[phenixbb] Additional conformations and partially occupied waters

Christian Roth christianroth034 at gmail.com
Mon Jan 11 04:14:12 PST 2016

Hi Helena,
Indeed you have to group the relevant aa and the respective water together
in a constrained group to avoid your problem and get the occupancies add up
to 1. This us described in the manual under occupancy refinement. I can't
access the manual at the moment to give you a more detailed answer.


On 11 Jan 2016 11:56, "Helena Taberman" <helena.taberman at uef.fi> wrote:

> Hi,
> I’m trying to refine a structure determined to 1.6 Å resolution. There’s
> several residues with additional conformations and waters with partial
> occupancies stating that they would be there when the conformation of the
> residues allows it. When I try to refine these conformations and partially
> occupied waters together the refinement kicks the second conformations and
> water molecules out of their densities, since they are obviously too close
> to the other additional conformations of the residues or the following
> residues. What could I do? Should I somehow group them together or what?
> Best regards,
> Helena
> Helena Taberman, Ph.D.
> University of Eastern Finland
> Department of Chemistry
> Joensuu Campus
> P.O. Box 111
> FI-80101 Joensuu, FINLAND
> Mobile: +358 50 337 2488
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