commands Help¶
Preset commands¶
- commands - Help on available commands (this file)
- command -h - Specific help on command
- command_list - Run tests from conf file or inline string
- checkall - Perform all checks without fixes
- load - Stores structure on local cache and provides basic statistics
System Configuration Commands¶
Commands to manipulate structure composition.
sequences [–output_fasta FASTA] - Print canonical and structure sequences in FASTA format
- –output_fasta Write sequences found to an external FASTA file
models [–select model_num(s)] [–superimpose] [–save_split]- Detect/Select Models
- Accept List of Models (comma separated) or Model number range
- –superimpose Superimposes currently selected models
- –save_split Split models as separated output files.
- –build_complex Builds an actual complex from Biounits stored as collection of models
chains [–select chain_ids | molecule_type] [–rename (auto|new label)] [–renumber (auto | [A:]ini0[-fin0]=[B:]ini1)] [–rem_inscodes] - Detect/Select/Reorganize Chains
- –select Select chains ids or chain types (PROTEIN|NA|DNA|RNA) to keep
- –rename Allow to fix unlabelled chains
- –renumber Allow to reorganize residues and chains by moving or renumbering fragments
- –rem_inscodes remove insertion codes when renumbering chains
- –rebuild rebuild chain and residue ids from backbone connectivity
inscodes - _Detects residues with insertion codes.
- –renumber Fixes insertion codes by renumering chain residues
altloc [–select occupancy| alt_id | list of res_id:alt_id] - Detect/Select Alternative Locations
metals [–remove All | None | Met_ids_list | Residue_list] - Detect/Remove Metals
ligands [–remove All | None | Res_type_list | Residue_list] - Detect/Remove Ligands
getss [–mark All | None | Residue_list] - Detect SS Bonds
- –mark - Replace relevant CYS by CYX to mark SS Bond (HG atom removed if present)
water [–remove Yes|No] - Remove Water molecules
rem_hydrogen [–remove Yes|No] - Remove Hydrogen atoms from structure
mutateside [–mut mutation_list|file:mutations_file] [–no_check_clashes] [–rebuild] - Mutate side chain with minimal atom replacement
- Allows multiple mutations (comma separated).
- mutation_list as file: accepts list of mutations in a external file
- Check generated clashes except –no_check_clashes set.
- –rebuild optimize side chains using Modeller (experimental).
add_hydrogen [–add_mode auto | pH | list | interactive | interactive_his] [–no_fix_side] [–keep_h] [–add_charges FF] - Add Hydrogen Atoms to the strucure
- –add_mode
- Auto - std changes at pH 7.0. His->Hie. pH: set pH value
- list - Explicit list as [*:]HisXXHid
- Interactive[_his]: Prompts for all selectable residues
- Fixes missing side chain atoms unless –no_fix_side is set.
- Existing hydrogen atoms are removed before adding new ones unless –keep_h is set.
- –add_charges FF adds partial charges (from RES_LIBRARY) and atom types from FF forcefield (Accepted: ATD, CMIP).
- Output format taken from file extension (Accepted: pdb, pdbqt, pqr) or –output_format.
- Residue names are modified according to ionization state (e.g. HIS-> HIE, HID, HIP). Use –keep_canonical_resnames to avoid this behaviour
Fix Structure Errors¶
Commands to detect and fix possible structure errors.
Amide [–fix All|None|Auto|Residue List] [–no_recheck] - Detect/Fix Amide atoms Assignment
- Auto option searches for the combinations of fixes that offer less contacts.
- Amide contacts are rechecked unless –no_recheck That can lead to infinite loops if done non-interactively.
chiral [–fix All|None|Residue List] [–no_check_clashes] - Detect/Fix Improper side chain chirality
- Checks for generated clashes unless –no_check_clashes set
fixside [–fix All |None|Residue List] [–no_check_clashes] - Complete side chains (heavy atoms, protein only)
- Checks generated clashes unless –no_check_clashes set
- –rebuild Rebuild complete side chain using Modeller
backbone [–fix_atoms All|None|Residue List] [–fix_chain All|None|Break list] [–add_caps All|None|Break list] [–extra_gap] [–no_recheck] [–no_check_clashes] - Analyze main chain missing atoms and fragments (protein only)
- –fix_atoms Add missing O, OXT backbone atoms.
- –fix_chain Missing fragments filled using comparative modelling (Modeller License needed)
- –add_caps Add ACE and NME residues as necessary, preserving existing atoms
- –extra_gap (Experimental) Recovers additional residues from model structure at either side of the break, helps to fix loop connections.
- Backbone is rechecked on each op unless –no_recheck is set. Use on non-interactive.
- Generated clashes are checked unless –no_check_clashes
Structure Warnings¶
Additional checks on structure quality. No fix available.
cistransbck - Analyzes cis-trans dihedrals on backbone atoms
clashes - Detect steric clashes in groups: Severe, Apolar, Polar Donors, Polar Acceptors, Ionic Positive, Ionic Negative