[phenixbb] Possible Twinned data

Kelly Daughtry kddaught at bu.edu
Thu Jun 9 12:52:10 PDT 2011


Yuri,
I would refine in parallel with and without the twin law and check the
resulting maps and R-factors.
I had a case where the twin fraction was 0.06, which I expected to be
negotiable. When I included the twin law in refinement, my R-factors
dropped dramatically.
It's usually the best rule of thumb that you have the right space group
/ molecular replacement solution / twinning / etc.

Good luck,
Kelly

*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
*******************************************************


On Thu, Jun 9, 2011 at 3:38 PM, Yuri <yuri.pompeu at ufl.edu> wrote:

> Hello phenixers,
> I am a little bit at loss since this is the first time I have encountered
> this situation.
> I just collected preliminary data on a ligand soaked crystal. It goes to
> about 1.85 A. The centrics and acentrics reflections tests look a little
> deviant from ideal untwinned. I was looking at my xtriage log
> file and it seemed to me like I have some twinned fraction. Phenix says
> not. I realize too my completeness is not good.
> Any educated insight would be helpful as I have never dealt with twinning
> (if this actually the case).
> Log file section:
> Wilson ratio and moments
>
> Acentric reflections
>   <I^2>/<I>^2    :1.650   (untwinned: 2.000; perfect twin 1.500)
>   <F>^2/<F^2>    :0.839   (untwinned: 0.785; perfect twin 0.885)
>   <|E^2 - 1|>    :0.649   (untwinned: 0.736; perfect twin 0.541)
>
>
> Centric reflections
>   <I^2>/<I>^2    :2.099   (untwinned: 3.000; perfect twin 2.000)
>   <F>^2/<F^2>    :0.749   (untwinned: 0.637; perfect twin 0.785)
>   <|E^2 - 1|>    :0.703   (untwinned: 0.968; perfect twin 0.736)
>
>
>
> NZ test (0<=z<1) to detect twinning and possible translational NCS
>
>
> -----------------------------------------------
> |  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
> -----------------------------------------------
> | 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
> | 0.1 |   0.052 |    0.095 |  0.171 |   0.248 |
> | 0.2 |   0.126 |    0.181 |  0.285 |   0.345 |
> | 0.3 |   0.197 |    0.259 |  0.371 |   0.419 |
> | 0.4 |   0.271 |    0.330 |  0.440 |   0.474 |
> | 0.5 |   0.334 |    0.394 |  0.499 |   0.520 |
> | 0.6 |   0.394 |    0.451 |  0.553 |   0.561 |
> | 0.7 |   0.447 |    0.503 |  0.600 |   0.597 |
> | 0.8 |   0.497 |    0.551 |  0.629 |   0.629 |
> | 0.9 |   0.541 |    0.593 |  0.660 |   0.657 |
> | 1.0 |   0.581 |    0.632 |  0.697 |   0.683 |
> -----------------------------------------------
> | Maximum deviation acentric      :  0.062    |
> | Maximum deviation centric       :  0.078    |
> |                                             |
> | <NZ(obs)-NZ(twinned)>_acentric  : -0.050    |
> | <NZ(obs)-NZ(twinned)>_centric   : -0.021    |
> -----------------------------------------------
>
>
>  L test for acentric data
>
>  using difference vectors (dh,dk,dl) of the form:
> (2hp,2kp,2lp)
>  where hp, kp, and lp are random signed integers such that
>  2 <= |dh| + |dk| + |dl| <= 8
>
>  Mean |L|   :0.441  (untwinned: 0.500; perfect twin: 0.375)
>  Mean  L^2  :0.270  (untwinned: 0.333; perfect twin: 0.200)
>
>  The distribution of |L| values indicates a twin fraction of
>  0.00. Note that this estimate is not as reliable as obtained
>  via a Britton plot or H-test if twin laws are available.
>
> Cheers,
> --
> Yuri Pompeu
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110609/ed5e6916/attachment.htm>


More information about the phenixbb mailing list