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