[ccp4bb] AW: [ccp4bb] twinning fun

2014-01-29 Thread Herman . Schreuder
Dear Bert,

The first thing I would do is to calculate the Matthews number: Does at least 
one monomer fit in the P622 asymmetric unit? If not, your crystals are 
definitively twinned.
As mentioned below, I would also check  the I^2/I^2 ratio, but I would do 
it with the data processed in P6, since processing true P6 data in P622 will 
produce a twinned ratio even when the P6 data was not twinned. If it turns out, 
that some crystals are twinned and others not, I would  look at the diffraction 
patterns to see if something funny is going on (ice rings, high background, 
strange spot shape etc.). In this case, I would try to solve the structure with 
untwinned crystals. Maybe less fun, but also less hassle, frustration and 
cleaner maps.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dirk 
Kostrewa
Gesendet: Dienstag, 28. Januar 2014 22:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] twinning fun

Dear Bert Van-Den-Berg,

as far as I understand this, if you have true P622, process the data in P6 and 
then test for twinning, both the Britton-test and H-test will indicate perfect 
merohedral twinning.
This is because the Britton-test checks for a sudden increase of negative 
intensities after de-twinning, which happens only at twin fractions close to 
0.5 if the intensities used for de-twinning are the same. But this is true if 
they are related by crystallographic symmetry.
The H-test relates the absolute difference to the sum of the presumably twinned 
intensities, which gives 0 for intensities related by crystallographic 
symmetry, again resulting in twin fractions close to 0.5.
In other words, intensities related by crystallographic symmetry would indicate 
perfect twinning in both of these tests.

A better test for perfect merohedral twinning would be the ratio of I^2/I^2 
which should be 2 for untwinned and 1.5 for perfectly twinned data, tested in 
the higher space group. These values are reported by data processing programs 
like XDS. Please, be aware that these ratios have rather strange values if you 
have an unusually high background (loop fiber diffraction, ice rings, etc.) or 
extremely weak data.

For a really good discussion of twin tests, see Yeates, Methods. Enzymol. 276, 
344-358, 1997.

Best regards,

Dirk.
Am 28.01.14 18:26, schrieb Bert Van-Den-Berg:
Dear all,

I recently collected several datasets for a protein that needs experimental 
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests 
with high confidence that the space group is P622. This is where the fun begins.
For some datasets (processed in P622), the intensity distributions are normal, 
and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is 
no twinning (twinning fractions  0.05). However, for other datasets (same cell 
dimensions), the intensity distributions are not normal (eg Z-scores  10). 
Given that twinning is not possible in P622, this suggests to me that the real 
space group could be P6 with (near) perfect twinning.

If I now process the normal L-test P622 datasets in P6, the twin-law based 
tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher probability of 
being solvable?

Is there any strategy for experimental phasing of (near) perfect twins? SAD 
would be more suitable than SIR/MIR? (I also have potential heavy atom 
derivatives).

Thanks for any insights!

Bert



--



***

Dirk Kostrewa

Gene Center Munich, A5.07

Department of Biochemistry

Ludwig-Maximilians-Universität München

Feodor-Lynen-Str. 25

D-81377 Munich

Germany

Phone:   +49-89-2180-76845

Fax: +49-89-2180-76999

E-mail:  kostr...@genzentrum.lmu.demailto:kostr...@genzentrum.lmu.de

WWW: www.genzentrum.lmu.dehttp://www.genzentrum.lmu.de

***


Re: [ccp4bb] twinning fun

2014-01-29 Thread Kay Diederichs
Dear Bert,

as Dirk has pointed out, if P622 is the correct space group, then the twinning 
statistics printed out if you process in P6 are meaningless.

Intensity statistics, like the ratio of I^2/I^2 , can be misleading if 
there is (e.g. pseudo-translational) NCS in the crystal; however, the effect of 
NCS on the value of the ratio of I^2/I^2 is opposite to that of twinning. 
Thus if a crystal is twinned and has NCS, you might not notice any problem in 
the ratio of I^2/I^2 .

The other statistics, like Britton and H-test, present the intensity statistics 
in a different way, but from my understanding do not give substantially 
different information.

The L-test does look at a different kind of information and therefore gives 
additional insight.

