[phenixbb] Problem with modified cysteine CME

Kendall Nettles knettles at scripps.edu
Wed Sep 16 12:55:30 PDT 2009

I am trying to refine a structure with modified cysteines, which refmac recognized as CME just fine. Phenix has CME listed in the mon_lib_list.cif, but the CME.cif file was not in the mon_lib/c/ directory. I  added it to the phenix mon_lib/c directory but phenix.refine still complained. I next added the CME.cif file ( copied from ccp4) as a command line input to phenix.refine, and added this to my parameters file:

refinement.pdb_interpretation.apply_cif_modification {
  data_mod = CME
  residue_selection = chain A and resid 381
  residue_selection = chain B and resid 381
  residue selection = chain B and resid 530

Still no luck.

Thanks for your help,
Kendall W. Nettles, PhD
Associate Professor
Department of Cancer Biology
The Scripps Research Institute
130 Scripps Way
Jupiter Fl 33458

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