[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] ->
Apply
Paul.
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