Reply-to: Help and discussion for users of IMP <IMP-USERS@LISTSRV.UCSF.EDU>
(I assume you attached a Python script here, which will upset UCSF's email system.)
> The low ~5-angstrom resolution of the substrate in the cryo map suggests that is not completely folded, but the program is modeling it in its fully folded state and aligns almost completely with the PDB I referenced it to in the topology file. I am wondering if I could modify the topology file to allow for a lesser degree of folding and more flexibility in this substrate?
Right, if you reference a PDB file in your topology and ask for it to be rigid, IMP isn't going to change its conformation (other than rigidly rotating and translating the entire subunit). If you think there's some sort of hinge motion going on, you could read in each domain separately and make each its own rigid body (usually grouping these into a super rigid body would give better sampling). If you think there's a low confidence region of the PDB, just remove it (e.g. delete the corresponding ATOM lines from the file) and IMP will use flexible beads in that region. I wouldn't recommend too much flexibility though because with only 20 crosslinks your system is rather under constrained.
> However, subsequent identical runs have given clash, unstable scores, lack of crosslink distance optimization, and drastically different positions of the substrate (CCT is fixed).
Sounds like inadequate sampling to me, probably as a result of the sparse data. IMP.sampcon should give the best idea of the precision you can claim for your model.
Ben
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle
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From: Help and discussion for users of IMP <IMP-USERS@LISTSRV.UCSF.EDU> on behalf of Cecilia Sanders <>
Sent: Monday, September 21, 2026 9:59 AM
To: IMP-USERS@LISTSRV.UCSF.EDU
Subject: [IMP-users] Help with validating IMP model, and also a topology file question
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