To: Help and discussion for users of IMP <>, Keren Lasker <>
Subject: Re: [IMP-users] problems when using multifit
From: Ben Webb <>
Date: Thu, 05 Jun 2014 12:02:30 -0700
Reply-to: Help and discussion for users of IMP <>
On 6/5/14, 12:00 AM, Fiona Bridget Naughton wrote:
1. I keep getting solutions in which the subunits are overlapping,
with identical subunits in exactly (or close to) the same place, leaving
empty space elsewhere in the map.
My guess would be you need to ask for more fits in this case, but Keren
is the ultimate authority here.
2. I would like to define x-links involving the subunits with
multiple copies, but the multifit application currently doesn't support
ambiguity for cross-links. I was planning to modify
ProteomicsEMAlignmentAtomics's add_all_restraints() method to add
x-links as ConnectivityRestraints instead, but I'm not sure how/where to
introduce these changes.
You would need to check out the IMP source code, modify the C++ code,
and rerun cmake and make. This will regenerate the Python bindings from
the C++ code (by running SWIG). Certainly some C++ experience would be
required here.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle