Re: [phenixbb] refining with f' and f" values

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