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.

Nevin

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