[phenixbb] geometry of disulfide and NAG

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Jan 22 10:22:56 PST 2009

Hi Li-Zhi,

>    Nigel, as you mentioned, the monomer library only define N2, C7, O7
> and C8 in the same plane. But just like Ca, C, O, N, Ca' in peptide bond
> need to be in the same plane, all these five atoms (C8, C7, O, N and C2)
> should be in the same plane. May I give a temporary name for NAG and
> provide corresponding cif file in the refinement? 

You can copy the NAG.cif file, make modifications, and add it to the
phenix.refine command line. The modified file will override the standard
file from the mon_lib directory.
I.e. you don't have to change the residue name.
But you can change the file name for clarity if you like, e.g. to


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