Hi Nat, I have selected "F(+),SIGF(+),F(-),SIGF(-)" as data labels in GUI during refinement. If I explain more about what I did, I merged Intensity+-, sigma+- from reflection file ( as amplitudes) with Rfree flags, F-obs, SIGFobs and HL coefficients of data.mtz file of a refinement. Then I used this with a pdb file and cif file (gor ligands) in refinement. Also I selected anomalous group in settings and asked to refine f' and f" for heavy atoms while giving 0.00 as the value.Then it gives an error message saying " use ML as target function" as I was using anomalous data. When I changed target to ML it gives error saying "if need to use phase restraints in refinement please change the target function to MLHL". As I am using experimental phases is it OK to uncheck "use experimental phase restraints" option and have ML as target function? 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. Thanks in advance for any help Subhani On Wed, Oct 31, 2012 at 3:32 PM, Nathaniel Echols wrote:

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I have a structure with heavy metals which I would like to refine anomalous scattering factors. I could get the f' and f" values from Autosol, when I gave the atom name and wavelength. But when I ran refinement with anomalous scattering giving .mtz file and pdb file from pHENIX refinement I got

On Wed, Oct 31, 2012 at 1:29 PM, Subhani Bandara wrote: the

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error "Invalid combination-F-obs not anomalous, provide anomalous reflections or fix all f" values. Then I used reflection file editor of GUI to create a mtz file that has anomalous data using the original reflection file and the mtz file of refinement. But still it gives an error. I must be doing something wrong, but cannot figure out what that is.

Did you select the correct labels in the configuration interface? There should be four columns (for instance, "F(+),SIGF(+),F(-),SIGF(-)". It may not automatically select the anomalous array, even though it probably should in this case.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

On Thu, Nov 1, 2012 at 8:43 AM, Subhani Bandara wrote:

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].)