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

Hi Nevin, I told Tom I would try to answer your question.

If I understand correctly, you have two structures (actually combined into one peptide chain in your example, 2gzv) but not a structure of their complex. You would like to see the 4-residue peptide bound to expected binding site of the PDZ domain.

Sorry, but Chimera does not predict how structures bind each other or find favorable conformations of a single peptide chain. You would first need to separate that structure into two different structures, then

(A) use some other program to predict how they bind each other. There are many "docking" programs that predict possible binding orientations given the structures of two molecules: DOCK, Autodock, Glide, etc. -- OR -- (B) if you already know or can guess how they should bind, you can open the two structures separately in Chimera and move them around into what you think is the correct position. You can freeze/unfreeze structures (so that you can move only one at a time) with the Active checkboxes in the Model Panel (Favorites... Model Panel).

Other tools that might be useful while you are doing this are - Find Clashes/Contacts http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html - Undo/Redo Move http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/undomove/ undomove.html - FindHBond http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html

The last idea I have is that if there is some other structure of a PDZ domain bound to its peptide in the expected site, you could this PDZ domain and this peptide to the respective parts of the known complex.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Sep 27, 2007, at 3:33 PM, Z. Nevin Gerek wrote:

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