[phenixbb] Occupancy refinement of secondary conformation doesn't add up to 1.00

Benjamin Stauch bs448c at gmail.com
Sat Jun 14 11:57:33 PDT 2014

Hi Phenix,

I do a refinement of a glycoprotein that has a NAG-NAG attached to an Asn.
The data set is very high resolution and I am positive there is indication
of a secondary conformation of the entire attachement.
I modeled a second conformation in Coot and run my refinement, with the
"adjust occupancy" option checked. After initially setting both occupancies
to 0.5, I am puzzled to see one of the NAGs to be refined to 0.45
(conformer A) and 0.75 (conformer B) occupancy .. For the other NAG, and
indeed all amino acid residues, things always add up like they should.

Additionally to this, I was wondering if there was an easy option to
restrain each conformer of the entire Asn-NAG-NAG group to have uniform
occupancies -- i.e. the Asn and both NAGs of conformer A to have identical

Thanks and best
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