[phenixbb] group on special position
pafonine at lbl.gov
Fri Sep 4 14:25:07 PDT 2020
thanks for confirming!
What if that ion on special position is partially occupied? In that case
you may want to refine its occupancy.. But clearly it's going to be
tricky to decouple partial occupancy due to symmetry and the one due to
On 9/4/20 14:22, Arthur Glasfeld wrote:
> Hi Pavel,
> Sorry for the delay in testing this out. It worked fine! I added one additional measure, fixing occupancy at 0.33 so it wouldn’t refine with the other partial occupancies in my model.
> Thanks so much for your help,
>> On Aug 17, 2020, at 7:22 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> For the archive record, to make this work:
>> - set occupancy of PO4 on special position to 0.33;
>> - use
>> custom_nonbonded_symmetry_exclusions="chain B and resseq 5"
>> (which selects that PO4) to make sure it does not clash with its symmetry copies.
>> On 8/13/20 10:18, Arthur Glasfeld wrote:
>>> Hi Karine,
>>> I did give that a try, but the phosphate jumped out of the density. My guess is that the symmetry relationship between O2, O3 and O4 means that if each is at full occupancy, they then occupy each of the three positions so there’s a clash between all three in each asymmetric unit. I’ve also tried setting O2 to 1.00 occupancy, and O3 & O4 to 0.00. Again, the phosphate jumps out of density...
>>>> On Aug 12, 2020, at 10:37 PM, Dr. Karine Röwer <karine.roewer at gmail.com> wrote:
>>>> Hi Arthur,
>>>> from the way I used to work in small molecule crystallography, I'd set the occupancy of the atoms on the symmetry axis to 0.33, and keep only one of the other three O atoms with an occupancy of 1. I'd expect phenix to generate the other two O atoms via symmetry operators, and applied to the atoms on the symmetry axis, you should get a total occupancy of 1. Does that help?
>>>> On Thu, Aug 13, 2020 at 2:56 AM Arthur Glasfeld <glasfeld at reed.edu> wrote:
>>>> I’ve run into a situation where I think I have a phosphate sitting on a 3-fold axis, where the P to O1 bond lies on the axis and the atoms O2, O3 and O4 are in symmetry-related positions. The data go to 1.6 Å, so it looks pretty convincing. I’m refining this in Phenix and have tried some tricks with occupancy - fixing the atoms at 0.33, but I get a lot of positive density in the Fo-Fc map and large B-factors. I’ve looked around but am not finding ideas on how to model this correctly in my structure file - the references I find are for monoatomic ions. Any advice would be welcome.
>>>> Arthur Glasfeld
>>>> Reed College
>>>> Portland, OR 97202
>>>> Office: (503)517-7679
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