[phenixbb] Problematic dataset

Peter Zwart PHZwart at lbl.gov
Sun Aug 5 13:27:26 PDT 2007


Hi Lucas,

It would be very informative to see the whole log file, especially the 
section on intensity statistics.

Furthermore, please run the data in P21 through xtriage and find that it 
is pseudo C222 with a single twin law.

I guess you have close to perfect twinning on the operator  -h,-h+k,-l 
(which will look different in P21).

Please try

phenix.refine twinning=True twin_law=<whatever xtriage gives you> 
model.pdb data.mtz

I hope you have choosen your free set with phenix.refine or 
iotbx.reflection_file_converter to get twin law compatible free set 
(done by default in phenix.refine, even if no twin law is specified).

Let me know if you have any other problems,

Peter


Lucas Bleicher wrote:
> I have a 1.9A dataset that could, in principle, be
> used to a molecular replacement solution. Phaser finds
> a solution which yields reasonable map to model
> agreement, but R factors do not fall down from values
> greater than 40%.
>
> It looked like a P21 (systematic absences are clear),
> so there was not much options on symmetry. I
> reprocessed the dataset in P1 and ran phenix.xtriage,
> and these lines called my attention:
>
> ---------------------------------------------
>  Analysing possible twin law :  -h,-k,l
> ---------------------------------------------
>
>
> Results of the H-test on a-centric data: 
>
>  (Only 50.0% of the strongest twin pairs were used)
>
> mean |H| : 0.053   (0.50: untwinned; 0.0: 50% twinned)
> mean H^2 : 0.005   (0.33: untwinned; 0.0: 50% twinned)
> Estimation of twin fraction via mean |H|: 0.447
> Estimation of twin fraction via cum. dist. of H: 0.449
>
>
> ---------------------------------------------
>  Analysing possible twin law :  -h,-h+k,-l
> ---------------------------------------------
>
>
> Results of the H-test on a-centric data: 
>
>  (Only 50.0% of the strongest twin pairs were used)
>
> mean |H| : 0.093   (0.50: untwinned; 0.0: 50% twinned)
> mean H^2 : 0.015   (0.33: untwinned; 0.0: 50% twinned)
> Estimation of twin fraction via mean |H|: 0.407
> Estimation of twin fraction via cum. dist. of H: 0.407
>
> ---------------------------------------------
>  Analysing possible twin law :  h,h-k,-l
> ---------------------------------------------
>
>
> Results of the H-test on a-centric data: 
>
>  (Only 50.0% of the strongest twin pairs were used)
>
> mean |H| : 0.085   (0.50: untwinned; 0.0: 50% twinned)
> mean H^2 : 0.013   (0.33: untwinned; 0.0: 50% twinned)
> Estimation of twin fraction via mean |H|: 0.415
> Estimation of twin fraction via cum. dist. of H: 0.417
>
>
> =========
>
> I have never dealt with twinned datasets before. Is
> there something I could try to do to obtain useful
> data from this?
>
> Lucas
>
> P.S.: Unfortunately, growing more crystals is not an option.
>
>
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