Hi Kendall,

the original Monomer Library contains lots of useless for refinement entries: for example, those that do not contain energy types, etc. At some point Ralf went ahead and cleaned the copy of Monomer Library that is used in PHENIX.

So, if you see something in the original CCP4 MonLib and at the same time it is not present in PHENIX copy of MonLib, that most likely means that there was something not right with the CIF file and it was removed.

Anyway, the solution for you is to run phenix.ready_set:

phenix.ready_set model.pdb

The above command will create the CIF file that you can use in refinement. It will also add H atoms to your model (xxx.updated.pdb file).

Pavel.


On 9/16/09 12:55 PM, Kendall Nettles wrote:
Problem with modified cysteine CME 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
--
Kendall W. Nettles, PhD
Associate Professor
Department of Cancer Biology
The Scripps Research Institute
130 Scripps Way
Jupiter Fl 33458

 

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