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rcsb / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry
GNU Lesser General Public License v2.1
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Multi Model X-RAY Structures (2Q4M) #90

Open lafita opened 8 years ago

lafita commented 8 years ago

If a structure is X-RAY and multi-model, and not a biological assembly, all the models are considered for symmetry, so identity symmetry axes are returned (and a lot of levels). A test case is 2Q4M.

This bug was introduced when providing support for biological assemblies, so a check should be made that the structure is a BA before using all models.

josemduarte commented 8 years ago

so a check should be made that the structure is a BA before using all models.

Or use the multi-chain bioassemblies

lafita commented 8 years ago

I agree Jose, but we have the problem that we cannot display them in Jmol. Definitely it will have to be changed when Jmol allows passing structures as MMCIF.

josemduarte commented 8 years ago

Oh jmol... forgot that :) Passing them as mmCIF to jmol should be quite easy now that we have mmCIF writers, shouldn't it?

lafita commented 8 years ago

Yes! Everything is ready from biojava side, but the latest Maven version of Jmol is a very old one, with buggy support for mmCIF. We either request for an update of their Maven version (which I think we already did), or we move away from Jmol.

josemduarte commented 8 years ago

Of course the maven problem... forgot that too! sorry about that.

Yes getting the latest jmol should be a priority... It even has a MMTF reader... perhaps we could even try to pass structures as MMTF.