Hi all, I have an anisotropic native data sets with heavy atoms and I want
to use the anomalous signal for the final refinement. Does anybody know how
to run the anisotropic sharpening and output the F(+)_ISOB, F(-)_ISOB? It
seems both the anisotropy server (UCLA) and phaser_anisotropy analysis
Hi,
I also have a question concerning anisotropic data. Collected a data set and
the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A).
So my first question is how to handle these data. I got only experience with
normal data using the ccp4 suite. Are there any
A first concern with that extreme anisotropy is at the integration and
scaling stages.
Large swaths of your detector are empty of reflections, but they will still
bias the way reference profiles are calculated at integration; while the
lots of reflections with intensities around 0 (but with
in
the third direction).
HTH,
Fred.
Message du 09/06/10 14:33
De : Marie Lacroix
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : [ccp4bb] Anisotropic data and an extremely long c axis
Hi,
I also have a question concerning anisotropic data. Collected a data set and
the best
Hi
Many years ago I coded up integration using anisotropic resolution
limits for Mosflm - it seemed to work well, but the refinement
programs available at the time really didn't like huge regions of
reciprocal space having no data in them - they preferred to have
measurements there with
Dear Marie,
I believe that the first of Fred's explanations can mostly be corrected for by
scaling (and it could partly be overcome by longer exposure times as long as
radiation damage does not kick in).
In your case, where one cell axis is about 10x as long as the other two, Fred's
second
lacroix.ma...@rocketmail.commailto:lacroix.ma...@rocketmail.com
Gesendet: Mittwoch, den 9. Juni 2010, 16:01:56 Uhr
Betreff: Re: AW: AW: [ccp4bb] Anisotropic data and an extremely long c axis
Does this coincide with the direction of better diffraction ?
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg
Frederic VELLIEUX wrote:
Anisotropy in the diffraction pattern could simply be due to the shape of the
crystals. The intensity of diffraction is a function of the volume of
diffracting matter that is hit by the X-ray beam. Think for example of a thin
plate crystal, which you rotate in the
I vaguely recall an email from Kay Diderich about 3 years ago to this board but
I couldn't find it, describing a neat method of distorting the diffraction
image to meet the ellipsoidal characteristics of the anisotropic diffraction.
But I might be confusion myself, anyhow Kay can you comment on
On 09/06/2010 16:49, James Holton wrote:
Operationally, I recommend treating anisotropic data just like
isotropic data. There is nothing wrong with measuring a lot of zeros
(think about systematic absences), other than making irrelevant
statistics like Rmerge higher. One need only glance at
Frank von Delft wrote:
On 09/06/2010 16:49, James Holton wrote:
Operationally, I recommend treating anisotropic data just like
isotropic data. There is nothing wrong with measuring a lot of zeros
(think about systematic absences), other than making irrelevant
statistics like Rmerge higher.
But at some point, getting a clear map might not be the goal. If you're in refinement mode, the weak reflections also provide information that your model needs to fit. I find I/sig(I) (or I/sig(I)) to be about as useful as
Rmerge (or its relatives). Ron
On Wed, 9 Jun 2010, James Holton
Katja Schleider schrieb:
Hi everybody,
is there a way to improve crystals that diffract strongly anisotropic?
We got data between 2.5 and 4.0 A and scala says we should cut these
data at 3.9 A. It's such a... I want to solve this structure!
greetings
Katja
Hi Katja,
check out
Hi everybody,
is there a way to improve crystals that diffract strongly anisotropic? We got
data between 2.5 and 4.0 A and scala says we should cut these data at 3.9 A.
It's such a... I want to solve this structure!
greetings
Katja
__
Do You
Hi Katja,
you may consider trying this:
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
but PLEASE do not deposit corrected data to PDB.
Also, I would just try to refine the structure and see how it goes (see
if you really need to use the above tool).
Pavel.
On 10/5/09 8:21 AM, Katja
I refrained from entering the fray during last month¹s discussion of
anisotropic data in refinement, but I wonder if there is any consensus
regarding treatment.
It seems to me that during refinement scaling to calcs should be superior to
even the very elegant likelihood methods. Another problem
I can't comment about your other questions but I will weigh in
on your refinement question.
I may misunderstand exactly what you mean by Fcalcs become
anisotropic but by my understanding, the answer is yes. I have
taken a model and set of structure factors from the PDB when the
model was
On 10/5/09 9:46 AM, Ben Spiller wrote:
For the refinement case, do others think that Fcalcs become
anisotropic? Or that the liklihood method developed by Read and
others is superior even at late stages?
FYI:
In phenix.refine (or CNS) the total model structure factor is defined as:
Fmodel
Concerning what Pierre asked, one point to remember at structure
refinement is to test and probably use TLS tensors. I had one case with
serious anisotropy in the data due a libration axis parallel to a
crystallographic axis. TLS lowered dramatically the R's and maps were neatly
better.
Dear all,
I am working on a data set which is severely anisotropic, with
diffraction limits of 2.6 A along the a* and b* direction but only 3.3 A
along the c* direction. I attached a screen shot of the Anisotropic
analysis (FALLOFF) output graph from SCALA.
My question is : what is the best
Dear Pierre,
there is also a Diffraction Anisotropy Server at UCLA that does
some scaling and truncating of anisotropic data, possibly making your
crystallographic life a bit easier ... but I don't have personal
experiences with this approach.
Have a look at
On Nov 22, 2007, at 14:43, Kay Diederichs wrote:
Pierre Barraud schrieb:
Dear all,
I am working on a data set which is severely anisotropic, with
diffraction limits of 2.6 A along the a* and b* direction but only
3.3 A along the c* direction. I attached a screen shot of the
Anisotropic
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