usage: ample [-h] [-config_file CONFIG_FILE] [-nproc NPROC]
[-work_dir WORK_DIR] [-alignment_file ALIGNMENT_FILE]
[-allow_his_tag [True/False]] [-blast_dir BLAST_DIR]
[-classic_mode True/False] [-ccp4i2_xml CCP4I2_XML]
[-coiled_coil [True/False]] [-devel_mode devel_mode]
[-dry_run True/False] [-early_terminate [True/False]]
[-ensembles ENSEMBLES] [-fasta FASTA]
[-fast_protein_cluster_exe FAST_PROTEIN_CLUSTER_EXE]
[-F flag for F] [-FREE flag for FREE]
[-ideal_helices [True/False]] [-helical_ensembles [True/False]]
[-helical_ensembles_set [{full,minimal}]]
[-improve_template improve_template] [-make_models [True/False]]
[-max_array_jobs MAX_ARRAY_JOBS] [-models models]
[-mr_sequence MR_SEQUENCE] [-mtz MTZ in] [-name job_name]
[-native_pdb native_pdb] [-native_mtz native_pdb]
[-nmr_model_in nmr_model_in] [-nmr_process NMR_PROCESS]
[-nmr_remodel [True/False]]
[-nmr_remodel_fasta NMR_REMODEL_FASTA] [-purge purge_level]
[-psipred_ss2 PSIPRED_FILE] [-quick_mode [True/False]]
[-restart_pkl RESTART_PKL] [-run_dir run_directory]
[-rvapi_document RVAPI_DOCUMENT] [-scwrl_exe path to scwrl]
[-show_gui [True/False]] [-single_model SINGLE_MODEL]
[-sf_cif SF_CIF] [-SIGF SIGF] [-top_model_only True/False]
[--version] [-webserver_uri WEBSERVER_URI]
| -config_file | user configuration file |
| -nproc | Number of processors [1]. For local, serial runs the jobs will be split across nproc processors. For cluster submission, this should be the number of processors on a node. Default: 1 |
| -work_dir | Path to the directory where the job will run (will be created if it doesn’t exist) |
| -alignment_file | |
| Alignment file in fasta format. For homologues the first line of each sequence must be the pdb file name | |
| -allow_his_tag | Allow HIS tags in the input sequence |
| -blast_dir | Directory where ncbi blast is installed (binaries in expected in bin subdirectory) |
| -classic_mode | Preset options to run the original AMPLE clustering/truncation options (1 cluster, 3 subclustering radii, 3 sidechains) |
| -ccp4i2_xml | Path to CCP4I2 XML file - if not None indicates we are running under CCP4I2 |
| -coiled_coil | Turn on Coiled-Coil mode for solving Coiled-Coil structures |
| -devel_mode | Preset options to run in development mode - takes longer |
| -dry_run | Check if input files and supplied options are valid. |
| -early_terminate | |
| Stop the run as soon as a success has been found. | |
| -ensembles | Path to directory containing existing ensembles |
| -fasta | protein fasta file. (required) |
| -fast_protein_cluster_exe | |
| path to fast_protein_cluster executable | |
| -F | Flag for F column in the MTZ file |
| -FREE | Flag for FREE column in the MTZ file |
| -ideal_helices | Attempt to solve the structure using ideal polyalanine helices (8 helices: from 5-40 residues) |
| -helical_ensembles | |
| Attempt to solve the structure using helical ensembles (minimal set of 12 ensembles used by default) | |
| -helical_ensembles_set | |
Possible choices: full, minimal Choose the set of helical ensembles to be used: full - 64 ensembles, minimal - 12 ensembles Default: “minimal” | |
| -improve_template | |
| Path to a template to improve - NMR, homolog | |
| -make_models | run rosetta modeling, set to False to import pre-made models (required if making models locally default True) |
| -max_array_jobs | |
| Maximum number of array jobs to run | |
| -models | Path to a folder of PDB decoys, or a tarred and gzipped/bziped, or zipped collection of decoys |
| -mr_sequence | sequence file for crystal content (if different from what’s given by -fasta) |
| -mtz | The MTZ file with the reflection data. |
| -name | 4-letter identifier for job [ampl] |
| -native_pdb | Path to the crystal structure PDB for benchmarking. |
