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:
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
**************************************
*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
salameh.m...@mayo.edu
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