[phenixbb] pseudo-translational symmetry refinement

Arthur Glasfeld glasfeld at reed.edu
Thu May 1 21:10:55 PDT 2008

Hi Peter,
Thanks for your thoughts.  I'll have to download the latest version  
sometime soon.  The off origin peak is 53% of the origin, so pretty  
substantial.  We will try TLS (I teach at an undergrad school, and I  
need to get the student out of classes long enough to get her to both  
learn new tricks and to execute them!)

I'd never heard of order-disorder twinning before.  It sounds like an  
ominous new bit of pathology that I need to acquaint myself with.  I  
found some papers on-line that deal with it.  Do you have any good  
references that explain it fully?

Thanks again for all your help (this isn't the first time I've  
imposed on your good nature!)


On Apr 30, 2008, at 9:23 PM, Peter Zwart wrote:
>> I hope it's OK if I chime in with this problem as well.  I am working
>>  with a site-directed mutant of a commonly studied protein in our
>>  lab.  It crystallize in P3121 and its unit cell is doubled along the
>>  c axis relative to a unit cell (P3221) that we have commonly seen
>>  with other mutants (the edges are roughly 55 x 55 x 88 or 55 x 55 x
>>  176).  Xtriage also picked up the pseuotranslational symmetry (0, 0,
>>  0.5), which is not surprising given the unit cell dimensions.
> If you are jusing the latest version (of of the lastes) it should
> actually tell you what the unit cell would be if the pseudo
> trans;lation would be a true crystallographic translation.
>>  I was aware of the problem with weak and strong reflectiions, but
>>  that is not so obvious in our case.  In HKLview one can see that in
>>  layers perpendicular to the c* axis, strong and weak reflections
>>  alternate out to about 8 Å, but the rest of the data (to 2.6 Å)
>>  appears - at least visibly - to be roughly consistent in intensity.
>>  Certainly when looking at the h0l or 0kl planes, there isn't any
>>  obvious alternation at higher resolution.
> If the differences are subtle / relatively minor, this is what is to
> be expected (watch out, a lot of hand waving):  at low resolution, the
> symmetry does not "appear to broken" resulting in strong modulations
> as if it were crystallographic symmetry. AT high resolution,
> deviations from ideality are so large that modulations are not so
> obvious anymore.
> What is the size of your off origin patterson peak as computed by  
> xtriage?
>> We quickly obtained a
>>  model by molecular replacement but have stalled in refinement at  
>> an R/
>>  Rfree of 30/38 (we have not tried TLS yet).  The most obvious
>>  difficulty with the model is seen using density fit analysis in coot
>>  - one domain of one of the subunits in the asymmetric unit (related
>>  by translation NCS to the other) has weak density.
> try TLS, it might help.
>>  Maybe this is just the luck of the draw - a crystal whose contents
>>  include 50% well ordered subunits and 50% not well ordered, but I'm
>>  curious if there is something obvious we should be trying.
> Not sure. 50% ordered and 50% not ordered sounds a lot like order
> disorder twins (OD). I am not sure what canb by done with that type of
> data in terms of refinement.
>>  By the
>>  way, xtriage found no evidence of twinning, and the data also passed
>>  muster with dataman (Padilla-Yeates) and Todd Yeates' server.
> Xtriage does use the Padilla Yeates test as the primairy vehicle for
> twin detemination, combined with the presence of twin laws of course.
> Beware that the presence of a full complement of nightmares such as OD
> twinning, merohedral twinning, pseudo symmetry etc etc can make
> intensity statistics look like all is fine.
> P
>>  Thanks in advance,
>>  Arthur Glasfeld
>>  Department of Chemistry
>>  Reed College
>>  P.S.  If anyone is interested I can send a figure with the hklview
>>  layers perpendicular to c* (hk0, hk1, hk2, hk3, hk4, hk5)
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> -- 
> -----------------------------------------------------------------
> P.H. Zwart
> Beamline Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
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