Stephen Graham wrote:
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.
Edit->Preferences->Geometry->CisPeptides->Yes
It seems that Coot does not add CISPEP cards for new cispeps, it only
strips them when the are in fact trans.
(i.e. Coot checks all cispep objects for begin trans, not all residues
for being cis).
Paul.
