board On Behalf Of Thomas, Leonard
M.
Sent: Monday, March 25, 2024 7:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] twinning or not?
WARNING: This message was sent by an external party. Report suspicious messages
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Hello,
I have run into a very odd
You can get apparent twinning if neighbouring spots are overlapped in any direction, and that may be worse with a home source with larger beam divergence. In that case a weak reflection may be corrupted by a neighbouring strong reflection, leading to intensity statistics characteristic of
Hi Len,
a possible theory: your crystals may be macroscopically twinned, i.e.
consisting of single crystals attached to each other in the way that the twin
operation describes.
At your home source, you employ a rather big beam that hits more than one
single crystal. So the data appear twinned.
Hello,
I have run into a very odd situation. Upon collection and data processing on a
crystal on my home source all pointers seemed to show twinning. Was not
surprised since previous crystals under different but related conditions have
showed significant twinning though the cell dimensions
] Im Auftrag von Marina
Ley
Gesendet: Donnerstag, 11. Juli 2019 12:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] twinning problems
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Hello everyone,
I have the following problem:
I have some really good data sets of about 1.6
Hello Marina,
In short: at first I'd build the model and refine it with the untwinned P3(2)21
data set until convergence. Then, I'd process all other data sets (including
the twinned ones) in that space group as well. If using XDS, I'd use the
XDS_ASCII.HKL of the untwinned data set as
Are all the trigonal cells related?
Eleanor
If so, you can use your untwinned data set as a guide to pointless to make
sure all others are in the same indexing system, assign all the spacegroups
to P3221
Then just start refinement with the key word twin from your good model.
Eleanor
On Thu, 11
Hello everyone,
I have the following problem:
I have some really good data sets of about 1.6 A which could be
processed in P 6 2 2 as well as in P 3 2 1.
Intensity statistics tests indicate twinning (merohedral, twinning
law: -h, -k, l, in P 3 2 1).
But I did not find a good MR solution (R
It is very common for a trigonal spacegroup H 32 to masquerade as C 2 2 21
Here is the log file for other cell.
Note that it is possible to reindex it with two cell dimensions equal and a
beta angle of 63 -
And the self rpotation shows a large rotation at 120 degrees
So go back to the data
Unit cell dimensions don’t really matter here. If it’s a centred lattice you
won’t be able to index it correctly in a primitive system even though C222 and
P222 both have a<>b<>c and alpha=beta=gamma=90.
Ditlev
---
Ditlev E. Brodersen
Lektor, Associate Professor
Department of Molecular
Hi Vijyay,
Did you tried with P212121 system?. RCSB has one structure with similar
unitcell and the corresponding pdb code is 3BMA. If you have not tried then
I hope it will solve the problem.
Thanks
damo
On Thu, Nov 29, 2018 at 11:44 AM Vijay Jayaraman <
bkvijay.jayara...@gmail.com> wrote:
>
Hi Vijay,
it could be pseudo-merohedral twinning of C2. In that case, any of the three
axes could be the unique one, so you must test all three possible settings.
Hopefully, reginement works well in one of these.
Best wishes,
Kay
On Thu, 29 Nov 2018 14:58:52 +, Vijay Jayaraman
wrote:
Hi all,
The data that we collected recently is in space group C 2 2 21 and appears to
be twinned. I could not find a twin law which I can use to detwin the data. The
R and R free doesn't drop below 0.4 even after multiple rounds of manual and
automated refinement. I have also attached the
Diederichs<mailto:kay.diederi...@uni-konstanz.de>
Verzonden: woensdag 1 maart 2017 23:38
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] Twinning and R-Free
Hi Alun,
that's difficult to understand for me. It is my understanding that for an
imperfect m
Hi Alun,
1. What does phenix.xtriage think of the dataset?
2. What kind of redundancy do you have in the dataset?
3. Sometimes with a large crystal and a small beam the twin fraction varies as
you rotate the crystal and illuminate different parts of the crystal (which can
have different twin
Hi Alun,
that's difficult to understand for me. It is my understanding that for an
imperfect model, refmac will indicate a twin fraction >0 even if in reality it
is 0. But alpha=0.372 sounds too high for that.
