Hi Len,
Twinning does not have to be a random spatial distribution within a crystal.
You can have large discrete domains that are effectively untwinned smaller
crystals assembled into the larger one – we have had several cases with
back-to-back growth of two crystals. In some cases, the
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 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
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:
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 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
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
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
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)
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
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 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
You are welcome. Let me also for the benefit of others who may
search the archives in the future, let me correct two errors
below - (typo and a miss-recollection).
Specially, I was thinking that phenix.refine was now able to refine
multiple twin laws, but according to Nat Echols on the phenix
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
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
Dear John,
It is not the sequence identity/similarity that counts, but how similar
the protein folds are. For many protein families, the fold is identical
although the sequence identity is very low. With 25% sequence identity
and presumably a protein from the same family, I give you a good chance
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
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
what does the twinning analysis by Phenix tell?
if you haven't done it yet i would think you should run the processed
data through phenix Xtriage and see
what is the twinning analysis tell you.
It also is a good program to solve your space group issues.
I think you might need a mtz file or
Respected Madam,
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
Hello
I guess you are using 5.5. In this version in the beginning twin fractions are
just initial values. They need to be refined. This are potential twin
operators. Further down in the log file there should be Rmerge for each twin
operator and estimated twin fractions. What are they? Can you
,
or refines against the original twinned data like (I believe) phenix and
shelxl.
Thx, BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: Tuesday, August 04, 2009 1:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
.
Thx, BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: Tuesday, August 04, 2009 1:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twinning
Try refinement with the newest REFMAC which will take twinning into
account.
...@jiscmail.ac.uk]
On
Behalf Of Eleanor Dodson
Sent: 23 April 2009 15:59
To: Kumar
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twinning or not?
Look at the moment plots after scalepack2mtz; if these are normal it
seems very unlikely you have twinning..
Eleanor
I know this subject
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Eleanor Dodson
Sent: 23 April 2009 15:59
To: Kumar
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twinning or not?
Look at the moment plots after scalepack2mtz
I dont think that is a twinning law, and that SG and cell dimensions are
unlikely to be twinned.
It could be really P1 I suppose with a twin operator -h,k,-l - ie the
SYM op is actually a twin operator..
But twinning usually shows up in the intensity statistic plots - have
you looked at the
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
People dont read the CCP4 documentation on twinning! Grrr
PG P3 can have 3 twinning operators; and these are:
k,h,-l ( or symm equiv) - if this is a crystallographic operator the
PG becomes P321
-h,-k,l (or symm equiv) - if this is a crystallographic operator the PG
becomes P6
-k,-h,-l (or
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
Dear J.Kryst -
I am basically very puzzled to see that a 3.1 A structure has R and
Rfree of 15.3 and 23.8 % respectively !
Is that the diffraction limit of the crystal or is it a home dataset
collected with rather short exposures?
Is the Wilson B very low by any chance ?
As for the gab,
There might be a few reasons for these R-values which seem to contradict
experience:
1) The starting phases result from MR where the model is very close and
from a data set at higher resolution. If your 3.1A data are of
respectable quality, the model would still correspond well to the
anneal to
avoid previous bias.
J.
- Original Message -
From: Tim Gruene [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, October 23, 2007 4:07 AM
Subject: {Spam?} Re: [ccp4bb] Twinning
There might be a few reasons for these R-values which seem to contradict
experience:
1
Hi,
How good/bad is the geometry of your model (as judged by the usual criteria
either in procheck of molprobity) ?
Boaz
- Original Message -
From: john kryst [EMAIL PROTECTED]
Date: Tuesday, October 23, 2007 7:04
Subject: [ccp4bb] Twinning
To: CCP4BB@JISCMAIL.AC.UK
Hi
PROTECTED]
AC.GWDG.DE
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, October 23, 2007 4:07 AM
Subject: {Spam?} Re: [ccp4bb] Twinning
There might be a few reasons for these R-values which seem to
contradict experience:
1) The starting phases result from MR where the model is very close and
from a data
should anneal to avoid previous bias.
J.
- Original Message - From: Tim Gruene [EMAIL PROTECTED]
AC.GWDG.DE
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, October 23, 2007 4:07 AM
Subject: {Spam?} Re: [ccp4bb] Twinning
There might be a few reasons for these R-values which seem
Hi John,
if I understand the make_cv_twin.inp correctly, then this script
takes care about separating reflections related by the twin law to
avoid a potential bias of the Free-R set with twin-law-related
reflections from the working set. At least, in the source of this
script I read the
try using phenix.refine and use TLS. it might help lowering Rfree (or
raising Rwork).
P
2007/10/23, john kryst [EMAIL PROTECTED]:
Hi CCP4bb ,
Thanks for your suggestions... here is the summary of the
structure...
I am working in deletion and point mutants. I have a mutant
Hi Dirk,
Nice cross validation flags for twin refinement do obey the twin law:
if (h,k,l) is in the free set, then (k, h, -l) should be as well.
Same is/should be true for work set btw.
In phenix, we generate test reflections that follow the lattice
symmetry (*). This means that even if you do
Hi Folks,
Thanks for the many useful responses. The answer to the conundrum is
indeed as some people suggested P212121 with a=b and twin operation
kh-1.
This is a very high-resolution dataset and I am using shelxl to refine
which allows inclusion of twinning (as does phenix.refine
Dear Eleanor,
many thanks for all your help and suggestions. We finally have solved
the mutant structure. The trick was to use the pseudo translation (there
was not any 2 fold axis in the self rotation) with MOLREP which found
two molecules and then applied the pseudo translation to provide
Dear Eleanor,
Yes the native is a dimer and we did the search using the dimer as a
model but we had similar results (i.e. all programs find one molecule).
The graphs from TRUNCATE show rather normal and I am attaching a gif
file with the plot for the cumulative intensity.
As for
You dont say whether the molecules in the native cell form a dimer - if
so I would search with that (you may need to turn off the packing search)
Or whether there is a pseudo translation vector in the mutant form..
Or what the data analysis graphs from TRUNCATE show - are they normal?
Eleanor
Hi Demetres,
not sure if this is going to be usefull, but here I go.
Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.
There is no obvious 'perfect'
Oh dear - this is tricky!
You could have a dimer in the asymmetric unit, or two monomers in the
asymm unit which generate dimers using the crystallographic 2 folds.
Things worth checking -
What does the self rotation show? Is there a clear 2 fold axis which is
different from the
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