[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [modeller_usage] Sidechains Refinement and Symmetry definition
- To: Giampaolo <giovannipaolo.dimartino AT gmail.com>
- Subject: Re: [modeller_usage] Sidechains Refinement and Symmetry definition
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Mon, 28 Mar 2011 16:20:51 -0700
- Cc: modeller_usage@listsrv.ucsf.edu
On 03/22/2011 11:33 AM, Giampaolo wrote:
I'm studying an homotetramer and i want to identify new sidechain
orientations on a specific helix segment without any more changes in the
protein structure of my initial pdb. So i tried the loopmodel routine:
loopmodel wasn't really designed or benchmarked for sidechain
optimization, but what you're doing looks pretty reasonable here.
?- Is it possible to preserve the symmetry of the sidechains over all
the subunits? or...to perform a total symmetry of the models by a
post-processing step of refinement?
If you want the sidechains to be identical, it may make more sense to
optimize a single chain, then construct the other chains by symmetry
operations. You can apply a symmetry restraint, but it will compete with
the loopmodel statistical potential, of course, so Modeller may not be
able to satisfy it as well as you might want.
Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage