On 12/5/18 7:06 AM, Andrea Graziadei wrote: > It is unclear to me what each of the fields means in the "proteins" section
The first three fields, from left to right, are: - protein name - first residue index (usually 1) - last residue index The remaining fields are used to specify file names of the protein, surface, and reference, but I think are generally unused.
> and the meaning of the first field in the "residue-xlink" section.
If set to 1, the interaction is also used as a filter in the construction of the junction tree, which is probably what you want.
> I assume "30" is the maximum distacnce from experimental data? > What potential is used for these restraints?
As far as I can tell from the code, the distance isn't used directly, but crosslink data just ensures that the given subunits are found in proximity via a connectivity restraint.
BTW, MultiFit hasn't been under active development for some time. For any more complex integrative modeling there are a number of more recent solutions in IMP - the PMI module is a good place to start.
Ben