[Chimera-users] reconstructing x-ray structure

Z. Nevin Gerek Nevin.Gerek at asu.edu
Thu Sep 27 15:33:33 PDT 2007

Hi Tom,

I want to find out coordinates between peptide and protein. In x-ray  
structures (such as: 2gzv it is a PDZ domain and peptide binds to  
alpha helix in this domain), peptide is attached into C-terminal of  
protein. At least they obtained bound structure with attaching  
peptide into C-terminal of protein. Originally, peptide binds to  
different place in the protein.
Is there anyway to find the right place of peptide using this x-ray  
structure in Chimera?
If I find positions between peptide and protein, eventually i will  
see peptide-protein interactions as in the right place.

I hope this clarifies my problem.


On Sep 27, 2007, at 3:05 PM, Thomas Goddard wrote:

> Hi Nevin,
>   Is your question about seeing a peptide in an x-ray density map?   
> Or is about contacts between peptide and protein atomic models (PDB  
> files)?
> > Is there any way to reconstruct x-ray structure data with the right
> > peptide binding information?
> I don't understand this question.  Can you provide more details.
> 	Tom

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