| -native_mtz | Path to the native MTZ containing FC and PHIC calculated phases for benchmarking. |
| -nmr_model_in | PDB with NMR models |
| -nmr_process | number of times to process the NMR models |
| -nmr_remodel | Remodel the NMR structures |
| -nmr_remodel_fasta | |
| The FASTA sequence to be used for remodelling the NMR ensemble if different from the default FASTA sequence | |
| -purge | Possible choices: 0, 1, 2 Delete intermediate files and failed MRBUMP results: 0 - None, 1 - Some, 2 - All possible |
| -psipred_ss2 | Psipred secondary structure prediction file |
| -quick_mode | Preset options to run quickly, but less thoroughly |
| -restart_pkl | Rerun a job using the pickled ample dictionary |
| -run_dir | Directory where the AMPLE work directory will be created [current dir] Default: “/home/docs/checkouts/readthedocs.org/user_builds/ample/checkouts/latest/docs” |
| -rvapi_document | |
| Path to an existing rvapi document (for running under jscofe) | |
| -scwrl_exe | Path to Scwrl4 executable |
| -show_gui | Pop up and display a stand-alone GUI |
| -single_model | Single structure model to be used to create ensembles |
| -sf_cif | Path to a structure factor CIF file (instead of MTZ file) |
| -SIGF | Flag for SIGF column in the MTZ file |
| -top_model_only | |
| Only process the top model in each ensemble | |
| --version | show program’s version number and exit |
| -webserver_uri | URI of the webserver directory - also indicates we are running as a webserver |
usage: ample [-h] [-submit_array [True/False]] [-submit_cluster [True/False]]
[-submit_pe_lsf SUBMIT_PE_LSF] [-submit_pe_sge SUBMIT_PE_SGE]
[-submit_max_array SUBMIT_MAX_ARRAY]
[-submit_num_array_jobs SUBMIT_NUM_ARRAY_JOBS]
[-submit_pe SUBMIT_PE] [-submit_queue SUBMIT_QUEUE]
[-submit_qtype {lsf,pbs,torque,slurm,sge,local}]
| -submit_array | Submit cluster jobs as an array |
| -submit_cluster | |
| Submit jobs to a cluster - need to set -submit_qtype flag to specify the batch queue system. | |
| -submit_pe_lsf | Cluster submission: string to set number of processors for LSF queueing system |
| -submit_pe_sge | Cluster submission: string to set number of processors for SGE queueing system |
| -submit_max_array | |
| The maximum number of jobs to run concurrently with SGE array job submission | |
| -submit_num_array_jobs | |
| The number of jobs to run concurrently with SGE array job submission | |
| -submit_pe | Cluster submission: string to set parallel environment |
| -submit_queue | The queue to submit to on the cluster. |
| -submit_qtype | Possible choices: lsf, pbs, torque, slurm, sge, local Cluster submission queue type Default: “local” |
usage: ample [-h] [-bbcontacts_file BBCONTACTS_FILE]
[-bbcontacts_format BBCONTACTS_FORMAT]
[-contact_file CONTACT_FILE] [-contact_format CONTACT_FORMAT]
[-disulfide_constraints_file DISULFIDE_CONSTRAINTS_FILE]
[-distance_to_neighbour DISTANCE_TO_NEIGHBOUR]
[-energy_function ENERGY_FUNCTION] [-native_cutoff NATIVE_CUTOFF]
[--no-contact-prediction NO_CONTACT_PREDICTION]
[-restraints_factor RESTRAINTS_FACTOR]
[-restraints_file RESTRAINTS_FILE]
[-restraints_weight RESTRAINTS_WEIGHT]
[-subselect_mode SUBSELECT_MODE]
| -bbcontacts_file | |
| Additional bbcontacts file. Requires normal contactfile | |
| -bbcontacts_format | |
| Residue contact file format. For available formats refer to the AMPLE documentation | |
| -contact_file | Residue contact file |
| -contact_format | |
| Residue contact file format. For available formats refer to the AMPLE documentation | |
| -disulfide_constraints_file | |
| Disulfide residue constraints for ab initio modelling | |
| -distance_to_neighbour | |
| Min. distance between residue pairs for contact (default=5) | |
| -energy_function | |
| Rosetta energy function for contact restraint conversion (default=FADE) | |