My questions would be -
a) is it a single dataset, or did you merge ? If the latter,
Hi Everyone,
I have a (2.5 - 2.3 Angstroms) data set the process as I4 or I222.
Aimless indicates twinning in both space groups and all the lower
symmetry space groups consistent with the reduced cell. Molecular
replacement works in I4 but not I222 etc. I can see new density for a
ligand we
Hi Rhys,
We had a similar problem where initial data processing suggested P6522
space group but the content of the crystal was too large to fit in the unit
cell (one well known symptom for twining). I reprocessed the data in P6,
P312, P321 and finally the solution was obtained in P6 (P65).
Hi,
I mentioned that R factors went down because they went down dramatically, from
33/36% to 22/24% (which shows that application of twinning does the right job
even if such R-factors cannot be compared), and I have ‘seen’ such dramatic
change for one of my small molecule refinements in old
Hi,
since several people mentioned R factors in this conversation I thought I
remind that R-factors are not comparable between refinements using twinning
and not. For example, R-factor decrease after switching to twin refinement
doesn't mean much; you can't use R factor drop as an argument for
As Aleks is suggesting, lower symmetry would be better.
I had similar issues with one of my protein with unit cell dimensions 57,
57, 256. Xtriage suggested suggested three 2-fold merohedral twin operators
(-h,-k,l; h,-h-k,-l; and –k,-h,-l). I went to lower symmetry (P31) and
applied twinning law
Dear Rhys,
I was not aware that twinning is not possible in P6322 however I agree with
Randy’s advise to check the lower symmetry P63 etc.
We were just collecting data which was apparently P6322 (according to automated
DLS processing: pointless) but the cell dimensions and our knowledge of the
Dear Rhys,
There's one important consideration to start from, which is that the space
groups P6322 and C2221 with their associated cell dimensions are two different
ways to describe the shapes of the unit cells and the positions of the spots.
You can see this by running
Dear All,
As I have approached my crystallography from a biological perspective,
sometimes so of the more mathematical/geometrical aspects sometimes perplex
me. I was wondering if anyone would be able to clarify what is going on
with some problematic crystals I'm working on.
I've grown crystals
e previous paragraph.
Colin
-Original Message-
From: Ethan A Merritt [mailto:merr...@u.washington.edu]
Sent: 06 November 2015 18:38
To: Nave, Colin (DLSLtd,RAL,LSCI)
Cc: ccp4bb
Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon
Process; was RE: [ccp4bb
7:33
> To: Nave, Colin (DLSLtd,RAL,LSCI)
> Cc: ccp4bb
> Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a
> Single-Photon Process; was RE: [ccp4bb] Twinning Question
>
>
> On Thursday, 05 November 2015 11:51:49 AM
> colin.n...@diamond.ac.uk<mailto:colin.
[mailto:merr...@u.washington.edu]
Sent: 04 November 2015 21:59
To: Nave, Colin (DLSLtd,RAL,LSCI)
Cc: ccp4bb
Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon
Process; was RE: [ccp4bb] Twinning Question
On Wednesday, 04 November, 2015 09:48:13 Colin Nave wrote:
> Domen
On Behalf Of Colin Nave
Sent: Thursday, November 05, 2015 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon
Process; was RE: [ccp4bb] Twinning Question
Ethan
My understanding is that one would have to have separate springs for each
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom
> Bellini
> Sent: 03 November 2015 18:05
> To: ccp4bb
> Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a
> Single-Photon Process; was RE: [ccp4bb] Twinning Question
>
> Dear All,
>
>
>
>
Dear Kristof,
Apart from things pointed out, a possibility to consider would also be the
presence of two different crystal types--of different compounds--in the same
reaction vessel.
Best regards,
Navdeep
---
On Wed, Aug 13, 2014 at 11:00:18AM +0200, Kristof Van Hecke wrote:
Dear,
I’m
Dear,
I’m struggling with the following (small molecule) problem:
We are trying to solve the structure of a metal-organic framework containing a
chiral compound.