If your measurements suffer from high background, diffuse scatter, ice rings, 
smeared reflections, additional crystals in the beam, or any other pathology, 
then all these tests may give distorted answers. In other words, even if 
twinning is not really present, any test designed to convert the deviation of 
data from ideality into an estimate of the twinning fraction will give you an 
alpha  0. So my experience is: if your data are very good, then the tests give 
good answers; if the data are mediocre or bad, don't necessarily believe the 
numbers. 

Finally, it's not only twinning of P6 that would give you P622, it's also 
twinning of P3x21, P3x12 that gives P6y22.

Hope this helps,

Kay




On Tue, 28 Jan 2014 17:26:23 +, Bert Van-Den-Berg 
bert.van-den-b...@newcastle.ac.uk wrote:

Dear all,

I recently collected several datasets for a protein that needs experimental 
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests 
with high confidence that the space group is P622. This is where the fun 
begins.
For some datasets (processed in P622), the intensity distributions are normal, 
and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is 
no twinning (twinning fractions  0.05). However, for other datasets (same 
cell dimensions), the intensity distributions are not normal (eg Z-scores  
10). Given that twinning is not possible in P622, this suggests to me that the 
real space group could be P6 with (near) perfect twinning.

If I now process the normal L-test P622 datasets in P6, the twin-law based 
tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher probability of 
being solvable?

Is there any strategy for experimental phasing of (near) perfect twins? SAD 
would be more suitable than SIR/MIR? (I also have potential heavy atom 
derivatives).

Thanks for any insights!

Bert



Re: [ccp4bb] twinning fun

2014-01-29 Thread Keller, Jacob

Try looking into tetartohedral twinning as well--I think I may have such a 
crystal, and it's tough going. And as Kay pointed out, try the various P3's. 
Since I have not yet been successful in figuring my similar case out, what do 
people on the list recommend as an approach to figuring this out--just trying 
every possible space group with various parameters? I would think there should 
be some actual advantages at the phasing step to having twins, such as a sort 
of NCS of intensities rather than amplitudes, weighted by twin fraction, but 
it doesn't seem that any software uses this. Perhaps there is a reason for that?

A paper on tetartohedral twinning I saw:

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):418-24. doi: 
10.1107/S0907444912006737. Epub 2012 Mar 16.
Tetartohedral twinning could happen to you too.
Roversi P, Blanc E, Johnson S, Lea SM.
Author information
Abstract
Tetartohedral crystal twinning is discussed as a particular case of 
(pseudo)merohedral twinning when the number of twinned domains is four. 
Tetartohedrally twinned crystals often possess pseudosymmetry, with the 
rotational part of the pseudosymmetry operators coinciding with the twinning 
operators. Tetartohedrally twinned structures from the literature are reviewed 
and the recent structure determination of tetartohedrally twinned triclinic 
crystals of human complement factor I is discussed.
PMID: 22505261 [PubMed - indexed for MEDLINE] PMCID: PMC3322600 Free PMC Article

JPK



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Wednesday, January 29, 2014 4:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] twinning fun

Dear Bert,

as Dirk has pointed out, if P622 is the correct space group, then the twinning 
statistics printed out if you process in P6 are meaningless.

Intensity statistics, like the ratio of I^2/I^2 , can be misleading if 
there is (e.g. pseudo-translational) NCS in the crystal; however, the effect of 
NCS on the value of the ratio of I^2/I^2 is opposite to that of twinning. 
Thus if a crystal is twinned and has NCS, you might not notice any problem in 
the ratio of I^2/I^2 .

The other statistics, like Britton and H-test, present the intensity statistics 
in a different way, but from my understanding do not give substantially 
different information.

The L-test does look at a different kind of information and therefore gives 
additional insight.

If your measurements suffer from high background, diffuse scatter, ice rings, 
smeared reflections, additional crystals in the beam, or any other pathology, 
then all these tests may give distorted answers. In other words, even if 
twinning is not really present, any test designed to convert the deviation of 
data from ideality into an estimate of the twinning fraction will give you an 
alpha  0. So my experience is: if your data are very good, then the tests give 
good answers; if the data are mediocre or bad, don't necessarily believe the 
numbers. 

