[phenixbb] coordinate refinement and maps

Subhani Bandara ramssb17 at gmail.com
Tue Nov 27 12:03:55 PST 2012

Hi all,

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

Thanks in advance for any help


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

> On Tue, Nov 20, 2012 at 12:41 PM, Subhani Bandara <ramssb17 at 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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