I'd like to thank you all, the problem is resolved. Apparently, in the pdb file, the carbonyl oxygen should be listed right after the carbonyl carbon not after the side chain atoms! M
********************************** 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 [email protected] ********************************** ________________________________ From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Salameh, Mohd A., Ph.D. Sent: Friday, December 18, 2009 5:32 PM To: [email protected] Subject: [ccp4bb] 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 ********************************** 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 [email protected] **********************************
