[phenixbb] group on special position

Pavel Afonine pafonine at lbl.gov
Thu Aug 13 11:12:53 PDT 2020

Hi Arthur, hi Karine,

this is definitely possible to do in Phenix but off the top of my head I 
can't remember how. What you have tried so far sounds about right to me 
but there might be subtle nuances. Would you mind sending me the model 
file so that I figure out the details and reply back with a how-to 
recipe? I'll use this as an opportunity to improve the documentation too!

I don't need the data file but if you share it too then I'll make sure 
the refinement works fine with whatever setup we'll come up with.

All files will be treated confidentially. Please send files to me only, 
not the whole phenixbb!


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...
> Thanks,
> Arthur
>> 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?
>> Cheers,
>> Karine
>> 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.
>> Thanks,
>> Arthur

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