On Thu, Feb 14, 2013 at 11:29 AM,
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. -Nat