[Chimera-users] Constrainted fitting

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 23 09:47:11 PDT 2013


Hi Christoph,
It depends on whether you believe your protein forms the dimer in the same way as the homolog with known dimeric structure.  It sounds like a reasonable hypothesis, at least, and I believe other people have done similar things.  You could try it and see if the shape of your modeled dimer appears to be compatible with the shape of the density.  If the fit is very poor, then you might consider alternative hypotheses.
Best
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 23, 2013, at 12:01 AM, Christoph Wigge wrote:

> Hi Elaine,
> Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution?
> Bests 
> Christoph 




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