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Hi Kendall,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Anyway, the solution for you is to run phenix.ready_set:<br>
<br>
phenix.ready_set model.pdb<br>
<br>
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).<br>
<br>
Pavel.<br>
<br>
<br>
On 9/16/09 12:55 PM, Kendall Nettles wrote:
<blockquote cite="mid:C6D6BAF2.16225%25knettles@scripps.edu" type="cite">
<title>Problem with modified cysteine CME</title>
<font face="Verdana, Helvetica, Arial"><span style="font-size: 12px;">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: <br>
<br>
refinement.pdb_interpretation.apply_cif_modification {<br>
data_mod = CME<br>
residue_selection = chain A and resid 381<br>
residue_selection = chain B and resid 381<br>
residue selection = chain B and resid 530<br>
}<br>
<br>
Still no luck. <br>
<br>
Thanks for your help, <br>
Kendall <br>
-- <br>
Kendall W. Nettles, PhD<br>
Associate Professor<br>
Department of Cancer Biology<br>
The Scripps Research Institute<br>
130 Scripps Way<br>
Jupiter Fl 33458<br>
<br>
</span></font>
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