Where can I set B-factor for water in phenix.refine
on the GUI version of phenix?
Do you mean resetting the B-factors for all waters, or the
B-factor for new solvent molecules when the water picking
option is selected? For the latter, it is here:
Settings menu->Ordered solvent...->Initial B-factor
value
(You may need to change the "user level" menu to
"intermediate" or "advanced" if you don't see that control at
first.)
If you want to reset B-factors for existing waters, open
Settings menu->Model modifications->Modify ADPs, enter
the selection for waters in the first control ("resname HOH"
is usually all you need), and enter a suitable value in "Set
isotropic B to:".
Of course in either case, by default phenix.refine will
re-refine those initial values.
-Nat