GetContacts

Interactive flareplot residue-contact visualization of a trajectory

The following steps will generate contacts from a simulation trajectory and convert them to a json file that can be uploaded and analyzed at gpcrviz.github.io/flareplot.

Assume you have a simulation represented with a topology file, top.pdb, and trajectory file, trj.dcd. We first generate a contact list (contacts.tsv) and then generate the time-flare (flareplot.json) with the commands:

    get_dynamic_contacts.py --topology top.pdb --trajectory trj.dcd --itypes hb --output contacts.tsv
    get_contact_flare.py --input contacts.tsv --output flareplot.json
  

Finally, go to gpcrviz.github.io/flareplot/?p=create and upload the flareplot.json file.

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Filtering interactions

If you are interested in only a subset of interactions there's two ways of getting these. The first is to use the --sele and --sele2 arguments when computing contacts. If, for example, you're only interested in interactions between residues 18-19 and 81-82 run:

    get_dynamic_contacts.py --topology top.pdb \
                            --trajectory trj.dcd \
                            --itypes hb \
                            --sele "resid 18 to 19" \
                            --sele2 "resid 81 to 82" \
                            --output contacts.tsv
    get_contact_flare.py --input contacts.tsv --output flareplot.json
  

Alternatively, you can generate all contacts and use a residue label file (see definition here) to decorate the flareplot with colors and edge-bundling as well as filtering away undesired residues:

    get_dynamic_contacts.py --topology top.pdb --trajectory trj.dcd --itypes hb --output contacts.tsv
    cat reslabels.tsv
      A:CYS:18  CYS18  red
      A:HIS:19  HIS19  red
      A:ALA:81  ALA81  blue
      A:ILE:82  ILE82  blue
    get_contact_flare.py --input contacts.tsv --flarelabels reslabels.tsv --output flareplot.json
  

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