On Thu, Nov 1, 2012 at 8:43 AM, Subhani Bandara
Then I merged only Intensity+-, sigma+- from reflection file ( as amplitudes) with Rfree flags of mtz file and used it with ML as target function. Then refinement started with high Rfree value (41% compared to 16% for current model) and ended up with 48% Rfree. But when I checked the map, occupancies of metals at general positions are matching with that of ligands.
Am I merging the correct data arrays? Are there anymore suggestions for this.
After inspection of the file containing anomalous data*, it's obvious that these are still the intensities, only mislabeled as amplitudes. When you're converting the intensities, you need to change the option "Output diffraction data as", and not "Force observation type" - the first one actually does the numerical conversion to get amplitudes, the second leaves the values alone but changes the data type in the MTZ file. Which I guess is what happened in your case. Actually running the conversion results in a dataset that reproduces your R-factors and has huge anomalous difference map peaks for the metals; I will send you this file separately. -Nat (* For the record: under "Reflection tools" there is a program called "Compare datasets", which will visualize pseudo-precession planes through reciprocal space for a pair of datasets, showing only those reflections in common. This makes it very easy to spot when something is wrong - the attached images show the difference between actual amplitudes [1], and intensities mislabeled as amplitudes [2].)
