[phenixbb] density level

CPMAS Chen cpmasmit at gmail.com
Sun Jan 13 11:38:00 PST 2013

Dear PhenixBBer,

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


At the same sigma level(1.5), the absolute density of the violet map is
0.32e/A^3 (phenix-dev-1266), while that of the blue map is
0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there is no
other difference on the data and model used.

Sam encountered a similar problem on the density.


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"

Or there is a work round for this issue?




Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130113/6350453c/attachment.htm>

More information about the phenixbb mailing list