Finally, it's not only twinning of P6 that would give you P622, it's also 
twinning of P3x21, P3x12 that gives P6y22.

Hope this helps,

Kay




On Tue, 28 Jan 2014 17:26:23 +, Bert Van-Den-Berg 
bert.van-den-b...@newcastle.ac.uk wrote:

Dear all,

I recently collected several datasets for a protein that needs experimental 
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests 
with high confidence that the space group is P622. This is where the fun 
begins.
For some datasets (processed in P622), the intensity distributions are normal, 
and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is 
no twinning (twinning fractions  0.05). However, for other datasets (same 
cell dimensions), the intensity distributions are not normal (eg Z-scores  
10). Given that twinning is not possible in P622, this suggests to me that the 
real space group could be P6 with (near) perfect twinning.

If I now process the normal L-test P622 datasets in P6, the twin-law based 
tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher probability of 
being solvable?

Is there any strategy for experimental phasing of (near) perfect twins? SAD 
would be more suitable than SIR/MIR? (I also have potential heavy atom 
derivatives).

Thanks for any insights!

Bert



Re: [ccp4bb] twinning fun

2014-01-29 Thread Eleanor Dodson
Dont forget that with twinning in apparent point group PG6/mmm the
true SG may be P6i or P3i21
See the twinning notes: http://www.ccp4.ac.uk/dist/html/twinning.html


Detecting twinning can be problematic -

My rule of thumb, following the procedure od ctruncate::

0) Check the matthews coefficient for likely number of molecules.
Half a molecule must mean you are assigning too high a symmetry count.
Lots of molecules means you need to check for non-crystallographic
translation etc.


1) Look at the I^2/I^2 plot after correction for anisotropy
If it isnt reasonably  straight with resolution you probably have some
data problems, and these can make all the tests pretty useless.

2) Is there a NC translation - truncate tells you that.
If not, and the data is OK,  you are unlikely to have twinning if
I^2/I^2 for acentrics is ~ 2, and  the L test looks OK.
H test and Britten tests a bit more influenced by other NC symmetry
considerations

3) If there IS NC translation I^2/I^2 for acentrics will probably
be  2  but the L test is still pretty reliable.

Good luck Eleanor

experimental phasing is tricky with perfect twinning but it has been
done. Sorry I have forgotten reference though..
Eleanor



On 29 January 2014 09:17, Kay Diederichs kay.diederi...@uni-konstanz.de wrote:
 Dear Bert,

 as Dirk has pointed out, if P622 is the correct space group, then the 
 twinning statistics printed out if you process in P6 are meaningless.

 Intensity statistics, like the ratio of I^2/I^2 , can be misleading if 
 there is (e.g. pseudo-translational) NCS in the crystal; however, the effect 
 of NCS on the value of the ratio of I^2/I^2 is opposite to that of 
 twinning. Thus if a crystal is twinned and has NCS, you might not notice any 
 problem in the ratio of I^2/I^2 .

 The other statistics, like Britton and H-test, present the intensity 
 statistics in a different way, but from my understanding do not give 
 substantially different information.

 The L-test does look at a different kind of information and therefore gives 
 additional insight.

 If your measurements suffer from high background, diffuse scatter, ice rings, 
 smeared reflections, additional crystals in the beam, or any other pathology, 
 then all these tests may give distorted answers. In other words, even if 
 twinning is not really present, any test designed to convert the deviation of 
 data from ideality into an estimate of the twinning fraction will give you an 
 alpha  0. So my experience is: if your data are very good, then the tests 
 give good answers; if the data are mediocre or bad, don't necessarily believe 
 the numbers.

 Finally, it's not only twinning of P6 that would give you P622, it's also 
 twinning of P3x21, P3x12 that gives P6y22.

 Hope this helps,

 Kay




 On Tue, 28 Jan 2014 17:26:23 +, Bert Van-Den-Berg 
 bert.van-den-b...@newcastle.ac.uk wrote:

Dear all,

I recently collected several datasets for a protein that needs experimental 
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests 
with high confidence that the space group is P622. This is where the fun 
begins.
For some datasets (processed in P622), the intensity distributions are 
normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that 
there is no twinning (twinning fractions  0.05). However, for other datasets 
(same cell dimensions), the intensity distributions are not normal (eg 
Z-scores  10). Given that twinning is not possible in P622, this suggests to 
me that the real space group could be P6 with (near) perfect twinning.

