[phenixbb] Gap between R and Rfree

Pavel Afonine PAfonine at lbl.gov
Thu Feb 25 11:58:51 PST 2010

Hi Young-Jin,

> Third, ncs may be the key... I re-processed hkl and cut the resolution 

I'm wondering why you cut the resolution?

> and did ncs=true. It first generated error message and suggested to put distance limit upto 3. 

With ncs=true phenix.refine will determine the NCS groups automatically. 
Since the currently used algorithm is very simple the NCS groups may not 
be chosen optimally (making it smart is in to-do list). This is why it 
is a good idea to check the automatically determined NCS groups, 
especially when you see a message that asks you to push the distance 
limit to a larger value. You can look in .geo file (the file that lists 
all the geometry restraints used in refinement)  for something like 
EXCESSIVE DISTANCE to see affected atoms and then check the map to see 
if these atoms should be forced to obey NCS and not represent the 
individuality of NCS related groups and therefore need to be excluded 
from NCS restraints.

Good luck!

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