I am using Dev1223 and need to generate LLG map from phenix.refine to see any additional anomalous scattering is there. In the output window of phenix.refine I added LLG map to map coefficients and checked write mtz file... option. I thought the the mtz file with LLG map will be written to the output folder of refinement where the other files are, but don't see any additional files generated other than usual files. Am I doing something wrong?

Subhani

On Tue, Nov 20, 2012 at 2:47 PM, Nathaniel Echols <nechols@lbl.gov> wrote:

On Tue, Nov 20, 2012 at 12:41 PM, Subhani Bandara <ramssb17@gmail.com> wrote:
> I am refining a protein with metal-ligand complexes. Is it possible to
> refine only y coordinates for an atom (on two fold) while keeping X and Z
> fixed using Phenix? Also is there a way to calculate something like
> anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to
> identify any additional atoms bound at metal sites.

Not sure about the first question, but the answer to the second is
yes, if you download the latest nightly build, phenix.refine is now
able to output an anomalous log-likelihood gradient (LLG) map from
Phaser, which will indicate where any unmodelled anomalous scattering
is present. This is most useful if you use the group_anomalous
strategy with any heavy atom selected (I would put S in this list),
and I suspect you need to refine them separately for optimal results
(i.e. each metal is its own group, rather than one group with the
selection "element FE" or whatever it is). You can also get an LLG
map from phenix.maps, but this simply guesses the anomalous scattering
based on the wavelength, and will probably be noisier than if you
refine f' and f''.

-Nat
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