbody movement between ligand and receptor.
-refine_mutable_only Refine only the mutable residues, i.e. all residues
within certain cutoff but not mutable will be ignored.
-refine_all_mutable Refine all mutable residues for each MC search step.
-refine_unbound Refine the unbound state using the specified
refinement method.By default, the unbound state is
defined as separating the ligand and the receptor from
the refined bound state without further optimization.
-MC Run Monte Carlo search with Prime residue mutation
backend.
-mc_nstep MC_NSTEP Number of Marte Carlo steps (default 2000).
-mc_noutput MC_NOUTPUT
Number of top mutations being reported (default 100).
-mc_temp MC_TEMP The temperature for controlling acceptance rate
(default 298).
-mc_write_trj Write MC sampling trajectory files. This option should
be used with -no_cleanup to keep the files in the work
directory.
-mc_nterm MC_NTERM Terminate if no new move accepted in X moves (default
X=1000000).
-mc_stability_weight MC_STABILITY_WEIGHT
The weight of stability in the optimization score in
the affinity calculation. The default is 0.0.
-mc_affinity_weight MC_AFFINITY_WEIGHT
The weight of affinity in the optimization score in
the affinity calculation. The default is 1.0.
-mc_stability_cutoff MC_STABILITY_CUTOFF
The cutoff to reject a mutation if the stability
increases more than a threshold. The default is 30.0.
-mc_affinity_cutoff MC_AFFINITY_CUTOFF
The cutoff to reject a mutation if the affinity
increases more than a threshold. The default is 30.0.
-mc_random_seed MC_RANDOM_SEED
The random seed for MC job (default 0)
-mc_random_start Start the the Monte Carlo search from a randomly
mutated structure
-minimizer_nbcutoff Experimental option. Sets the non-bonded cutoff for
the Python Minimizer (default is 14A if Python
Minimizer is used for refinement, and 40A if Prime is
used for refinement).
-no_cleanup Do not clean up intermediate files.
-NOJOBID Do not run the script under job control
-HOST <host_list> Run job remotely on the indicated host entry. (if
-NJOBS is used, subjobs are run on the -subhost list)
-subhost <subhost_list>
Run subjobs on this host. By default, same as the
-HOST list.
-NJOBS <#jobs> Number of subjobs to generate. By default, the
workflow is run as one job.
-LOCAL Do not use a temporary directory. Keep files in the
current directory.
-WAIT Do not return a prompt until the job completes.
-SAVE Return zip archive of job directory at job completion.
-add_res_scan_wam Whether to add "RESIDUE SCANNING" wam to output file.
-merge_mae PREVIOUS_OUTPUT_STRUCTURE
Run using output of incomplete job to fill in missing
results.