[Chimera-users] Minimize

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 4 08:38:35 PDT 2009

Hi Alex,
I would never recommend minimization as part of a pipeline to prepare  
structures for DelPhi calculations.  Is there some reason you expect  
these structures to be particularly bad?  The minimization is intended  
for when you have done some manual building, or mutation, or docking,  
and want to clear up some local bad contacts or highly strained  
geometries.  It is only a local minimization, and will not "refine"  
the structure if that requires crossing any energy barriers.

I don't know what the issue with "spec" and "freeze" are, but they  
worked fine when I tried them today.  There must be a selection for  
"freeze" to have any effect. "spec" only controls which models are  
minimized, so if you only have one model open at a time there is no  
reason to use it.

For preparing structures for DelPhi, you might want to look at the  
Dock Prep tool (under Tools... Structure Editing).  It has several  
structure "regularization" options such as changing selenomethionine  
to methionine, removing solvent, removing alternate locations of  
atoms, and rebuilding missing sidechains (although not backbone), as  
well as hydrogen addition.  However, don't bother with the charge  
addition since that will be irrelevant to the DelPhi calculation ---  
DelPhi looks up charges from a separate parameter file.

Actually "minimize" calls Dock Prep to fix up the structure  
beforehand.  I say just use Dock Prep directly and don't bother with  
charge addition and don't minimize, unless there is some reason to  
think the structures are particularly warped.

The main thing to worry about for an accurate DelPhi calculation is  
getting the charges and radii assigned correctly from the DelPhi  
parameter files.  You should check the DelPhi log file.  That is a  
DelPhi issue, fairly separate from Chimera.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 3, 2009, at 1:32 PM, Alex Gawronski wrote:

> Hello,
> I'm preparing proteins for Delphi analysis using Chimera's minimize  
> function (from a script). However this process is very time  
> consuming. Is using minimize necessary to get accurate results from  
> Delphi? If not, what is necessary? I've played around with the  
> "spec" and "freeze" parameters and they either seem to have no  
> affect or throw an error (which I submitted as a bug). What do you  
> suggest I do?
> Thanks,
> Alex Gawronski
> Carleton University

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