[phenixbb] Changing an amino acid to an unusual amino acid

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Wed Jun 3 10:28:02 PDT 2015

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] -> 


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