The space group is most probably Pc, but when refining, SHELX gives the error
“Possible racemic twin or wrong absolute structure -
Hi, Pc may not be the space group for your crystal, if the molecule is
chiral. Seems like the data were forced to be reduced to a mirror_related
SG. Lijun
On Aug 13, 2014 2:00 AM, Kristof Van Hecke kristofrg.vanhe...@gmail.com
wrote:
Dear,
I’m struggling with the following (small molecule)
Twin laws are possible if there are 2 ways to index your cell, and
non-merefedral twinning is possible in any system depending on the cell.
I am not sure of the small molecule tools to check twinning though.
Eleanor Dodson
On 13 August 2014 05:58, Lijun Liu lijunli...@gmail.com wrote:
Hi, Pc
Hi folks
Pc *must* have both enantiomers, since it's got a glide plane ( =
mirror + translation parallel to mirror).
So the sample *cannot* be enantiopure if the space group is Pc (or P2/
c)...
BTW, Pc isn't a centrosymmetric space group.
Unless I'm wrong...
On 13 Aug 2014, at Wed13 Aug
Betreff: Re: [ccp4bb] Twinning in space group Pc
Hi, Pc may not be the space group for your crystal, if the molecule is chiral.
Seems like the data were forced to be reduced to a mirror_related SG. Lijun
On Aug 13, 2014 2:00 AM, Kristof Van Hecke
kristofrg.vanhe
Betreff: Re: [ccp4bb] Twinning in space group Pc
Hi, Pc may not be the space group for your crystal, if the molecule is
chiral. Seems like the data were forced to be reduced to a mirror_related
SG. Lijun
On Aug 13, 2014 2:00 AM, Kristof Van Hecke kristofrg.vanhe...@gmail.com
wrote
how many (quasi) equivalent positions do you think the chiral compound can
adopt in the organo-metal framework?
Or the organo-metal framework in the crystal?
If it's two, you can probably do alternate conformations - if there are more,
it could become impossible, even in P1.
Mark J van Raaij
Dear Kristof,
Have you tried to solve it with the new SHELXT? You can force it to
consider only chiral (Sohnke) space groups by putting -c on the command
line.
Best wishes, George
On 13.08.2014 11:00, Kristof Van Hecke wrote:
Dear,
I’m struggling with the following (small molecule)
: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Dear Herman
On 24 April 2014 22:32,
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:
The X-ray coherent length is depending on the crystal, not the synchrotron and
my gut feeling is that it is at least several hundred unit
, April 24, 2014 7:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Dear Herman
On 24 April 2014 22:32,
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:
The X-ray coherent length is depending on the crystal, not the synchrotron and
my gut
] On Behalf
Of Ian Tickle Sent: Thursday, April 24, 2014 7:01 PM To:
CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning
VS. Disorder
Dear Herman On 24 April 2014 22:32,
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com
wrote:
The X-ray coherent length is depending
variation of
magnitude proportional to the degree of variation in that direction.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ian Tickle Sent: Thursday, April 24, 2014 7:01 PM To:
CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS.
Disorder
@JISCMAIL.AC.UK] on behalf of James Holton
[jmhol...@lbl.gov]
Sent: Thursday, April 24, 2014 6:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
There are two kinds of coherence length: transverse and longitudinal.
Longitudinal coherence is often quoted
Thanks to all—I’ve got the paper now
JPK
From: Keller, Jacob
Sent: Friday, April 25, 2014 1:58 PM
To: 'Oliver Zeldin'
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Does anyone know of a place where one can obtain this reference for free? I
would contact
...
Sincerely,
Chen
On Apr 25, 2014, at 3:21 PM, Keller, Jacob kell...@janelia.hhmi.org wrote:
Thanks to all—I’ve got the paper now
JPK
From: Keller, Jacob
Sent: Friday, April 25, 2014 1:58 PM
To: 'Oliver Zeldin'
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] AW: [ccp4bb] Twinning VS
, unit cell etc. to find out what is going on.
