crosslinkingMS database with custom ambiguity groups
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
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
Dear Andrea, Yes! This is correct!
Sent from my iPhone
> On 2 Jan 2024, at 14:42, Andrea Graziadei via IMP-users imp-users@salilab.org 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 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 > _______________________________________________ > IMP-users mailing list > imp-users@salilab.org > https://salilab.org/mm/postorius/lists/imp-users.salilab.org/
participants (2)
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Andrea Graziadei -
Riccardo Pellarin