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

[Bryan W. Lepore]

using phenix 1.3b rc6 cctbx_tag 2007_11_18_2203

have a few questions :

1.
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?

2.
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?

3. 
in "data_mod = 5pho", does 5pho come from 5pho.cif?  and it still needs to 
be on the command line?

-bryan