[phenixbb] Reliable twinning fraction estimation
Xiao Lei
xiaoleiusc at gmail.com
Wed Dec 10 14:45:47 PST 2014
Hi Tom,
I paste the patterson analysis from the xtriage log file here. This shows
no significant pseudotranslation is detected.However in the summary of the
log file it gives me some PM (pseudo-merohedral) possiblities.
Patterson analyses
------------------
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord. : 0.269 -0.000 -0.001
Distance to origin : 18.194
Height (origin=100) : 2.560
p_value(height) : 1.000e+00
The reported p_value has the following meaning:
The probability that a peak of the specified height
or larger is found in a Patterson function of a
macro molecule that does not have any translational
pseudo symmetry is equal to 1.000e+00.
p_values smaller than 0.05 might indicate
weak translational pseudo symmetry, or the self vector of
a large anomalous scatterer such as Hg, whereas values
smaller than 1e-3 are a very strong indication for
the presence of translational pseudo symmetry.
Patterson analyses
- Largest peak height : 2.560
(corresponding p value : 1.00000)
The largest off-origin peak in the Patterson function is 2.56% of the
height of the origin peak. No significant pseudotranslation is detected.
-------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws
<I^2>/<I>^2 : 1.554 (untwinned: 2.0, perfect twin: 1.5)
<F>^2/<F^2> : 0.878 (untwinned: 0.785, perfect twin: 0.885)
<|E^2-1|> : 0.557 (untwinned: 0.736, perfect twin: 0.541)
<|L|>, <L^2>: 0.375, 0.199
Multivariate Z score L-test: 11.683
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,-l,k+l | PM | 0.359 | 0.127 | 0.118 | 0.022 |
| h,k+l,-k | PM | 0.359 | 0.127 | 0.118 | 0.022 |
| h,-k-l,k | PM | 0.074 | 0.428 | 0.429 | 0.435 |
| h,l,-k-l | PM | 0.074 | 0.428 | 0.429 | 0.435 |
| h,-k,-l | PM | 0.370 | 0.117 | 0.118 | 0.022 |
| -h,k,-k-l | PM | 0.361 | 0.124 | 0.118 | 0.022 |
| -h,-k-l,l | PM | 0.362 | 0.127 | 0.118 | 0.022 |
| -h,-l,-k | PM | 0.058 | 0.441 | 0.448 | 0.441 |
| -h,l,k | PM | 0.362 | 0.123 | 0.117 | 0.033 |
| -h,-k,k+l | PM | 0.075 | 0.427 | 0.428 | 0.452 |
| -h,k+l,-l | PM | 0.077 | 0.425 | 0.427 | 0.418 |
------------------------------------------------------------------
Xiao
On Wed, Dec 10, 2014 at 2:17 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> wrote:
> Hi Xiao,
> Yes, that is pretty convincing. One more thing to check: In your xtriage
> output what does it say about Patterson peaks? (Is there any translational
> pseudo-symmetry?) If not...you're probably done, yes it is nearly
> perfectly twinned.
> All the best,
> Tom T
>
> On Dec 10, 2014, at 3:13 PM, Xiao Lei wrote:
>
> Hi Tom,
>
> Thank you very much for your advice, I just tried Xtriage analysis of
> the data scaled as P1, the Wilson moment is 1.554, this result shows that
> the dataset is nearly perfect twinned.
>
> I paste the part of the log file of xtriage below.
>
>
> Analyses of the absences table indicates a number of likely space group
> candidates, which are listed below. For each space group, the number of
> absent violations are listed under the '+++' column. The number of present
> violations (weak reflections) are listed under '---'. The last column is a
> likelihood based score for the particular space group. Note that
> enantiomorphic spacegroups will have equal scores. Also, if absences were
> removed while processing the data, they will be regarded as missing
> information, rather then as enforcing that absence in the space group
> choices.
>
>
>
> -----------------------------------------------------------------------------------
> | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- |
> score |
>
> -----------------------------------------------------------------------------------
> | P 1 | 0 | 0.00 | 0.00 | 0 | 0 |
> 0.000e+00 |
>
> -----------------------------------------------------------------------------------
>
>
>
>
> Wilson ratio and moments
>
> Acentric reflections
> <I^2>/<I>^2 :1.554 (untwinned: 2.000; perfect twin 1.500)
> <F>^2/<F^2> :0.878 (untwinned: 0.785; perfect twin 0.885)
> <|E^2 - 1|> :0.557 (untwinned: 0.736; perfect twin 0.541)
>
> Xiao
>
> On Wed, Dec 10, 2014 at 1:24 PM, Terwilliger, Thomas Charles <
> terwilliger at lanl.gov> wrote:
>
>> Hi Xiao,
>>
>> Here are some things to check before concluding whether the data are
>> twinned:
>>
>> 1. What are the Wilson moments (2 for untwinned 1.5 for perfect twin)?
>>
>> 2. Is it possible you have the wrong space group? If the data are
>> overmerged then you could get this result. Perhaps your space group is
>> really P31 or something like that? What are your merging statistics? Try
>> an analysis with data in lower-symmetry space groups (you can always get
>> the Wilson moments in P1 and that will often be a good indicator).
>>
>> All the best,
>> Tom T
>>
>> On Dec 10, 2014, at 1:37 PM, Xiao Lei wrote:
>>
>> > Dear All,
>> >
>> > I have a x-ray dataset of a protein-DNA complex to 2.8 A resolution
>> with space group P312 checked by phenix xtriage for twinning. The estimated
>> twin fraction from the output of xtriage is: 0.115 (Britton analysis);
>> 0.119 (H test) and 0.022 (maximum likelihood method). However, the L-test
>> graph in xtriage shows my observed data almost perfectly overlay with
>> theoretical perfect twin data. In addition, when I tried to use phenix to
>> do refinement with twin law -h,-k,l, the log file shows my twin fraction
>> estimation is 0.49, which is very high and much bigger than Britton
>> analysis and H test estimation.
>> >
>> > As far as my understanding is that if a twin fraction is lower than
>> 15%, I still have hope to solve the structure (molecular replacement in
>> this case) with reasonable R value, but if the twin fraction is 0.49, which
>> is almost a perfect twin, which makes detwin impossible and refinement will
>> stall at high R values (in my case, R free start: 0.4199; R work start:
>> 0.4121; and R free final: 0.4038 and R work final: 0.3640 after running
>> phenix refinement with twin law -h, -k, l).
>> >
>> > My question: which twin fraction estimation is more reliable? is my
>> data almost perfectly twined?
>> >
>> > I attached the graphs of L test, Britton analysis and twin estimation
>> from phenix xtriage and part of log file from phenix refine here.
>> >
>> > Many thanks in advance.
>> >
>> > Xiao
>> > <p312_phenix_refine.png><P312_estimated
>> twin_fraction.png><P312_Britton_plot.pdf><P312_Ltest.png>_______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
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