Hi,
I tried to processed it as P321. It seemed that it might be right. The
Rmerge increased
just a little. Then I used phenix.xtriage and sfcheck to check it. The
results are as following:
phenix.xtriage:
Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws
- <I^2>/<I>^2 : 2.084
- <F>^2/<F^2> : 0.827
- <|E^2-1|> : 0.666
- <|L|>, <L^2>: 0.400, 0.227
Multivariate Z score L-test: 9.082
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.
Statistics depending on twin laws
-----------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
-----------------------------------------------------------------
| -h,-k,l | M | 0.461 | 0.102 | 0.065 | 0.022 |
-----------------------------------------------------------------
Patterson analyses
- Largest peak height : 4.288
(corresponding p value : 0.98768)
The largest off-origin peak in the Patterson function is 4.29% of the
height of the origin peak. No significant pseudotranslation is detected.
The results of the L-test indicate that the intensity statistics
are significantly different than is expected from good to reasonable,
untwinned data.
As there are twin laws possible given the crystal symmetry, twinning could
be the reason for the departure of the intensity statistics from normality.
It might be worthwhile carrying out refinement with a twin specific target
function.
sfcheck:
Pseudo-translation is not detected.
Minimal estimated error : 0.0864
Perfect twinning test <I^2>/<I>^2 : 2.0191
Partial Twinning test:
-h,-k,+l
Polar angles: 0.00 0.00 180.00
Alpha(twin fraction),Npair,Ior,Tol : 0.148 118812 2 0.000
Then, what should I do? I did not deal with any twinning dataset. Any
comments and suggestions
will be greatly appreciated. Thanks!
Yingjie
On Thu, Oct 16, 2008 at 12:24 AM, Eleanor Dodson <[EMAIL PROTECTED]>wrote:
> I should have said - most likely explanation is point group is reall P321
>
> Eleanor
>
>
>
>> 2008/10/15, Eleanor Dodson <[EMAIL PROTECTED]>:
>>
>>
>>> I cant follow this very well.
>>> Try SFCHECK as well which will do the same tests and give a differently
>>> formatted output..
>>> or TRUNCATE which gives you plots of these stats v resolution..
>>>
>>> <I^2>/<I>^2 : 2.351 This is higher than the expected value of 2 for
>>> untwinned data. (1.5 for perfectly twinned data)
>>> However it can be distorted by non-crystallographic translation, but you
>>> dont seem to have that..
>>> Or by experimental errors and you need to inspect it in resolution
>>> ranges
>>> to detect that - assuming your low res data is more accurate than the
>>> high
>>> res.
>>>
>>> Eleanor
>>>
>>>
>>>
>>>
>>>
>>> Yingjie Peng wrote:
>>>
>>>
>>>
>>>> Dear guys,
>>>>
>>>> I have collected a dataset with the sg as P31. I ran pehnix.xtriage to
>>>> analyse the data with
>>>> following result:
>>>>
>>>> Twinning and intensity statistics summary (acentric data):
>>>>
>>>> Statistics independent of twin laws
>>>> - <I^2>/<I>^2 : 2.351
>>>> - <F>^2/<F^2> : 0.788
>>>> - <|E^2-1|> : 0.766
>>>> - <|L|>, <L^2>: 0.446, 0.270
>>>> Multivariate Z score L-test: 3.358
>>>> 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.
>>>>
>>>>
>>>> Statistics depending on twin laws
>>>>
>>>>
>>>>
>>> ------------------------------------------------------------------
>>>
>>>
>>>> | Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
>>>>
>>>>
>>>>
>>> ------------------------------------------------------------------
>>>
>>>
>>>> | -h,-k,l | M | 0.460 | 0.043 | 0.039 | 0.022 |
>>>> | h,-h-k,-l | M | 0.054 | 0.423 | 0.459 | 0.478 |
>>>> | -k,-h,-l | M | 0.476 | 0.042 | 0.043 | 0.022 |
>>>>
>>>>
>>>>
>>> ------------------------------------------------------------------
>>>
>>>
>>>> Patterson analyses
>>>> - Largest peak height : 4.693
>>>> (corresponding p value : 0.95672)
>>>>
>>>>
>>>> The largest off-origin peak in the Patterson function is 4.69% 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.
>>>> Even though no twinning is suspected, it might be worthwhile carrying
>>>> out
>>>> a refinement using a dedicated twin target anyway, as twinned structures
>>>> with
>>>> low twin fractions are difficult to distinguish from non-twinned
>>>>
>>>>
>>> structures.
>>>
>>>
>>>> The correlation between the intensities related by the twin law
>>>> h,-h-k,-l
>>>> with an
>>>> estimated twin fraction of 0.42 %
>>>> is most likely due to an NCS axis parallel to the twin axis. This can be
>>>> verified by
>>>> supplying calculated data as well.
>>>>
>>>>
>>>> Is it perfect twinning or partial twinning? I am supposed to do MR with
>>>>
>>>>
>>> this
>>>
>>>
>>>> dataset.
>>>> What should I do next with this dataset? Thanks very much.
>>>>
>>>> Best regards,
>>>>
>>>> Yingjie
>>>>
>>>>
>>>> Yingjie PENG, Ph.D. student
>>>> Structural Biology Group
>>>> Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
>>>> Shanghai Institute of Biological Sciences (SIBS)
>>>> Chinese Academy of Sciences (CAS)
>>>> 320 Yue Yang Road, Shanghai 200031
>>>> P. R. China
>>>> 86-21-54921117
>>>> Email: [EMAIL PROTECTED]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>
>
