[phenixbb] Problem with modified cysteine CME

Pavel Afonine PAfonine at lbl.gov
Wed Sep 16 13:36:42 PDT 2009

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).


On 9/16/09 12:55 PM, Kendall Nettles wrote:
> 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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> phenixbb at phenix-online.org
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