[phenixbb] poor phasing

[Francis E Reyes]

On Apr 27, 2009, at 9:20 AM, Peter Zwart wrote:

>>    R_abs_twin observed data   : 0.012
>>    R_abs_twin calculated data : 0.300
>>
>> Is R_abs_twin the same thing as Robs_twin in Lebedev, Vagin,
>> Murshudov. Acta Cryst. (2006). D62, 83-95 ?
>>
>> And I guess I have rotational pseudo symmetry with Rcalctwin < 1/2.
>
> Correct.
>
>> Interestingly when I run xtriage when the data is scaled into P 41 21
>> 2 I get the following stats
>> R vs R statistic:
>>   R_abs_twin = <|I1-I2|>/<|I1+I2|>
>>   Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95
>>
>>    R_abs_twin observed data   : 0.012
>>    R_abs_twin calculated data : 0.521
>>
>> since r_abs_twin or r_obs_twin ~= 0, that's an indicator for perfect
>> twinning.
>
> when data is scaled in P 41 21 2 and you still get twin laws, it means
> your cell still has higher symmetry.
> what are your unit cell parameters?


Sorry Peter


I err'd. When the data is scaled in P 41 21 2, xtriage reports the  
summary twinning analysis as follows:


-------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
   - <I^2>/<I>^2 : 1.971
   - <F>^2/<F^2> : 0.792
   - <|E^2-1|>   : 0.731
   - <|L|>, <L^2>: 0.484, 0.318
        Multivariate Z score L-test: 1.741
        The multivariate Z score is a quality measure of the given
        spread in intensities. Good to reasonable data are expected
        to have a Z score lower than 3.5.
        Large values can indicate twinning, but small values do not
        necessarily exclude it.


No (pseudo)merohedral twin laws were found.


Patterson analyses
   - Largest peak height   : 5.297
    (corresponding p value : 0.86379)


The largest off-origin peak in the Patterson function is 5.30% of the
height of the origin peak. No significant pseudotranslation is detected.

The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.

-------------------------------------------------------------------------------


In this case, the only indicator for perfect twinning is 'Large values  
can indicate twinning, but small values do not necessarily exclude  
it.' ?

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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