check_structure

Structure Checking from MDWeb

check_structure performs MDWeb structure checking set as a command line utility. It is intended to prepare a structure for molecular dynamics simulation.

It includes structure manipulation options like selecting models or chains, removing components of the system, completing side chains and backbone, and quality checking as residue quirality, amide orientation, or vdw clashes.

check_structure can be run interactively. It will prompt for any missing parameter or information, but also can be run standalone providing a list of operations.

usage: check_structure [-h] [-i INPUT_STRUCTURE_PATH] [--file_format {mmCif,pdb,cif,xml}] [--coords_only]
                       [--sequence FASTA_SEQ_PATH] [--pdb_server PDB_SERVER] [--cache_dir CACHE_DIR_PATH]
                       [--nocache] [--overwrite_cache] [--copy_input COPY_INPUT] [--modeller_key MODELLER_KEY]
                       [--res_lib RES_LIBRARY_PATH] [--data_lib DATA_LIBRARY_PATH] [-o OUTPUT_STRUCTURE_PATH]
                       [--output_format {pdb,pdbqt,pqr,cmip,cif,mmCif}] [--keep_canonical_resnames] [--rename_terms]
                       [--json JSON_OUTPUT_PATH] [-nv] [-v] [--limit ATOM_LIMIT] [--time_limit TIME_LIMIT] [--debug]
                       [--build_warnings] [--force_save] [--check_only] [--non_interactive] [--version]
                       command ...

positional arguments:

command - Command to execute (required)

command_options - Specific command options (optional)

• On a interactive session, parameters required for command execution will be prompted as necessary, but can be also introduced as command options in the command line. see Commands Help.

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Arguments for input:

-i –input INPUT_STRUCTURE_PATH - Input structure.

• Formats pdb(qt)|cif|pqr. Taken from file extension. pdbqt accepted, but read as pdb.
• Remote pdb:{pdbid}[.format] | {url}. See also –file_format for selecting download format (default: cif). For remote downloads as pdb: using pdb format, sequences are also automatically downloaded.
• Biounits/Assemblies pdb:{pdbid}.{bn}. Biounits/assemblies. Default format mmCIF.

–file_format {mmCif,cif,pdb,xml} - Format for retrieving structures (mmCif(default)|cif|pdb|xml)

–build_warnings - Show structure building warnings (may indicate PDB errors)

–coords_only - Loads structure coordinates, discards chain labels and residue ids from input

–sequence FASTA_SEQ_PATH - Input canonical sequence in FASTA format

• accepted local files, URLs, or pdb:{pdbid}. Required for PDB/PQR structures.
• Note that sequence is automatically obtained when downloading structures from wwPDB

–pdb_server PDB_SERVER - DEPRECATED. pdb: defaults to wwPDB, use direct urls ofor other servers

–cache_dir CACHE_DIR_PATH - Path for structure’s cache directory (default: ./tmpPDB)

–nocache - Do not cache downloaded structures

–overwrite_cache - Overwrite cached file if any

–copy_input DIR - Copy the downloaded structure in the indicated folder

–limit ATOM_LIMIT - Limit on number of atoms (0: no limit, default: 1000000)

–time_limit TIME_LIMIT - Set limit on the execution time (sec), (0: nolimit. default: 3600)

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Additional data input

–res_lib RES_LIBRARY_PATH - Override default residue library (AMBER prep format)

–data_lib DATA_LIBRARY_PATH - Override default data library

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Arguments for output

-o –output OUTPUT_STRUCTURE_PATH - Output structure.

• cif|pdb|pdbqt|pqr|cmip formats available (use file extension or –output_format to set format)

–output_format OUTPUT_FORMAT - Format for the Output.

• cif|pdb|pdbqt|pqr|cmip formats available (if empty file extension is used)

–keep_canonical_resnames - Revert output to canonical residue names when modified by any operation

–json JSON_OUTPUT_PATH - Store a summary of all activities on a json file

–force_save - Force saving an output file even if no modification

–rename_terms - Label N-term and C-term as NXXX and CXXX residues in output files

-nv –quiet - Reduces output, removing labels and progress info

-v –verbose - Additional progress info

–debug - Add debug information (Memory usage, timings)

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Configuration arguments

–check_only - Perform checks only, structure is not modified

–non_interactive - Do not prompt for missing parameters

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Miscelanea

–modeller_key MODELLER_KEY - User key for Modeller, required for backbone rebuild unless included in Modeller installation. Register at https://salilab.org/modeller/registration.html

-h, –help - show this help message and exit

–version - show program’s version number and exit

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