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Fwd: Re: model_refinement



----- Forwarded message from Oliver Hucke <> -----

Date: Tue, 02 Sep 2003 10:03:00 -0700
From: Oliver Hucke <>
To: Modeller Care <>
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 <>
>X-Mailer: The Bat! (v1.52f)
>Reply-To: Denis Volkov <>
>X-Priority: 3 (Normal)
>Message-ID: <>
>To: modeller <>
>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
> 
>
> 
>

-- 
­
____________________________________________________________

Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific Ave 
Seattle, WA 98195
T:(206)685-7046
_______________________________




----- End forwarded message -----