Handling multiple protein chains

[amiel-ab]

Hi,

Thanks for sharing your tool,

In the input_dynamic.txt it is mentionned that we should refer to a specific active region but how are we able to specify the residues if there are multiple protein chains ?

Amiel

[abrownless1]

Hi Amiel,

Thanks for pointing this out! I have a few suggestions immediately that I hope will be useful, and in the meantime I am working on making the solutions to this more robust.

The active region does use MDAnalysis selection language, so you should be able to specify a single region by adding the 'segid' or 'chainID' keywords. So for example if you are calling the python layer directly:

initialize_network(structure_directory, topology_file=None, trajectory_file=None, network_type='water-protein', include_hydrogens=False, custom_selection=None, active_region_reference='resid 180 and chainID A', ...):

It may be the case that this is currently only possible through directly calling the python layer rather than through the input files, so I will make sure the input files are able to work the same way and provide an update later.

I do also recognize that this chain ID information can often be lost when converting from a starting crystal structure to a structure used to run MD, in which case the added 'chainID selection' may not be useful. In this case, it is probably best practice currently to save a pdb and trajectory which is a subset of your whole structure (perhaps one monomer+waters or just excluding duplicated residues from the second monomer) to avoid these issues for the time being. Working on a more robust solution for this now, but that would be my immediate suggestion to try.