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

[Riccardo Pellarin <>]

Dear Andrea,
Yes! This is correct!


Sent from my iPhone

> On 2 Jan 2024, at 14:42, Andrea Graziadei via IMP-users <> wrote:
> 
> 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
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