On 6/5/14, 12:00 AM, Fiona Bridget Naughton wrote: > 1. I keep getting solutions in which the subunits are overlapping, > with identical subunits in exactly (or close to) the same place, leaving > empty space elsewhere in the map.
My guess would be you need to ask for more fits in this case, but Keren is the ultimate authority here.
> 2. I would like to define x-links involving the subunits with > multiple copies, but the multifit application currently doesn't support > ambiguity for cross-links. I was planning to modify > ProteomicsEMAlignmentAtomics's add_all_restraints() method to add > x-links as ConnectivityRestraints instead, but I'm not sure how/where to > introduce these changes.
You would need to check out the IMP source code, modify the C++ code, and rerun cmake and make. This will regenerate the Python bindings from the C++ code (by running SWIG). Certainly some C++ experience would be required here.
Ben