Re: [IMP-users] crosslinking with multiple copies of subunits
To: Help and discussion for users of IMP <>
Subject: Re: [IMP-users] crosslinking with multiple copies of subunits
From: Ben Webb <>
Date: Tue, 4 Oct 2016 12:55:15 -0700
On 09/27/2016 04:29 AM, Josh Bullock wrote:
I was wondering, how does IMP handle crosslinks when there are multiple
copies of the same subunit (created in IMP using the create_clone()
function) ?
Ambiguity *should* be handled automatically.
If an inter-subunit crosslink is satisfied in IMP with an
intra-crosslink, does this stop the crosslink from contributing to the
scoring ?
The restraint doesn't statically pick one interaction and freeze that;
rather (as I far as I understand it) each possible interaction is a
minimum on the restraint's energy surface, so the assignment can change
during a simulation.
Also, experimentally it is possible to clarify which crosslinks are
definitely intra-subunit (via SDS-PAGE). However there doesn't seem to
be any way to flag this on a crosslink in IMP, unless I'm missing
something ... ?
That I don't know, but Riccardo would.
Ben
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle