[phenixbb] Refinement using data with pseudo translational symmetry

Gino Cingolani Gino.Cingolani at jefferson.edu
Sun Mar 18 09:15:49 PDT 2012

Hi Bret,
I think the apparent higher symmetry (P212121 vs P21) is due the (pseudo)-twinning operator
(a 2-fold axis). So refinement with a twin law (h,-k,-l) will work only in the lower
symmetry space group (P21). I hope it helps.


Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
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"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Bret Wallace [bretw319 at gmail.com]
Sent: Sunday, March 18, 2012 12:07 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Refinement using data with pseudo translational symmetry


I have been using the auto.ncs function in phenix, but I haven't really looked to see if they are properly defined myself.


At this point I have not tried using the ordered_solvent command in phenix yet to find waters.  I will try that real quick before I bother you to have a look at it.  I'll let you know the updated R's afterwards.


It is interesting that you say that, because I after I lowered the symmetry to P21, and re-ran xtriage, it mentioned that I had pseudo-merohedral symmetry, but I didn't pursue that further. My beta-angle was also ~90.2 in this case, and the twinning operator is the same (h, -k, -l).

I will detwin and re-refine and see what happens,

Thanks everyone and I'll let you know what works,
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