My 2 cents,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Chen Zhao
Gesendet: Donnerstag, 24. April 2014 22:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinning VS. Disorder
Dear all,
Hello! I am kinda confused
. April 2014 22:13
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] Twinning VS. Disorder
Dear all,
Hello! I am kinda confused and am thinking about the definition of
twinning and disorder. I am just a starting student and might make some
fundamental mistakes.
1) Twinning is a macroscopic
Dear Herman
On 24 April 2014 22:32, herman.schreu...@sanofi.com wrote:
The X-ray coherent length is depending on the crystal, not the synchrotron
and my gut feeling is that it is at least several hundred unit cells, but
here other experts may correct me.
I assume you meant that the
One can have microdomains without a significant increase in misorientation
e.g. shift dislocations between domains. However, some misorientation is bound
to occur. Not sure I understand your statement And as the blocks get
smaller, the distinction between changing unit cell parameters and
and mosaic block interchangeably. Let
me know if you are making a distinction
-Original Message-
From: Keller, Jacob [mailto:kell...@janelia.hhmi.org]
Sent: 14 March 2014 16:32
To: ccp4bb
Subject: Re: [ccp4bb] twinning problem ?
At the limit, the microdomain picture leads to powder-diffraction
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] twinning problem ?
Hi Zbyszek
I think this has deviated significantly from twinning problems!
I certainly don't claim the 1998 study was typical. The crystal was large by
present day standards, no cryoprotectant was used and non uniform
drying/cooling rates might
Dear Jacob,
Measurement of the reciprocal space maps at reflections with triple axis
diffractometry allows experimental separation of mosaicity and strain
(variation in unit cell parameter) effects. See eg Boggon et al 2000 Acta Cryst
D56, 868-880 http://dx.doi.org/10.1107/S090744495837 for
Unless you are interested in finding curious objects, what would you do with
protein quasicrystal? The practices of macromolecular crystallography is about
determining 3-dimensional structure of objects being crystallized. Protein
quasicrystal are really unlikely to diffract to high enough
[mailto:kell...@janelia.hhmi.org]
Sent: 13 March 2014 15:55
To: ccp4bb
Subject: Re: [ccp4bb] twinning problem ?
Unless you are interested in finding curious objects, what would you do with
protein quasicrystal? The practices of macromolecular crystallography is about
determining 3-dimensional
On 03/13/2014 10:55 AM, Keller, Jacob wrote:
Unless you are interested in finding curious objects, what would you do with
protein quasicrystal? The practices of macromolecular crystallography is about
determining 3-dimensional structure of objects being crystallized. Protein
quasicrystal are
cases, such a set up could reveal certain types of twinning
(so I have left the subject of the email unchanged!)
Regards
Colin
-Original Message-
From: Zbyszek Otwinowski [mailto:zbys...@work.swmed.edu]
Sent: 13 March 2014 21:33
To: ccp4bb
Subject: Re: [ccp4bb] twinning problem ?
On 03
Zbyszek - do you have any measure of unintegrated streaks?
It could be a help to at least have a rough score.
Eleanor
On 11 March 2014 20:04, Zbyszek Otwinowski zbys...@work.swmed.edu wrote:
Shape of the diffraction spots changes in the statistical disorder --
twinning continuum. At both
Dear Stephen,
I have seen a similar effect in the structure of
F1-ATPase complexed with the full length inhibitor protein. The inhibitor is a
dimer, and it actually couples 2 copies of the ATPase, but it crystallised with
only one copy of the ATPase per asymmetric unit.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] twinning problem ?
Dear Stephen,
I have seen a similar effect in the structure of
F1-ATPase complexed with the full length inhibitor protein. The inhibitor is a
dimer, and it actually couples 2 copies of the ATPase
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] twinning problem ?
Dear Stephen,
I have seen a similar effect in the structure of
F1-ATPase complexed with the full length inhibitor
protein. The inhibitor is a dimer, and it actually
couples 2 copies of the ATPase, but it
crystallised
: Wednesday, March 12, 2014 12:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] twinning problem ?
