[phenixbb] cif mods, .def, .cifs...

Bryan W. Lepore bryan.lepore at umassmed.edu
Tue Jun 17 18:58:23 PDT 2008

using phenix 1.3b rc6 cctbx_tag 2007_11_18_2203

have a few questions :

can .cif modifications such as

refinement.pdb_interpretation.apply_cif_modification {
   data_mod = 5pho
   residue_selection = resname GUA and name O5T

(from http://www.phenix-online.org/documentation/refinement.htm#anch281 )

be copy/pasted into the .def file so a .params file doesn't have to be 
given on the command line?  i.e. can't _everything_ go in the .def?

in the example where it says "data_mod_5pho" at the top of the .cif file, 
is phenix looking for a file - .pdb, .params, .. - with that prefix?

in "data_mod = 5pho", does 5pho come from 5pho.cif?  and it still needs to 
be on the command line?


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