Example file with gaussian objects

[arose]

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

[benmwebb]

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]

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

[benmwebb]

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]

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

[brindakv]

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

[arose]

That would would be really great!

[benmwebb]

@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.