Dear Stephen,
I have seen a similar effect in the structure of
F1-ATPase complexed with the full length inhibitor protein. The inhibitor is
a dimer
For any sample, crystalline or not, a generally valid description of
diffraction intensity is it being a Fourier transform of electron density
autocorrelation function.
I thought for non-crystalline samples diffraction intensity is simply the
Fourier transform of the electron density, not its
On 03/12/2014 04:15 PM, Keller, Jacob wrote:
For any sample, crystalline or not, a generally valid description of
diffraction intensity is it being a Fourier transform of electron density
autocorrelation function.
I thought for non-crystalline samples diffraction intensity is simply the
The Fourier transform of electron density is a complex scattering amplitude
that by the axiom of quantum mechanics is not a measurable quantity. What is
measurable is the module squared of it. In crystallography, it is called either
F^2 (formally equal F*Fbar) or somewhat informally diffraction
On 03/12/2014 09:02 PM, Keller, Jacob wrote:
The Fourier transform of electron density is a complex scattering amplitude
that by the axiom of quantum mechanics is not a measurable quantity. What is
measurable is the module squared of it. In crystallography, it is called either
F^2 (formally
Sorry - hadnt finished..
The twinning tests are distorted by NC translation - usually the L test is
safe, but the others are all suspect..
On 11 March 2014 14:09, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
What is the NC translation? If there is a factor of 0.5 that makes SG
Shape of the diffraction spots changes in the statistical disorder --
twinning continuum. At both ends spots shape is like in diffraction from
crystals without such disorder. However, in the intermediate case,
electron density autocorrelation function has additional component to
one resulting
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
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
-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
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
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
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
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
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
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
Dear Bulletin Board,
Prodded by pdb annotators, which are very hesitant to accept coordinate files
when their Rfactor does not correspond with our Rfactor, I had a look again
into some old data sets, which I suspect are twinned. Below are the results of
some twinning tests with the Detwin
-3292
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: Thursday, June 20, 2013 6:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Twinning problem
Dear Bulletin Board,
Prodded by pdb annotators, which are very
Hello everyone
sorry for the intervention with some basic questions regarding twinning
In continuation with the discussion with Liang i would like to ask a
question which i faced..i have also solved a structure and the statistics
depending on twin laws as described through xtriage, phenix is as
Hi, All,
I got a set of P2(or P21) data for MR. However, the Phenix-Xtriage
indicated that it could be a pseudo-merohedral twinning. Does anyone know
how to deal with such kind of twinning problem? Thanks.
Best,
Liang
get the twin law and either refine with phenix.refine twin_law=-h,-k,l or
whatever it suggests, or just add into your Refmac script the line TWIN and it
will figure out the twin law for you.
You can also detwin data but then you might be throwing away a lot of data.
We've now had two cases
Hello,
I would suggest to use several tools (in addition to Phenix's) - CCP4's
detwin, the plots generated by truncate before detwinning, the Yeates
twinning server and there might be others - to get a good idea of what
the twinning fraction is.
Here we've had success using CCP4's detwin to
Dear John,
In a hexagonal crystal class the possible point groups are
P3 (only a 3-fold axis)
P321(3-fold plus 2-fold relating hkl and kh-l)
P312 (3-fold and 2-fold relating (hkl and -k,-h,-l)
P6 ( 6 fold axis only)
P622 (6-fold plus 2-fold relating hkl and k,h,-l)
pointless will tell you which
@JISCMAIL.AC.UK
Subject: [ccp4bb] twinning in hexagonal system
Hello All,
This is regarding twinning in a data set.
I collected a native data set to resolution, 1.8 A. I used XDS suite
to process and scale the data set. It scaled well in P622 and I found
systematic absence (l=6n present).
Hence
Hello All,
This is regarding twinning in a data set.
I collected a native data set to resolution, 1.8 A. I used XDS suite
to process and scale the data set. It scaled well in P622 and I found
systematic absence (l=6n present).
