> Is there an easy way in coot to identify all cis- peptide bonds in a > structure?
Extensions->Modelling->Residues with Cis Peptide Bonds... *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487673 fax: (+46) 08-327626 email: [email protected] ----- Original Message ----- From: Stephen Graham <[email protected]> Date: Wednesday, January 28, 2009 11:40 am Subject: [COOT] Flag all cis- peptide bonds To: [email protected] > Hi all, > > Is there an easy way in coot to identify all cis- peptide bonds in a > structure? In section 7.8.4 of the manual it states that "Unexpected > CIS peptide bonds show up red" in the omega analysis graph... I guess > all my ones are 'expected' (i.e. Xaa-Pro) as they are not red. I > tried opening a file then immediately saving it (as I thought mmdb > added CISPEP cards to output PDB files these days) but no joy. > > Am I missing something simple? > > Stephen > > P.S. I'm running coot 0.5.2 Northumberland (revision 1691) on > ubuntu 8.10 > > -- > Dr Stephen Graham > Nuffield Medical Fellow > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > Roosevelt Drive > Oxford OX3 7BN > United Kingdom > Phone: +44 1865 287 549 >
