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ihmwg / IHMCIF

📖 mmCIF support for hybrid/integrative models
https://pdb-dev.wwpdb.org
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Example file with gaussian objects #62

Open arose opened 6 years ago

arose commented 6 years ago

Hi, is there an example file available that includes gaussian objects, i.e. _ihm_gaussian_obj_site?

benmwebb commented 6 years ago

To the best of my knowledge, no. In the IMP world we do often represent proteins as sets of Gaussians (to more easily fit them against EM density represented as a sum of Gaussians) but we only deposit our highest resolution representation in PDB-Dev, which is a set of sphere objects.

arose commented 6 years ago

Thanks. Can IMP be used to create a ihm/mmcif cif file?

benmwebb commented 6 years ago

If your objective is just to make a syntactically correct IHM mmCIF file, the python-ihm library is the easiest way to do it - here's a worked example. An actual scientific application of it can be seen here.

But yes, IMP supports writing of mmCIF files as part of its IMP::pmi module. This takes IMP's own data structures and uses the python-ihm library to map them to PDB's data model and then write that to mmCIF. A recent study published in Nature is here. This code is probably harder to follow though unless you are familiar with IMP's own data structures.

arose commented 6 years ago

Thanks @benmwebb. I mostly would like to have an example IHM mmCIF file that includes gaussians for web-based visualization development.

brindakv commented 5 years ago

@benmwebb, would it be possible to generate an example of a low resolution structure that uses a Gaussian object representation?

arose commented 5 years ago

That would would be really great!

benmwebb commented 5 years ago

@benmwebb, would it be possible to generate an example of a low resolution structure that uses a Gaussian object representation?

Sure, but it would certainly be a fantasy - we don't have any real structures that use Gaussians. I may be able to coarsen one of our existing systems, but it'll take a while.