Protein Superimposition?

Victor Jongeneel vjongene at eliot.unil.ch
Fri Jun 2 06:50:40 EST 1995


In article <D95qDK.Hvy at cnn.nas.nasa.gov>
Wilson S. Ross <bross at splatter.nas.nasa.gov> wrote:
> |> :    After a ProMod homology modeling session [exapsy web site], I need
> |> : to generate superimpositions of the alpha carbons of the 3D structures of
> |> : the theoretical model and the pdb protein used for modelling. 
> 
> There might be something in http://www.amber.ucsf.edu/amber/0Net/list.html
> under "protein.structure" or "programs.anal" or, in "programs," the
> MODELLER writeup looks promising:
> 
>   ... the user provides an alignment of a sequence 
>   to be modeled with known related structures and MODELLER
>   will automatically calculate a full-atom model.
> 
> Bill Ross
> 

In fact, ProMod supplies the model in the same coordinate space as the 
"reference" protein used for modelling, so you should be able to fetch it from 
PDB and superimpose it onto the model without further processing.  
Alternatively, you can do a MATCH using the "expert mode" of Swiss-Model.

Good luck!

Victor Jongeneel
-- 
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|C. Victor Jongeneel, PhD, Associate Member     |
|Ludwig Institute for Cancer Research           |
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|Tel: +41-21-692-5994   FAX: +41-21-653-4474    |
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