So I guess the answer is 'yes, I was missing something simple'. That's perfect.
Many thanks On 28/01/2009, Bernhard Lohkamp <[email protected]> wrote: > > > 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 > > > -- 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
