[phenixbb] xray and neutron joint refinement

Nathaniel Echols nechols at lbl.gov
Thu Feb 14 11:41:42 PST 2013

On Thu, Feb 14, 2013 at 11:29 AM,  <amakal at chem.uw.edu.pl> wrote:
> After the first refinement I ended up with xxx_data.mtz (attached), in which
> both Fobs and R-free flags for both x-ray and neutron data are specified.
> However, phenix.refine GUI still does not recognize the 'neutron' part of
> the input.
> In order to proceed with newly-generated r-free flags for neutrons I was
> forced to extract neutron data into separate file and neutron r-free flags
> into yet another separate file, read-in both additional files into the GUI
> and then specify from a drop-down menu what each of the files contained.
> Is there any way for phenix to read in all four coefficients (Fobs, neutron
> Fobs and associated R-free flags) from a single mtz file?

Yes, you should be able to do this.  The only problem that I see is
that it doesn't automatically pull out the neutron data, and even
after you specify that the file contains neutron data, the default
label is still F-obs-xray - I think I can fix this, although it's only
going to work for obvious labels (e.g. the *_data.mtz file from
phenix.refine).  In these cases I can also make it use the neutron
data automatically, but I don't want to do this in other
circumstances, because it's quite common to have multiple data arrays
present in an MTZ file, and they'll usually just be different forms of
the same thing (e.g. merged amplitudes and anomalous intensities).

Anyway, you simply add the file, it gets recognized as containing
X-ray data and flags, then you either right-click the "Data type"
field, or select the file and click "Modify file type", and select
"Neutron data" and "Neutron R-free" in the menu.  The data and flags
labels will be automatically populated, and then you can change them
to the appropriate arrays.  I'm using the most recent code (equivalent
to 1.8.2-1296, which you are encouraged to install), but it should
work in build 1280 as well.


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