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 Ed