[phenixbb] coordinate refinement and maps

Nathaniel Echols nechols at lbl.gov
Tue Nov 27 12:11:47 PST 2012

On Tue, Nov 27, 2012 at 12:03 PM, Subhani Bandara <ramssb17 at gmail.com> wrote:
> I am using Dev1223  and need to generate LLG map from phenix.refine to see
> any additional anomalous scattering is there. In the output window of
> phenix.refine I added LLG map to map coefficients and checked write mtz
> file... option. I thought the the mtz file with LLG map will be written to
> the output folder of refinement where the other files are, but don't see any
> additional files generated other than usual files. Am I doing something
> wrong?

No, the LLG map coefficients should be part of the same MTZ file that
all of the other map coefficients are written.  At present I don't
think they will be automatically opened in Coot when launched from the
Phenix GUI (I will look into fixing this), nor will the "Auto-open
MTZ" function in Coot recognize them.  Instead, you need to select
"Open MTZ, mmCIF, fcf, or phs" in Coot, pick the MTZ file, and once
you get to the map setup dialog, choose "LLG" and "PHLLG" or whatever
you decided to name the columns, and check "Is a difference map?".
Randy's recommendation was to only look at peaks greater than the
maximum negative value, so I would scroll up the contour level until
all of the negative LLG density disappears.


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