[modeller_usage] how to constrain automodel to remain closer to the template

To: modeller_usage@listsrv.ucsf.edu

Subject: [modeller_usage] how to constrain automodel to remain closer to the template

From: "Jake Gunn-Glanville" <dr.jake AT gmail.com>

Date: Fri, 19 Sep 2008 08:06:09 -0700

I have been modeling a protein with a template I am quite confident in, and a loop that I would like to use a separate template for. When I generate 200 models, they all seem to show a great deal of structural diversity. Curious, I developed 20 models of a solved structure against itself, and found a bit of diversity in all of these resulting models as well. Is there a good way to constrain automodel so that it diverses less from the templates when thre are no obvious residue clashes forcing it to make adjustments?

--
Jacob Glanville
Informatics Associate
Rinat Biotherapeutics & Bioinnovation Center; Pfizer Inc.
415 497 3552