This document is for OpenStructure version 2.4, the latest version is 2.7 !

Molecular Checker (Molck)

Where can I find the Molck executable?

The Molck executable can be found at <YOUR-OST-STAGE-DIR>/bin

Basic Usage

To check one PDB file (struc1.pdb) with Molck, use the following command:

molck --complib <PATH TO COMPOUND LIB> struc1.pdb

The checked and cleaned file will be saved by default ad struc1-molcked.pdb.

Similarly it is possible to check a list of PDB files:

molck --complib <PATH TO COMPOUND LIB> struc1.pdb struc2.pdb struc3.pdb

All Options

The molck executable supports several other command line options, please find them following:

Usage: molck [options] file1.pdb [file2.pdb [...]]
  --complib=path       Location of the compound library file. If not provided,
                       the following locations are searched in this order:
                       1. Working directory,
                       2. OpenStructure standard library location (if the
                          executable is part of a standard OpenStructure
  --rm=<a>,<b>         Remove atoms and residues matching some criteria:
                       - zeroocc - Remove atoms with zero occupancy
                       - hyd - Remove hydrogen atoms
                       - oxt - Remove terminal oxygens
                       - nonstd - Remove all residues not one of the
                                  20 standard amino acids
                       - unk - Remove unknown atoms not following
                               the nomenclature
                       Default: hyd
  --fix-ele            Clean up element column
  --stdout             Write cleaned file(s) to stdout
  --out=filename       Write cleaned file(s) to disk. % characters in the
                       filename are replaced with the basename of the input
                       file without extension. Default: %-molcked.pdb
  --color=auto|on|off  Whether output should be colored. Delault: auto
  --map-nonstd         Maps modified residues back to the parent amino acid,
                       for example: MSE -> MET, SEP -> SER.

Molck Python API

Within OST, one can also call the Molck() function directly on entities to get the same effect as with the binary.


Enter search terms or a module, class or function name.


Documentation is available for the following OpenStructure versions:

dev / 2.7 / 2.6 / 2.5 / (Currently viewing 2.4) / 2.3.1 / 2.3 / 2.2 / 2.1 / 2.0 / 1.9 / 1.8 / 1.7.1 / 1.7 / 1.6 / 1.5 / 1.4 / 1.3 / 1.2 / 1.11 / 1.10 / 1.1

This documentation is still under heavy development!
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.