| -native_cutoff | Distance cutoff for reference contacts in native structure (default=8A) |
| --no-contact-prediction | |
Do not predict contacts Default: False | |
| -restraints_factor | |
| Factor (* Sequence length) determining number of contact restraints to use (default=1.0) | |
| -restraints_file | |
| Residue restraints for ab initio modelling | |
| -restraints_weight | |
| Additional energy weighting of restraints in Rosetta | |
| -subselect_mode | |
| Long-range decoy satisfaction subselection mode - one of [linear | scaled | cutoff] | |
usage: ample [-h] [-all_atom [True/False]] [-frags_3mers FRAGS_3MERS]
[-frags_9mers FRAGS_9MERS] [-make_frags [True/False]]
[-multimer_modelling MULTIMER_MODELLING]
[-nmodels number of models] [-nr nr]
[-rg_reweight radius of gyration reweight]
[-rosetta_executable ROSETTA_EXECUTABLE] [-rosetta_db ROSETTA_DB]
[-rosetta_dir ROSETTA_DIR]
[-rosetta_fragments_exe ROSETTA_FRAGMENTS_EXE]
[-rosetta_flagsfile ROSETTA_FLAGSFILE]
[-rosetta_version ROSETTA_VERSION] [-transmembrane [True/False]]
[-transmembrane_old [True/False]]
[-transmembrane_octopusfile TRANSMEMBRANE_OCTOPUSFILE]
[-transmembrane_spanfile TRANSMEMBRANE_SPANFILE]
[-transmembrane_lipofile TRANSMEMBRANE_LIPOFILE]
[-use_homs [True/False]]
| -all_atom | Do all-atom Rosetta modelling (adds “-return_full_atom true” to rosetta arguments |
| -frags_3mers | Path to file with pre-existing Rosetta 3mer fragments |
| -frags_9mers | Path to file with pre-existing Rosetta 3mer fragments |
| -make_frags | set True to generate Rosetta 3mers and 9mers locally, False to import fragments |
| -multimer_modelling | |
| Generate multimeric models. Accepted values: [‘dimer’, ‘trimer’, ‘tetramer’] | |
| -nmodels | number of models to make (default: 1000) |
| -nr | Path to the NR non-redundant sequence database |
| -rg_reweight | Set the Rosetta -rg_reweight flag to specify the radius of gyration reweight. |
| -rosetta_executable | |
| Path to ROSETTA executable for modelling | |
| -rosetta_db | Path to the Rosetta database directory |
| -rosetta_dir | The Rosetta install directory |
| -rosetta_fragments_exe | |
| Location of the Rosetta make_fragments.pl script | |
| -rosetta_flagsfile | |
| Location of file with Rosetta modelling commands | |
| -rosetta_version | |
| The version number of Rosetta | |
| -transmembrane | Do Rosetta modelling for transmembrane proteins (Ovchinnikov protocol) |
| -transmembrane_old | |
| Do Rosetta modelling for transmembrane proteins (Yarov-Yarovoy protocol) | |
| -transmembrane_octopusfile | |
| Octopus transmembrane topology predicition file | |
| -transmembrane_spanfile | |
| Span file for modelling transmembrane proteins | |
| -transmembrane_lipofile | |
| Lips4 file for modelling transmembrane proteins | |
| -use_homs | Select ROSETTA fragments from homologous models |
usage: ample [-h] [-cluster_dir CLUSTER_DIR] [-cluster_method CLUSTER_METHOD]
[-ensembler_timeout ENSEMBLER_TIMEOUT] [-gesamt_exe gesamt_exe]
[-homologs [True/False]] [-homolog_aligner homolog_aligner]
[-ensemble_max_models ENSEMBLE_MAX_MODELS]
[-mustang_exe mustang_exe] [-num_clusters NUM_CLUSTERS]
[-percent percent_truncation]
[-percent_fixed_intervals PERCENT_FIXED_INTERVALS [PERCENT_FIXED_INTERVALS ...]]
[-score_matrix SCORE_MATRIX]
[-score_matrix_file_list SCORE_MATRIX_FILE_LIST]
[-side_chain_treatments SIDE_CHAIN_TREATMENTS [SIDE_CHAIN_TREATMENTS ...]]
[-spicker_exe SPICKER_EXE]
[-subcluster_radius_thresholds SUBCLUSTER_RADIUS_THRESHOLDS [SUBCLUSTER_RADIUS_THRESHOLDS ...]]
[-subcluster_program SUBCLUSTER_PROGRAM]
[-theseus_exe Theseus exe] [-thin_clusters [True/False]]
[-truncation_method TRUNCATION_METHOD]
[-truncation_pruning TRUNCATION_PRUNING]
[-truncation_scorefile TRUNCATION_SCOREFILE]
[-truncation_scorefile_header TRUNCATION_SCOREFILE_HEADER [TRUNCATION_SCOREFILE_HEADER ...]]
