----- Forwarded message from Oliver Hucke ohucke@u.washington.edu -----

Date: Tue, 02 Sep 2003 10:03:00 -0700 From: Oliver Hucke ohucke@u.washington.edu To: Modeller Care modeller-care@salilab.org Subject: Re: model_refinement

Hi Denis,

did you compare the quality of the structure calculated with modeller with that of the template(s)? If the quality of the model is really worse something might be wrong with your alignment. Did you do the manual adjustment of the input alignment on basis of the analysis of the quality of the first models? This usually helps a lot. I do not think that it is necessary to use charmm or another external molecular mechanics package to improve the quality of your model. Modeller actually uses (an older version of) the charmm force field for the molecular mechanics part of the optimization.

Best, Oliver

Modeller Care wrote:

>------ Forwarded Message > >From: Denis Volkov D.Volkov@artcustoms.ru >X-Mailer: The Bat! (v1.52f) >Reply-To: Denis Volkov D.Volkov@artcustoms.ru >X-Priority: 3 (Normal) >Message-ID: 43123585810.20030902125313@artcustoms.ru >To: modeller modeller_usage@salilab.org >Subject: model_refinment > > >Hello everyone, >I successfully used Modeller to model unknown protein. Now I'd like >to sent my model to Protein Data Bank. So i checked my structure >using Procheck and find some problems, namely some bad contacts,etc. >In order to clean a structure i used Charmm program for energy >minimization. But after it i obtain structure with bad angles and >bond lengths. Can anybody know how to clean a structure well for >PDBank and what programs should be use for it. >Thanks in advance >Denis Volkov > >Enzyme Laboratory,IBCH RAS > > > >