Hence thought the space group may be P6122/P6522. SFCHECK did
Hello
Space groups with point groups 622 and 432 merohedral twinning is not possible
(they are the highest groups possible for proteins).
If you could merge in 622 it means that Rmerge was very small. It is very
likely that point group is either 622 or 6 with very strong rotational symmetry
Hi all,
I am worried about mixing working and free reflexions during TWIN refinement.
Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of
twinning?
I mean in that way that the possible twinning operators are taken into account
for a following
refmac job using the TWIN
Hi all,
I am worried about mixing working and free reflexions during TWIN refinement.
Is there any keyword in UNIQUEIFY to generate a R-free flag in the case of
twinning?
I mean in that way that the possible twinning operators are taken into account
for a following
refmac job using the TWIN
This is a problem not properly addressed - if you generate your
FreeRflags in the highest possible Laue group for a system - eg P6/mmm
if you SG is trigonal, then add these to the lower symmetry reflection
list you are safe. It really should be done at the pointless stage but
it isnt..
Here
Thanks Ian,
I understood now.
Great lesson for me.
Best regards
Fulvio Saccoccia
Il giorno ven, 20/05/2011 alle 18.14 +0100, Ian Tickle ha scritto:
The true values of the components of the twin can't in general be
equal since they come from _different_ reflections that are unrelated
by
Thanks Ian,
I tried to do this:
I took the file containing
hkl I and sigI
and generated a new file containing
hkl I/2 and sigI
because I know, from the refined structure that the twin fraction is
nearly 0.5. Now, using this new file the wilson plot give me a more
reliable estimated B
No, simply applying a single overall scale factor to the intensities
can't possibly make any difference to the Wilson B since the fall-off
with resolution will remain unchanged. The Wilson plot is a plot of
ln(mean(I')/S) in shells of constant d* vs d*^2, where I' is I
corrected for symmetry and
Thanks Ian,
but your reply confused me a little.
I hope you can explain me where I was wrong.
I know that
I(twin)=tf*I(h1)+(1-tf)*I(h2)
I supposed that having tf=0.5 I could take the I(twin), dividing by 2 I
will get both I(h1) and I(h2), that are the two component (that are
equal in
The true values of the components of the twin can't in general be
equal since they come from _different_ reflections that are unrelated
by the true crystal symmetry (they are only related by the
pseudo-symmetry of the twin).
Let's say:
Itwin(h1)=tf*I(h1)+(1-tf)*I(h2)
where I(h1) and I(h2) are
Hi Fulvio
There are 2 different issues here: the Wilson plot scale B factor on
the one hand and Wilson statistics on the other. The first are not
affected by twinning since they depend only on the intensity averages
in shells. The second refers to the distribution of intensities (i.e.
the
Ok, so another question in my mind:
the data come from a collection interrupted after the first 200 frames
and restarted after 1 hour to recover the missed 160 frames.
The first and second group of frames, if separately indexed, give cell
parameter values that differ of about 1A for axes and 1
Hi Fulvio,
Yes, it can. An increase in cell parameters can indicate a failure of the
cooling system or (more likely) radiation damage of the crystal.
For refinement you probably do not need all those 360 frames,
unless you collected thin frames and your space group is P1
I suggest you integrate
That translation is interesting - R3 indexed as hexagonal has a
crystallographic translation of 0.667 0.333 0.333, so this one
indicated by SFCHECK is related.
The twinning is not very severe so it should refine OK from the PHASER
solution.
Is that so?
Eleanor
On 04/08/2011 05:50 AM,
this can screw up your statistics on twinning and this can be due to
the NCS rotation
axis (or will be based on what you say) parallel to a crystallographic
symmetry axis.
just check that. it should still refine though but this will have
opposite effect to twinning,
so it can be
Yes - that is true.
Any crystal might be split, and give diffraction with overlapping
lattices- ie show non-merohedral twinning. If you are lucky/careful you
might only get a few spots which overlap after integration of one of the
lattices- not enough to be detected as twinning from the
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