Hello,
I see now this is addressed by adding a "UniqueID" column to the crosslink csv that is read by IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter, which if I understand correctly sets up ambiguous restraints between all crosslinks with the same UniqueID when passed onto IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.
Andrea
On Wed, 27 Dec 2023 at 12:45, Andrea Graziadei graziadei.a@gmail.com wrote: > > Hello, > > I have a crosslinking MS dataset beteween 3 proteins, A, B and C. B > and C are different proteins that share 30% identical sequence in > chunks. Thus, I have crosslinks from A to B that are unambiguous, and > others that may be from A to B or from A to C, as they go to a shared > sequence. For homodimers, IMP handles this automatically. > > How do I construct the crosslink database to specify ambiguity at the > restraint level? is there a column I can add to the crosslink csv that > has a a selection e.g. residue 5 of protein A is crosslinked to > residue 17 of protein B or residue 29 of protein C? > > Many thanks, > > Andrea