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haddock2mmcif

🚧 Attention 🚧

This code is under development and subject to change. Please report any bugs by opening an issue in the repository.

Encode information from a HADDOCK run into a .cif to be deposited in PDB-Dev.

Currently the follow information is encoded in the .cif

  • Models are represented as:

    1. Whole structure as rigid
    2. Interface as flexible, defined by the flcut parmameter in run.cns

  • Top4 models from each clusters within ModelGroup, ranked by their top4 HADDOCK score

  • Restraints as Dataset represented as DerivedDistanceRestraint

    1. Ambiguous, Active/Passive as ResidueFeature with probability defined by ncvpart in run.cns read from ambig.tbl
    2. Unambiguous, the ResidueFeature are read from unambig.tbl

To-be-implemented

  • HADDOCK-score

Installation

$ git clone https://github.com/haddocking/haddock2mmcif
$ cd haddock2mmcif
$ python setup.py develop
$ cd tools
$ g++ -o contact-chainID contact-chainid.cpp
$ cd ..

Usage

The input for haddock2mmcif is the folder of a run-directory, either downloaded from the web server or executed locally.

$ cd example_data
$ tar zxvf 6269-E2A-HPR.tgz
$ haddock2mmcif --output example.cif E2A-HPR/