Dear Ian and James,
Here I learned something new. I assumed that coherence length would be limited
by crystal quality, e.g. mosaicity and microdomains etc. which apparently is
not the case. For me, one of the characteristics of twinning is that there is
no interference between the twin domains.
Is the following being neglected?
In a crystal with these putative mosaic microdomains, there will be
interference between microdomains at their edges/borders (at least), but since
most microdomains are probably way smaller than the coherence length of 3-10
microns, presumably all unit cells in
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Dear Jakob,
your Gedankenexperiment on powder diffraction is not correct. You
would record a powder diffraction pattern if you rotated a single
crystal around the beam axis and record the result on a single image.
This rotation does not affect the mos
Hi Pavel,
> I agree that you bias R-free after the real-space refinement
>
>
> well, ok, isn't it enough to realize that this is bad and should be avoided ?
> (I
> guess we all know we should never bias Rfree!)
>
>
> My point was that we normally do not calculate R-free after re
A postdoctoral position is available in the Department of Microbiology and
Molecular Genetics at Rutgers University - New Jersey Medical School to study
structural mechanisms regulating bacterial signaling and perform SAR studies of
antimicrobial compounds. In addition to a recent Ph.D., the id
>your Gedankenexperiment on powder diffraction is not correct. You would record
>a powder diffraction pattern if you rotated a single crystal around the beam
>axis and record the result on a single image.
If you wanted to do it with a single crystal, you would have to rotate the
crystal through
Thank you Piotr, this is very useful to know.
Cheers,
Eugene
On 24 Apr 2014, at 22:18, Piotr Sliz wrote:
> Eugene,
>
> SBGrid Consortium supports certain paid programs such as Pymol, Schrodinger,
> and Geneious, and academic laboratories have access to a limited pool of
> tokens. For more se
Dear James,
I have a slightly different way to think about transverse coherence. I
heard Mark Sutton give a talk about this at the APS a few years ago, and
here are graphics from a similar talk given by Alec Sandy at BNL:
http://www.bnl.gov/nsls2/workshops/docs/XPCS/XPCS_Sandy.ppt
The eqn.
Hi Robbie,
> I agree that you bias R-free after the real-space refinement
> >
> >
> > well, ok, isn't it enough to realize that this is bad and should be
> avoided ? (I
> > guess we all know we should never bias Rfree!)
> >
> >
> > My point was that we normally do not calculate R-free
Dear colleagues,
I know this is not related to ccp4 but I am in need of an answer and many
of you work with cells etc.
My building had a major malfunction of electricity and the power backup did
not kick in. My -80C freezer was without power for over 24 hours until I
found out. Because it is sm
Dear Jacob,
In terms of the effect of crystal (lattice) defects on diffraction spot
profiles, there are two great papers by Colin Nave that discuss this:
http://journals.iucr.org/d/issues/1998/05/00/issconts.html and
http://journals.iucr.org/d/issues/1998/05/00/issconts.html . There is also
this p
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes
* qtpisa and pisa
- New features
+ concentration dependence of predicted oligomeric states to aid the
identification of biological units in protein's working conditions
+ mu
Jackie,
We grow cells routinely and freeze pellets after fermentation. In general,
proteins are fairly stable until you break cells so you are probably ok
unless your protein is very heat labile and it sat at room temperature for
hours. However as I mentioned, there is a kind of buffering from t
Does anyone know of a place where one can obtain this reference for free? I
would contact Darwin himself, but I suspect he wouldn’t write back. I think
this is the original paper proposing the mosaic block model, and I’d really
like to see his reasoning.
Darwin, C. G. (1922). Philos. Mag. 43, 8
Depositing a new X-ray crystal structure to the PDB archive?Try the new
and improved wwPDB Deposition system at
http://deposit.wwpdb.org/deposition/.
Since the new system went live on January 27^th , 2014, ~700 structures
have been deposited and promptly annotated.Detailed information on the
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 Darw
I was getting very excited here for a second. Deposition of X-ray data?
Is this finally possible? Raw diffraction data, in other words?
Image files?
Sadly, the text of the email doesn't support that conclusion.
Andreas
On 25/04/2014 8:16, Rachel Kramer Green wrote:
Depositing a new X-r
Dear all
written below is the log file of an anomalous data processed through
SHELXC..my question is ..what is the strength of anomalous signal ?? as it
is said "For zero signal and should be about 0.80". Then
in the present case is there really a signal or can be assumed no
signal..we are expec
Dear all
sorry about my previous mail where i forgot to mention that the data was
collected on home source at Cuk alpha and at 1.54A.
written below is the log file of an anomalous data processed through
SHELXC..my question is ..what is the strength of anomalous signal ?? as it
is said "For zero s
should be above 0.80
There seems to be plenty of signal there with all values above 1.02. We have
solved structures with less multiplicity and lower .
There is a different criteria of "signal" for when you know the positions of
the anomalous substructure atoms and when you need to find the po
Thanks to all who replied to my message.
The most logical explanation to the observed phenomenon is likely the
following. During crystallization, Sr ions from the crystallization solution
kick out a fraction of the Mg(OH)6 ions from the binding site in question. The
cavity of the binding site i
Thank you all for your comments/references and now I have a better
understanding of what could be actually happening. But I have a feeling that
disorder, where the twin domains can interfere with each other, is not actually
so unusual. And in some cases MR might be possible to reveal a partial
Hi,
My condolences. This is not a fun experience!
Your plasmids will be OK :)
Glycerol stocks may be rescued as long as after going to room temperature
they did NOT get frozen again. Re-freeze will greatly reduce viability -
but even after one re-freeze you should be able to streak the glycerol
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