[phenixbb] Partially occupied SO4 and waters

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Tue Oct 20 17:03:57 PDT 2009

You can do grouped occupancy refinement, which will force the
het atoms associated with each AC to follow the side chain
occupancies, which will prevent the sum of protein and
hetatom occupancies exceeding a value of one. NB
the het atoms must have altloc flags in the PDB.

You can try refining  occupancies without groups 
(Phenix refine occupancies for any atoms with Q < 1)
but without groups you might find everything sums to > 1.

Pavel may have better suggestions.

From: Chris Waddling [waddling at msg.ucsf.edu]
Sent: Tuesday, October 20, 2009 7:57 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Partially occupied SO4 and waters

I have a partially occupied sulfate ion that is refining to 55% along with
one of two arginine side chains.   Associated with the second conformation
of the arginine, there is positive density for three partially occupied

In Shelxl, I can use the PART identifier to specify that the sulfate ion and
the waters are not present simultaneously and are associated with their
respective Arg side chain conformation.  Is there a way to do this in



Dr. Christopher A. Waddling, Ph.D.
University of California at San Francisco

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