[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [IMP-users] extracting distance from CrossLinkingMassSpectrometryRestraint with state ambiguity



Thats right - but instead of returning the shortest distance between the two, it returns the distance corresponding to the latest state to be added. This makes crosslink violation analysis (and distance-based model filtering) pretty difficult...

Andrea


On Fri, 16 Jul 2021, 02:17 Ben Webb, <">> wrote:
On 7/2/21 6:37 AM, Andrea Graziadei wrote:
> I am modeling a multistate system in PMI using
> CrossLinkingMassSpectrometryRestraint  in imp-2.15, and trying to
> adapt imp-sampcon for the purpose.
...
> After running replica exchange, i am trying to extract distances for
> my crosslinks (in theory 2 per protein copy, one in state 0 and one in
> state 1).

If I'm understanding your setup correctly, each crosslink need only be
satisfied by one of the two states, so you would only get one distance.

        Ben
--
" target="_blank" rel="noreferrer">                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle