[cctbxbb] Inserting F000 into reflection (mtg) file

[Pavel Afonine]

Hi Nick,

> I’ve been looking through the cctbx/phenix scripts and although there’s a script for estimating F000 (phenix.f000), I can’t find any way of inserting it into an mtz file to make it accessible for easy map generation. Is this implemented anywhere/what do people use as the best way of doing this?
>
> If the insertion of F000 into an mtz file has been purposefully avoided, I presume it's done because we don't want the possibility of someone refining a model where F000 is used in refinement. Unless there’s another reason?

have a look at fft_map method of miller class (cctbx/miller/__init__.py) 
- it takes f_000 as an optional parameter.

If you just want to add it to existing miller_array then it is something 
like this:

f_obs_new = f_obs_old.customized_copy(
   indices = f_obs_old.indices().append((0,0,0)),
   data = f_obs_old.data().append(VALUE))

then you can dump into MTZ file:

mtz_dataset = f_obs_new.as_mtz_dataset(column_root_label="F-obs")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")

You need to have an estimate of F000 (which includes contributions from 
macromolecule and bulk-solvent).

Pavel