[chimerax-users] General question about MODELLER

[Elaine Meng]

Hi Tiglath,
According to this post, Modeller already minimizes the structure.

<https://salilab.org/archives/modeller_usage/2009/msg00162.html> 

Elaine

> On Nov 19, 2020, at 4:26 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Tiglath,
> I believe that Modeller does try to give reasonable bond lengths, angles, etc. but I do not know the details.  For details you would need to read the Modeller manual and other documentation on comparative modeling:
> <https://salilab.org/modeller/documentation.html>
> 
> Minimization usually has very little effect on a structure, especially if it doesn't have any severe strains or clashes, so my personal guess on whether you need to use it is no. However, you should make these scientific decisions yourself based on your knowledge of the structure and your project.  
> 
> QMEAN is not one of the scores that Modeller gives, and I don't know anything about it, so you'd probably also want to read more about it.  E.g. web-searching gives some links
> <https://swissmodel.expasy.org/qmean/help>
> <https://pubmed.ncbi.nlm.nih.gov/17932912/>
> 
> You could always try minimizing and seeing if it makes much difference in the structure or in its QMEAN score, and if any structural changes make sense or not.  You could still choose to use the original output from Modeller instead.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Nov 19, 2020, at 3:24 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
>> 
>> Hi
>> I have a question about using MODELLER. I've built models of a protein that I'm currently studying and wanted to know if it's necessary to minimize regions of the protein that may have poor quality based on the QMEAN score. Or does MODELLER minimize these regions when building homology models?
>> Thanks
>> Tiglath 
>