| -cluster_dir | Path to directory of pre-clustered models to import |
| -cluster_method | |
| How to cluster the models for ensembling. Options: spicker|spicker_tm | |
| -ensembler_timeout | |
| Time in seconds before timing out ensembling | |
| -gesamt_exe | Path to the gesamt executable |
| -homologs | Generate ensembles from homologs models (requires -alignment_file) |
| -homolog_aligner | |
| Program to use for structural alignment of homologs (gesamt|mustang) | |
| -ensemble_max_models | |
| Maximum number of models permitted in an ensemble | |
| -mustang_exe | Path to the mustang executable |
| -num_clusters | The number of Spicker clusters of the original decoys that will be sampled [1] |
| -percent | percent interval for truncation |
| -percent_fixed_intervals | |
| list of integer percentage intervals for truncation | |
| -score_matrix | Path to score matrix for spicker |
| -score_matrix_file_list | |
| File with list of ordered model names for the score_matrix | |
| -side_chain_treatments | |
| The side chain treatments to use. Options: polyala|reliable|allatom|unmod | |
| -spicker_exe | Path to spicker executable |
| -subcluster_radius_thresholds | |
| The radii to use for subclustering the truncated ensembles | |
| -subcluster_program | |
| Program for subclustering models [gesamt] | |
| -theseus_exe | Path to theseus executable |
| -thin_clusters | Create ensembles from 10 clusters with 1 + 3A subclustering and polyAlanine sidechains |
| -truncation_method | |
| How to truncate the models for ensembling: percent | |
| -truncation_pruning | |
| Whether to remove isolated residues (single) | |
| -truncation_scorefile | |
| CSV file containing per residue scores - COLUMN ONE MUST BE RESIDUE INDEX STARTING FROM 1 | |
| -truncation_scorefile_header | |
| column headers to be used to create ensembles | |
usage: ample [-h] [-arpwarp_cycles ARPWARP_CYCLES]
[-buccaneer_cycles BUCCANEER_CYCLES] [-do_mr [True/False]]
[-domain_termini_distance DOMAIN_TERMINI_DISTANCE]
[-existing_mr_solution EXISTING_MR_SOLUTION]
[-early_terminate_SHELXE_CC EARLY_TERMINATE_SHELXE_CC]
[-early_terminate_SHELXE_ACL EARLY_TERMINATE_SHELXE_ACL]
[-molrep_only [True/False]] [-mrbump_dir MRBUMP_DIR]
[-mr_keys MR_KEYS [MR_KEYS ...]] [-mr_sg_all True/False]
[-nmasu NMASU] [-phaser_kill phaser_kill]
[-phaser_only [True/False]] [-phaser_rms phaser_rms]
[-refine_rebuild_arpwarp True/False]
[-refine_rebuild_buccaneer True/False]
[-shelx_cycles SHELX_CYCLES]
[-shelxe_exe path to shelxe executable]
[-shelxe_max_resolution SHELXE_MAX_RESOLUTION]
[-shelxe_rebuild [True/False]]
[-shelxe_rebuild_arpwarp [True/False]]
[-shelxe_rebuild_buccaneer [True/False]]
[-use_scwrl [True/False]] [-use_shelxe [True/False]]
| -arpwarp_cycles | |
| The number of ArpWarp cycles to run | |
| -buccaneer_cycles | |
| The number of Bucanner rebuilding cycles to run | |
| -do_mr | Run or skip the Molecular Replacement step |
| -domain_termini_distance | |
| distance between termini for insert domains | |
| -existing_mr_solution | |
| Existing MR solution to give to MRBUMP | |
| -early_terminate_SHELXE_CC | |
| SHELXE_CC criteria for when a job has succeeeded | |
| -early_terminate_SHELXE_ACL | |
| SHELXE_ACL criteria for when a job has succeeeded | |
| -molrep_only | Only use Molrep for Molecular Replacement step in MRBUMP |
| -mrbump_dir | Path to a directory of MRBUMP jobs (see restart_pkl) |
| -mr_keys | Additional keywords for MRBUMP - are passed through without editing |
| -mr_sg_all | Try all possible space groups in PHASER Molecular Replacement step in MRBUMP |
| -nmasu | Manually specify the number of molecules in the asymmetric unit - sets the NMASu MRBUMP flag |
| -phaser_kill | Time in minutes after which phaser will be killed (0 to leave running) |
| -phaser_only | Only use Phaser for Molecular Replacement step in MRBUMP |
| -phaser_rms | RMS value for phaser |
| -refine_rebuild_arpwarp | |
| True to use ARPWARP to rebuild the REFMAC-refined MR result. | |
| -refine_rebuild_buccaneer | |
| True to use Buccaneer to rebuild the REFMAC-refined MR result. | |
| -shelx_cycles | The number of SHELXE cycles to run when rebuilding. |
| -shelxe_exe | Path to the SHELXE executable |
| -shelxe_max_resolution | |
| Maximum permitted resolution for rebuilding with SHELXE | |
| -shelxe_rebuild | |
| Rebuild SHELXE traced pdb with buccaneer and arpwarp | |
| -shelxe_rebuild_arpwarp | |
| Rebuild SHELXE traced pdb with arpwarp | |
| -shelxe_rebuild_buccaneer | |
| Rebuild SHELXE traced pdb with buccaneer | |
| -use_scwrl | Remodel sidechains of the decoy models using Scwrl4 |
| -use_shelxe | True to use SHELXE |