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] [–keep_min_contacts KEEP]

  • –remove - Remove Water molecules

  • –keep_min_contacts KEEP - _Remove All Water molecules with less then KEEP contacts

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 (protein only)

clashes - Detect steric clashes in groups: Severe/covalent, Apolar, Polar Donors, Polar Acceptors, Ionic Positive, Ionic Negative

  • Severe: any atom pair with at bond distance or below. Note that it can correspond to an actual covalent bond.

  • Apolar: two non interacting atoms too close

  • Polar Donors: Two hydrogen bond donors too close

  • Polar Acceptors: Two hydrogen bond acceptors too close

  • Ionic: Two charged atoms of the same charge too close