On 03/06/15 00:40, Schubert, Carsten [JRDUS] wrote:
However in your case it looks as if the CRO residue may not be defined as a polymer, i.e. part of a protein chain in the monomer library you are using.
I think that you're right.
In Windows the monomer library is located in C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The aminoacids or modified aminoacids considered part of the peptide chain have all ‘peptide’ in the header, CRO does not. That is probably the reason why coot does not make any bonds.
That's right.
This would probably cause problems later on with Phenix as well. You could pull out the CRO.cif into your directory, modify it to make it a peptide and read it into coot and phenix during refinement.
Edit -> Restaints -> CRO -> [Group] -> {modify to} L-peptide [Return] -> Apply Paul.