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HADDOCK Scriptorium - Producing restraints for gapped structures

Some protein structures are not determined at sufficient resolution to discern all the residues in the density map. Alternatively, very flexible regions of a peptide chain cannot be determined trivially by x-ray crystallography. Finally, structures such as those of antibody molecules are composed of several chains that must keep a particular structure throughout the computational simulation in order to have a biological meaning.

The script here deposited identifies gaps in structures and produces suitable distance constraints that prevent unnatural deformations of the peptide chain(s). The gaps can be of two types, although these are merely informative, as they are treated in the same manner:

  • Sequence Gaps: whenever there is a break in the residue numbering in the PDB file, eg. 1,2,5,6,...
  • Distance Gaps: whenever the alpha carbons of two adjacent residues are located further than a certain distance threshold in Ångstrom (default, 4Å).

The script is written in Python and requires no additional dependencies. Use it by simply calling it with the structure you wish to be checked as the first argument (structure.pdb in the following example):

python gap_check.py structure.pdb
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Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
"The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858) and the EOSC-hub (project# 777536) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid."
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.


The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858