If I now process the normal L-test P622 datasets in P6, the twin-law based 
tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher probability of 
being solvable?

Is there any strategy for experimental phasing of (near) perfect twins? SAD 
would be more suitable than SIR/MIR? (I also have potential heavy atom 
derivatives).

Thanks for any insights!

Bert



Re: [ccp4bb] twinning fun

2014-01-29 Thread Randy Read
Also, if you have translational NCS then recent versions of Phaser can correct 
for the statistical effects and give you I^2/I^2 moment tests that are 
diagnostic of twinning.  This works pretty well for 2-fold tNCS (i.e. one major 
Patterson peak corresponding to one or more pairs of molecules separated by the 
same translation).  If there's higher order tNCS, then this works less well in 
the current version.  We give some examples in the paper describing the 
algorithm: http://journals.iucr.org/d/issues/2013/02/00/dz5268/dz5268.pdf.

Best wishes,

Randy Read

On 29 Jan 2014, at 13:30, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:

 Dont forget that with twinning in apparent point group PG6/mmm the
 true SG may be P6i or P3i21
 See the twinning notes: http://www.ccp4.ac.uk/dist/html/twinning.html
 
 
 Detecting twinning can be problematic -
 
 My rule of thumb, following the procedure od ctruncate::
 
 0) Check the matthews coefficient for likely number of molecules.
 Half a molecule must mean you are assigning too high a symmetry count.
 Lots of molecules means you need to check for non-crystallographic
 translation etc.
 
 
 1) Look at the I^2/I^2 plot after correction for anisotropy
 If it isnt reasonably  straight with resolution you probably have some
 data problems, and these can make all the tests pretty useless.
 
 2) Is there a NC translation - truncate tells you that.
 If not, and the data is OK,  you are unlikely to have twinning if
 I^2/I^2 for acentrics is ~ 2, and  the L test looks OK.
 H test and Britten tests a bit more influenced by other NC symmetry
 considerations
 
 3) If there IS NC translation I^2/I^2 for acentrics will probably
 be  2  but the L test is still pretty reliable.
 
 Good luck Eleanor
 
 experimental phasing is tricky with perfect twinning but it has been
 done. Sorry I have forgotten reference though..
 Eleanor
 
 
 
 On 29 January 2014 09:17, Kay Diederichs kay.diederi...@uni-konstanz.de 
 wrote:
 Dear Bert,
 
 as Dirk has pointed out, if P622 is the correct space group, then the 
 twinning statistics printed out if you process in P6 are meaningless.
 
 Intensity statistics, like the ratio of I^2/I^2 , can be misleading if 
 there is (e.g. pseudo-translational) NCS in the crystal; however, the effect 
 of NCS on the value of the ratio of I^2/I^2 is opposite to that of 
 twinning. Thus if a crystal is twinned and has NCS, you might not notice any 
 problem in the ratio of I^2/I^2 .
 
 The other statistics, like Britton and H-test, present the intensity 
 statistics in a different way, but from my understanding do not give 
 substantially different information.
 
 The L-test does look at a different kind of information and therefore gives 
 additional insight.
 
 If your measurements suffer from high background, diffuse scatter, ice 
 rings, smeared reflections, additional crystals in the beam, or any other 
 pathology, then all these tests may give distorted answers. In other words, 
 even if twinning is not really present, any test designed to convert the 
 deviation of data from ideality into an estimate of the twinning fraction 
 will give you an alpha  0. So my experience is: if your data are very good, 
 then the tests give good answers; if the data are mediocre or bad, don't 
 necessarily believe the numbers.
 
 Finally, it's not only twinning of P6 that would give you P622, it's also 
 twinning of P3x21, P3x12 that gives P6y22.
 
