[phenixbb] refining with f' and f" values

Subhani Bandara ramssb17 at gmail.com
Thu Nov 1 08:43:54 PDT 2012

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

Am I merging the correct data arrays? Are there anymore suggestions for

Thanks in advance for any help


On Wed, Oct 31, 2012 at 3:32 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Wed, Oct 31, 2012 at 1:29 PM, Subhani Bandara <ramssb17 at gmail.com>
> wrote:
> > 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
> the
> > error "Invalid combination-F-obs not anomalous, provide anomalous
> > reflections or fix all f" values. Then I used reflection file editor of
> > 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
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