[phenixbb] calculating anomalous differences from a model

Nathaniel Echols nechols at lbl.gov
Thu Apr 3 09:40:11 PDT 2014

On Thu, Apr 3, 2014 at 9:28 AM, Alastair Fyfe <afyfe at soe.ucsc.edu> wrote:

>  A related question: is there a current example of  using phaser to
> calculate SAD LLG maps from a refined model not refined with phenix.refine?
> In the past I have used the description posted here:
> http://www.phenix-online.org/pipermail/phenixbb/2008-July/012399.html
> However phaser syntax and keywords seem to have changed a bit as this no
> longer works.  Also, have the derived FLLG and PHLLG columns been renamed ?

You can do this in phenix.maps (which runs Phaser for you internally) -
just specify "LLG" as the map_type, and you can name the columns whatever
you want (FLLG and PHLLG are good choices, but the GUI will fill something
in for you automatically).  You should also specify the wavelength, of
course, otherwise it's going to look pretty similar to the simple anomalous
difference map since no anomalous scattering is modeled.  The f'' won't
actually be refined, but it's a pretty good first approximation, and the
result definitely more sensitive towards missing weak scatterers.

You can also get the LLG map from phenix.refine (so why use anything
else?), but that requires performing anomalous group refinement (there is a
wavelength parameter but it is not widely used at the moment).  My tests
indicate that Phaser's anomalous refinement is more accurate, however.

This is probably yet another item for the FAQ list.

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