[IMP-users] Re: crosslinkingMS database with custom ambiguity groups

[Andrea Graziadei <>]

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 <> 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