[Chimera-users] average structure of superimposed models

[sette at uniroma2.it]

And if your models have the same sequence you should try to use suppose

http://structbio.vanderbilt.edu/~jsmith/suppose/

bye
Marco



Def. Quota "Elaine Meng" <meng at cgl.ucsf.edu>:

> Hi Sum,
> Sorry, Chimera does not calculate average structures.
>
> According to the publication describing the Superpose web server, it  
> can generate an average backbone, but only if all the structures  
> have the same atoms (e.g. different conformations of the same  
> protein).
>
> Superpose server:
> <http://wishart.biology.ualberta.ca/SuperPose/>
> Publication describing it:
> <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441615/>
>
> A long time ago I used a program named MPOSE to make a consensus CA  
> "template" from a set of related structures, but I don't have that  
> program anymore and don't know if it is available.  It is described  
> in this paper:
>
> T.D. Wu, S.C. Schmidler, T. Hastie, and D.L. Brutlag, "Modeling and  
> Superposition of Multiple Protein Structures Using Affine  
> Transformations: Analysis of the Globins" Pac Symp Biocomput 3:509  
> (1998).
> <http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p509.html>
>
> One should be aware that an average or consensus structure can be  
> very distorted and energetically unreasonable, depending on how it  
> was computed.  There are many issues such as whether to average  
> coordinates for each atom or  internal coordinates such as angles.
>
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Dec 23, 2010, at 12:00 AM, Sumitro Harjanto wrote:
>
>> Hi Elaine,
>> I have superimposed a few highly similar models of the same protein  
>> family. They are >80% identical in sequences. I would like to find  
>> an ‘average’ structure as a  representative model of these  
>> proteins. Can I achieve this through Chimera..?
>> Cheers,
>> Sum
>
>
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>
>



Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette at uniroma2.it
e-mail:        m77it at yahoo.it
Tel.:          +39-0672594424
Fax:           +39-0672594328


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