I'm trying to use the multifit application on a system with multiple copies of some subunits, but I'm having a couple of problems:
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. If I reduce the max penetration allowed/increase the penetration coefficient, I get no solutions. Are there any other parameters I should try changing? (It's not at all clear what many of the parameters in the alignment.param file are for, so I don't know which others might be relevant). Or anything else I could do?
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. Editing the .h/.cpp files in my folder has no effect, and I get errors when changing multifit's __init__.py due to various functions/classes not being defined (they're imported to the .h/.cpp file instead of defined in __init__). I know little about python/c++ beyond syntax, so I may be going about this the wrong way. Do I need to be doing something involving swig? Or something else?
Any help will be greatly appreciated!