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 waters. 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 Phenix? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco
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. Mark ________________________________________ From: Chris Waddling [[email protected]] Sent: Tuesday, October 20, 2009 7:57 PM To: [email protected] 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 waters. 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 Phenix? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Chris, yes, you can do it in phenix.refine. Use constrained groups for this: http://www.phenix-online.org/documentation/refinement.htm#anch20 and do not forget to assign proper altloc identifiers for involved atoms (so they don't get pushed apart by non-bonded term). Please let me know if you have any questions or problems with this. Pavel. On 10/20/09 4:57 PM, Chris Waddling wrote:
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 waters.
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 Phenix?
Thanks,
Chris
-- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco
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participants (3)
-
Chris Waddling -
Mayer, Mark (NIH/NICHD) [E] -
Pavel Afonine