On Thu, Nov 1, 2012 at 8:43 AM, Subhani Bandara
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".
Okay, I wasn't aware that MLHL was limited to non-anomalous data. Good to know.
As I am using experimental phases is it OK to uncheck "use experimental phase restraints" option and have ML as target function?
If this is the same structure you sent me data for earlier, I don't think you need experimental phases - they're more helpful at lower resolution, or when you're more worried about model bias, but you have high resolution data and a very good model.
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.
That doesn't sound right... is this the reprocessed dataset or the original? Can you please send me (off-list!) all of the input files (again, sorry!), including the original reflection file with intensities, and one of us will take a look. I suspect there is a simple explanation but it's impossible to guess without seeing the exact inputs. FYI, I would just refine against intensities directly, since phenix.refine will convert them internally using French-Wilson treatment to correct negative intensities. The reflection file editor is somewhat dumber in its handling of intensities - I have since changed the code to use French-Wilson instead but this isn't released yet. -Nat