 Hope this helps,
 
 Kay
 
 
 
 
 On Tue, 28 Jan 2014 17:26:23 +, Bert Van-Den-Berg 
 bert.van-den-b...@newcastle.ac.uk wrote:
 
 Dear all,
 
 I recently collected several datasets for a protein that needs experimental 
 phasing.
 The crystals are hexagonal plates, and (automatic) data processing suggests 
 with high confidence that the space group is P622. This is where the fun 
 begins.
 For some datasets (processed in P622), the intensity distributions are 
 normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest 
 that there is no twinning (twinning fractions  0.05). However, for other 
 datasets (same cell dimensions), the intensity distributions are not normal 
 (eg Z-scores  10). Given that twinning is not possible in P622, this 
 suggests to me that the real space group could be P6 with (near) perfect 
 twinning.
 
 If I now process the normal L-test P622 datasets in P6, the twin-law 
 based tests (britton and H-test in xtriage) give high twin fractions (0.45- 
 0.5), suggesting all my data is twinned.
 Does this make sense (ie can one have twinning with normal intensity 
 distributions)?
 If it does, would the normal L-test datasets have a higher probability of 
 being solvable?
 
 Is there any strategy for experimental phasing of (near) perfect twins? SAD 
 would be more suitable than SIR/MIR? (I also have potential heavy atom 
 derivatives).
 
 Thanks for any insights!
 
 Bert
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 

Re: [ccp4bb] twinning fun

2014-01-29 Thread Keller, Jacob
Two more papers on twinning I found informative:

===

Acta Cryst. (2003). D59, 2004-2016[ doi:10.1107/S0907444903021085 ]

Twinned crystals and anomalous phasing
Z. Dauter
Abstract: Merohedral or pseudomerohedral twinning of crystals cannot be 
identified from inspection of the diffraction patterns. Several methods for the 
identification of twinning and the estimation of the twin fraction are suitable 
for macromolecular crystals and all are based on the statistical properties of 
the measured diffraction intensities. If the crystal twin fraction is estimated 
and is not too close to 0.5, the diffraction data can be detwinned; that is, 
related to the individual crystal specimen. However, the detwinning procedure 
invariably introduces additional inaccuracies to the estimated intensities, 
which substantially increase when the twin fraction approaches 0.5. In some 
cases, a crystal structure can be solved with the original twinned data by 
standard techniques such as molecular replacement, multiple isomorphous 
replacement or multiwavelength anomalous diffraction. Test calculations on data 
collected from a twinned crystal of gpD, the bacteriophage [lambda] capsid 
protein, show that the single-wavelength anomalous diffraction (SAD) method can 
be used to solve its structure even if the data set corresponds to a perfectly 
twinned crystal with a twin fraction of 0.5.

Keywords: twinning; merohedral; pseudomerohedral; anomalous scattering; SAD.

===

Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):99-107. Epub 2007 Dec 5.
Surprises and pitfalls arising from (pseudo)symmetry.
Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD.
Author information
Abstract
It is not uncommon for protein crystals to crystallize with more than a single 
molecule per asymmetric unit. When more than a single molecule is present in 
the asymmetric unit, various pathological situations such as twinning, 
modulated crystals and pseudo translational or rotational symmetry can arise. 
The presence of pseudosymmetry can lead to uncertainties about the correct 
space group, especially in the presence of twinning. The background to certain 
common pathologies is presented and a new notation for space groups in unusual 
settings is introduced. The main concepts are illustrated with several examples 
from the literature and the Protein Data Bank.
PMID: 18094473 [PubMed - indexed for MEDLINE] PMCID: PMC2394827 Free PMC Article


Re: [ccp4bb] twinning fun

2014-01-29 Thread Jrh
Dear Bert,
In my own review:-
http://www.tandfonline.com/doi/abs/10.1080/08893110802360925?journalCode=gcry20#.UulGyGtYCSM
molecular replacement emerged in my mind as the most robust option for 
structure determination in such a case, apart from finding an untwinned crystal 
form of course.
Best wishes,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 28 Jan 2014, at 17:26, Bert Van-Den-Berg bert.van-den-b...@newcastle.ac.uk 
wrote:

 Dear all,
 
 I recently collected several datasets for a protein that needs experimental 
 phasing.
 The crystals are hexagonal plates, and (automatic) data processing suggests 
 with high confidence that the space group is P622. This is where the fun 
 begins.
 For some datasets (processed in P622), the intensity distributions are 
 normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that 
 there is no twinning (twinning fractions  0.05). However, for other datasets 
 (same cell dimensions), the intensity distributions are not normal (eg 
 Z-scores  10). Given that twinning is not possible in P622, this suggests to 
 me that the real space group could be P6 with (near) perfect twinning.
 
