SIMBAD: Sequence Independent Molecular replacement Based on Available Database
usage: simbad-full [-h] [-ccp4_jobid CCP4_JOBID] [-chunk_size CHUNK_SIZE]
[-debug_lvl {info,debug,warning,error,critical}]
[-name NAME] [-output_pdb OUTPUT_PDB]
[-output_mtz OUTPUT_MTZ] [-run_dir RUN_DIR]
[-results_to_display RESULTS_TO_DISPLAY] [-tmp_dir TMP_DIR]
[-work_dir WORK_DIR] [-webserver_uri WEBSERVER_URI]
[--cleanup] [--display_gui] [--process_all] [--skip_mr]
[--version] [-nproc NPROC] [-submit_qtype {local,sge}]
[-submit_queue SUBMIT_QUEUE] [-cont_db CONT_DB]
[-max_contaminant_results MAX_CONTAMINANT_RESULTS]
[-organism ORGANISM] [-morda_db MORDA_DB]
[-max_morda_results MAX_MORDA_RESULTS] [-latt_db LATT_DB]
[-max_lattice_results MAX_LATTICE_RESULTS]
[-max_penalty_score MAX_PENALTY_SCORE]
[-amore_exe AMORE_EXE] [-npic NPIC]
[-min_solvent_content MIN_SOLVENT_CONTENT] [-pklim PKLIM]
[-rotastep ROTASTEP] [-rot_program {amore,phaser}]
[-shres SHRES] [-sga {enant,all}]
[-mr_program {molrep,phaser}] [-refine_program {refmac5}]
[-refine_cycles REFINE_CYCLES] [-pdb_db PDB_DB]
[-phaser_kill PHASER_KILL] [-F F] [-SIGF SIGF] [-FREE FREE]
[-DANO DANO] [-SIGDANO SIGDANO]
mtz
| mtz | The path to the input mtz file |
| -ccp4_jobid | Set the CCP4 job id - only needed when running from the CCP4 GUI |
| -chunk_size | Max jobs to submit at any given time Default: 0 |
| -debug_lvl | Possible choices: info, debug, warning, error, critical The console verbosity level Default: “info” |
| -name | The identifier for each job [simbad] Default: “simbad” |
| -output_pdb | Path to the output PDB for the best result |
| -output_mtz | Path to the output MTZ for the best result |
| -run_dir | Directory where the SIMBAD work directory will be created Default: “.” |
| -results_to_display | |
The number of results to display in the GUI Default: 10 | |
| -tmp_dir | Directory in which to put temporary files from SIMBAD |
| -work_dir | Path to the directory where SIMBAD will run (will be created if it doesn’t exist) |
| -webserver_uri | URI of the webserver directory - also indicates we are running as a webserver |
| --cleanup | Delete all data not reported by the GUI Default: False |
| --display_gui | Show the SIMBAD GUI Default: False |
| --process_all | Trial all search models Default: False |
| --skip_mr | Skip Molecular replacement step Default: False |
| --version | Print the SIMBAD version |
| -nproc | Number of processors. 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 |
| -submit_qtype | Possible choices: local, sge The job submission queue type Default: “local” |
| -submit_queue | The queue to submit to on the cluster. |
| -cont_db | Path to local copy of the contaminant database Default: /empty/path/share/simbad/static/contaminants |
| -max_contaminant_results | |
The maximum number of contaminant results to return Default: 20 | |
| -organism | Select a specific host organism using the UniProt mnemonic organismidentification code |
| -morda_db | Path to local copy of the MoRDa database |
| -max_morda_results | |
The maximum number of contaminant results to return Default: 200 | |
| -latt_db | Path to local copy of the lattice database Default: /empty/path/share/simbad/static/niggli_database.npz |
| -max_lattice_results | |
The maximum number of lattice results to return Default: 20 | |
| -max_penalty_score | |
The maximum lattice penalty score allowed Default: 7 | |
| -amore_exe | Path to amore executable Default: “/empty/path/libexec/amore-rs” |
| -npic | Number of peaks to output from the translation function map for each orientation Default: 50 |
| -min_solvent_content | |
The minimum solvent content present in the unit cell with the input model Default: 30 | |
| -pklim | Peak limit, output all peaks above <pklim> Default: 0.5 |
| -rotastep | Size of rotation step Default: 1.0 |
| -rot_program | Possible choices: amore, phaser Program with which to perform rotation search Default: “amore” |
| -shres | Spherical harmonic resolution Default: 3.0 |
| -sga, --sgalternative | |
Possible choices: enant, all Check alternative space groups | |
| -mr_program | Possible choices: molrep, phaser Path to the MR program to use. Default: “molrep” |
| -refine_program | |
Possible choices: refmac5 Path to the refinement program to use. Default: “refmac5” | |
| -refine_cycles | The number of refinement cycles to run [default: 30] |
| -pdb_db | Path to local copy of the PDB, this is needed if there is no internet access |
| -phaser_kill | Time in minutes after which phaser will be killed (0 to leave running) Default: 30 |
| -F | Flag for F column in the MTZ |
| -SIGF | Flag for SIGF column in the MTZ |
| -FREE | Flag for FREE column in the MTZ |
| -DANO | Flag for the DANO column in the MTZ |
| -SIGDANO | Flag for the SIGDANO column in the MTZ |