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molstar / pdbe-molstar

Molstar PDBe implementation
Apache License 2.0
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loading multiple structures loses non-covalent interaction rendering. Can it be maintained? #71

Closed ljmartin closed 2 years ago

ljmartin commented 2 years ago

Hi PDBe-Molstar, Thanks for a great package. I'd like to load a protein structure (PDB), then separately a ligand structure (SDF). I'd like also to visualize the non-covalent interactions, as would be done with ligandView or by clicking on the ligand in a full single structure.

However, when loading the structures separately, the non-covalent interactions aren't visualized. Is there any way to maintain these?

Compare, for example, the ligand view of retinoic acid in 1CBS with the two loaded separately. Example ligand interactions are here - basically hydrogen bonding between the carboxylic acid and the tyrosine and arginine is of interest.

Doing the same in pdbe-molstar doesn't show the hydrogen bonding interactions, presumably because the molecules are considered separate, and not just non-bonded (see below for example).

Thanks

Example HTML follows. Note that, because I'm including the raw PDB and SDF data as plaintext blobs, it's a bit long. It's also worth noting that, when doing this, CPU usage appears pinned to ~100%.

here's a plunker

mandarsd commented 2 years ago

Hi, You are right about why the interactions are not shown. Unfortunately PDBe implementation has no support for such functionality. You'll have to write your own Mol* plugin to accomplish it. The discussion here - https://github.com/molstar/molstar/issues/578 might be a good reference for you.

ljmartin commented 2 years ago

Thanks a lot @mandarsd for the molstar link - that will work.