 If I now process the normal L-test P622 datasets in P6, the twin-law based 
 tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
 suggesting all my data is twinned.
 Does this make sense (ie can one have twinning with normal intensity 
 distributions)? 
 If it does, would the normal L-test datasets have a higher probability of 
 being solvable?
 
 Is there any strategy for experimental phasing of (near) perfect twins? SAD 
 would be more suitable than SIR/MIR? (I also have potential heavy atom 
 derivatives).
 
 Thanks for any insights!
 
 Bert


[ccp4bb] twinning fun

2014-01-28 Thread Bert Van-Den-Berg
Dear all,

I recently collected several datasets for a protein that needs experimental 
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests 
with high confidence that the space group is P622. This is where the fun begins.
For some datasets (processed in P622), the intensity distributions are normal, 
and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is 
no twinning (twinning fractions  0.05). However, for other datasets (same cell 
dimensions), the intensity distributions are not normal (eg Z-scores  10). 
Given that twinning is not possible in P622, this suggests to me that the real 
space group could be P6 with (near) perfect twinning.

If I now process the normal L-test P622 datasets in P6, the twin-law based 
tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), 
suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher probability of 
being solvable?

Is there any strategy for experimental phasing of (near) perfect twins? SAD 
would be more suitable than SIR/MIR? (I also have potential heavy atom 
derivatives).

Thanks for any insights!

Bert


Re: [ccp4bb] twinning fun

2014-01-28 Thread Dirk Kostrewa

Dear Bert Van-Den-Berg,

as far as I understand this, if you have true P622, process the data in 
P6 and then test for twinning, both the Britton-test and H-test will 
indicate perfect merohedral twinning.
This is because the Britton-test checks for a sudden increase of 
negative intensities after de-twinning, which happens only at twin 
fractions close to 0.5 if the intensities used for de-twinning are the 
same. But this is true if they are related by crystallographic symmetry.
The H-test relates the absolute difference to the sum of the presumably 
twinned intensities, which gives 0 for intensities related by 
crystallographic symmetry, again resulting in twin fractions close to 0.5.
In other words, intensities related by crystallographic symmetry would 
indicate perfect twinning in both of these tests.


A better test for perfect merohedral twinning would be the ratio of 
I^2/I^2 which should be 2 for untwinned and 1.5 for perfectly 
twinned data, tested in the higher space group. These values are 
reported by data processing programs like XDS. Please, be aware that 
these ratios have rather strange values if you have an unusually high 
background (loop fiber diffraction, ice rings, etc.) or extremely weak data.


For a really good discussion of twin tests, see Yeates, Methods. 
Enzymol. 276, 344-358, 1997.


Best regards,

Dirk.

Am 28.01.14 18:26, schrieb Bert Van-Den-Berg:

Dear all,

I recently collected several datasets for a protein that needs 
experimental phasing.
The crystals are hexagonal plates, and (automatic) data processing 
suggests with high confidence that the space group is P622. This is 
where the fun begins.
For some datasets (processed in P622), the intensity distributions are 
normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) 
suggest that there is no twinning (twinning fractions  0.05). 
However, for other datasets (same cell dimensions), the intensity 
distributions are not normal (eg Z-scores  10). Given that twinning 
is not possible in P622, this suggests to me that the real space group 
could be P6 with (near) perfect twinning.


If I now process the normal L-test P622 datasets in P6, the twin-law 
based tests (britton and H-test in xtriage) give high twin fractions 
(0.45- 0.5), suggesting all my data is twinned.
Does this make sense (ie can one have twinning with normal intensity 
distributions)?
If it does, would the normal L-test datasets have a higher 
probability of being solvable?


Is there any strategy for experimental phasing of (near) perfect 
twins? SAD would be more suitable than SIR/MIR? (I also have potential 
heavy atom derivatives).


Thanks for any insights!

Bert


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***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***