>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" an
hink we are both using "domain" 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
4 7:04 PM
To: CCP4BB@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
d
he various
effects.
Of course, in some 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
Sub
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 r
>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 r
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
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 eq
>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 diffractio
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
Four
>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 it
atures
> of the crystallized protein?
>
> JPK
>
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew
> Leslie
> Sent: Wednesday, March 12, 2014 12:25 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject:
t;
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Andrew Leslie
> Sent: Wednesday, March 12, 2014 12:25 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] twinning problem ?
>
> Dear Stephen,
>
>
Behalf Of Andrew
Leslie
Sent: 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
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.
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 wrote:
> Shape of the diffraction spots changes in the statistical disorder <-->
> > twinning continuum. At both ends spots shape is l
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 f
Hi,
If there's an NCS translation, recent versions of Phaser can account for it and
give moment tests that can detect twinning even in the presence of tNCS. But I
agree with Eleanor that the L test is generally a good choice in these cases.
However, the fact that you see density suggests that
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 wrote:
> What is the NC translation? If there is a factor of 0.5 that makes SG
> determination complicated..
> Elean
What is the NC translation? If there is a factor of 0.5 that makes SG
determination complicated..
Eleanor
On 11 March 2014 14:04, Stephen Cusack wrote:
> Dear All,
> I have 2.6 A data and unambiguous molecular replacement solution for
> two copies/asymmetric unit of a 80 K protein for a cry
Dear All,
I have 2.6 A data and unambiguous molecular replacement solution
for two copies/asymmetric unit of a 80 K protein for a crystal integrated
in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9.
Refinement allowed rebuilding/completion of the model in the noraml way
but the
26-5036
FAX: 1-650-926-3292
-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 annotato
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 progr
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 f
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
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 wi
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
To the CCP4 community,
I have collected data from an RNA molecule that extends to 2.9 angstroms,
exhibit mosaicity less than 0.9 degrees and generally show nice, round spots.
The crystals look cubic and are not birefringent (suggesting a cubic lattice).
However, the data index poorly with
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