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Hi Mohd,

- if it is a regular peptide bond then they are linked automatically and this problem should never happen, otherwise there must be something not right with your input PDB file.

- check in .geo file if this particular bond is restrained;

If you send me (and not to the whole bb) the PDB file, or at its fragment containing this and a couple of adjacent residues, then I probably tell more about what the problem is.

Pavel.

PS> There is a PHENIX bulletin board:

http://www.phenix-online.org/


On 12/18/09 2:31 PM, Salameh, Mohd A., Ph.D. wrote:
[log in to unmask]" type="cite"> phenix refinement peptide bond poor geometry

Dear all,

I’m about to deposit  a structure into the protein data bank and I’m encountering a disturbing problem, I have a protein site where the peptide bond is not properly linked, the distance of C-N bond is 2.23 Angstrom, I tried to restrain that site by modifying my def file but the problem persist after refinement. I wonder if anybody can help resolving this problem. Thanks and happy holidays! Mohd

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Mohd A. Salameh, Ph.D.

Mayo Clinic Cancer Center

Griffin Cancer Research building,Rm 331

4500 San Pablo Rd

Jacksonville, FL 32224

Tel: (904) 953-0046

Fax: (904) 953-0277

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