Dear all,
I have a set of MS/XL restraints which I'd like to use to predict the structure of a putative homodimeric protein. Some of the XL are expected to happen within the same chain, others between the two distinct chains of the homodimer. The way I tackled the ambiguity issue so far is to explicitly generate all the possible XL/chain combinations and use this expanded list as an input for an adapted version of the human complement modeling script ( https://salilab.org/Complement) using IMP v2.9. Is there a better way to deal with ambiguity in IMP? I also found the AmbiguousCompositeRestraint https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints_1_1proteomics_1_1AmbiguousCompositeRestraint.html class, but didn't yet manage to find an example script using it. I'd be grateful for any suggestions you could provide me in this respect.
Thanks so much and all the best, Francesco