[phenixbb] WAS: changing TLS groups mid refinement

Edward A. Berry BerryE at upstate.edu
Mon May 17 09:49:48 PDT 2010

Pavel Afonine wrote:
> Do you have rock solid evidence that substituting missing (unmeasured)
> Fobs with 0 would be better than just using actual set (Fobs>0) in
> refinement?
Phil Jeffrey wrote:
> Fobs = 0 clearly conveys some information (i.e. the reflection is weak). Simply deleting the data is the worst case scenario

The problem seems to be that phenix is using Fobs=0 as a "missing number flag" which
precludes its use as a valid measurement.

I second the truncate advice, not actually truncating the reflections at zero but 
histogram-shifting them above zero (French & Wilson).

Even without the French & Wilson, the number of refelection that are precisely 0.00000
must be rather small. However if all negative intensities are set to zero
there could be a lot, and it might still be good to refine against them,
since they must have been pretty weak. Any change which increases
their calculated value should be penalized relative to one that decreases it


More information about the phenixbb mailing list