IMP-users December 2023

imp-users@salilab.org

3 participants
3 discussions

crosslinkingMS database with custom ambiguity groups
by Andrea Graziadei 02 Jan '24

02 Jan '24

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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IMP 2.20.0 release
by Ben Webb 22 Dec '23

22 Dec '23

IMP 2.20.0 is now available. This includes improved support for mmCIF files, reduced memory utilization, and preliminary support for converting RMF format directly to mmCIF. See https://integrativemodeling.org/2.20.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

1 0

IMP usage question
by yann.sterckx＠uantwerpen.be 12 Dec '23

12 Dec '23

Hi, I'm very new to IMP and have perhaps a naive question. We are working on a protein that is partially intrinsically disordered. We have a conformational ensemble that nicely fits to SAXS data set, but our aim is to include data from other methods to refine the ensemble. We have CD spectroscopy data and CCS from ion mobility MS. We were wondering whether IMP is suited to calculate the conformational ensemble using all three data sources (SAXS, CD spectroscopy, CCS by ion mobility MS) as input restraints? Clearly, IMP can handle the SAXS, but handling of CD and CCS was less clear to us. Thank you and best wishes, Yann

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IMP-users December 2023