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

[Ralf W. Grosse-Kunstleve]

Hi Bryan,

> 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?

Yes, you can simply append the block above to the end of the file.
Or find the pdb_interpretation scope and insert

  apply_cif_modification {
    data_mod = 5pho
    residue_selection = resname GUA and name O5T
  }

there.

> 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?

No. The only requirement is that you give phenix.refine a cif file
(with any name or extension, but I suggest you use .cif) that has
a data_mod_5pho block as shown in the phenix.refine docs.

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

The 5pho is matched against data_mod_5pho in any cif file. It is not
used to look for certain file names.
phenix.refine reads in all files in the order given, finds out which
ones are cif files, and collects all cif definitions (chem_comp, link,
mod, parameters for non-bonded interactions). Potentially definitions
from one file can override definitions from previous files. At the
end it looks up the modification with the identifier "5pho" in the
pool of all cif modifications it found in all files.

Ralf