On Tue, Nov 27, 2012 at 12:03 PM, Subhani Bandara
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. -Nat