[phenixbb] weaker density in maps

William G. Scott wgscott at chemistry.ucsc.edu
Sat Feb 27 10:11:10 PST 2010

I noticed that phenix makes by default two sets of maps, one of which has some sort of filling for missing reflections.  The one that doesn't do this correction I have found will preserve weak features better (in my most memorable case, water number six on a Mn++ ion). I never tried the gui, but maybe you are looking at the other map by default with that.

On Feb 26, 2010, at 2:29 PM, David Garboczi wrote:

> We sometimes build model into density at ~0.8 sigma, refine, and the Rfree becomes lower.  So we believe that we put model where it should be.
> Running the same data and same model in phenix under default conditions at the command line, we obtain maps that do not show the weaker features in which we believe in CNS.
> We are wondering if we can believe the weaker density or is it that we are not toggling something on in phenix.
> We routinely view the phenix-generated maps after transforming them to dsn6 files in mapman.
> thanks,
> Dave
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