[phenixbb] density level

Nathaniel Echols nechols at lbl.gov
Sun Jan 13 12:21:00 PST 2013

On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:
> I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my
> surprise, the absolute electron density on the 2Fo-Fc map is quite
> different.

The electron density maps (or coefficients) generated by Phenix are
not on an absolute scale, and the values displayed by Coot are more or
less irrelevant.  The scaling method changed significantly between
1.6.4 and 1.8, so I'm not surprised that the map levels did too.

> By the way, is there a simple way to keep only F and SIGF column of the
> autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce
> columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may
> not be necessary as it is pointed in the maillist, since the intensity is
> already transformed to amplitude after truncation in autoxds.
> I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix
> treats it as containing anomalous data. the following is extracted from the
> refine pdb file
> MIN(FOBS/SIGMA_FOBS)              : 1.16
> REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.11
> REMARK   3   NUMBER OF REFLECTIONS             : 143207
> Also, in the auto generated def file,
> xray_data.labels = "F, SIGF, DANO, SIGDANO"

This is intentional - why would you want to throw out information?
However, you can always use either the reflection file editor (in the
latest builds) or the French & Wilson GUI to convert IMEAN to F.


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