Hi Yoni,
If you used the standard .dmg installer, you could try opening a Terminal
window and executing the following commands:
echo $SHELL
If the output says: /bin/bash then do
source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh & ccp4i
If the output says: /bin/tcsh or /bin/csh then do
source
To the CCP4 Community
X-ray Crystallographer and Project Leader Position at Emerald Bio
Emerald Bio is an integrated gene-to-structure collaborative research
organization specializing in drug discovery services with laboratories near
Seattle, WA and Boston, MA. Our scientists provide integrat
I had a very similar problem with data collected on a particular beamline. The
issue was that I had to reverse the spindle direction in imosflm settings.
Also, when I load data from this beamline into imosflm the program rotates the
images by 90 degrees for some reason (this does not happen in
On curve fitting:
http://twitpic.com/8jd081
--
From: "DUMAS Philippe (UDS)"
Sent: Thursday, October 18, 2012 1:52 PM
To:
Subject: Re: [ccp4bb] PNAS on fraud
Le Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)"
a écrit:
Dear Oliver,
The representation of B12 has been updated in the wwPDB's Chemical
Component Dictionary and related PDB entries. They will be available
with next week's update of the archive.
Sincerely,
Rachel Green
***
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.ru
That must be an NMR journal :-)
Jürgen
On Oct 18, 2012, at 3:34 PM, Anastassis Perrakis wrote:
On 18 Oct 2012, at 21:30, Bosch, Juergen wrote:
Tassos,
just to clarify what you are saying in the Journal with 2% deposition after
submission, 98% have been deposited prior to submission (the way
On 18 Oct 2012, at 21:30, Bosch, Juergen wrote:
> Tassos,
>
> just to clarify what you are saying in the Journal with 2% deposition after
> submission, 98% have been deposited prior to submission (the way it should
> be). Is that what you are saying or am I reading that wrong ?
Yes, that is w
Tassos,
just to clarify what you are saying in the Journal with 2% deposition after
submission, 98% have been deposited prior to submission (the way it should be).
Is that what you are saying or am I reading that wrong ?
Or are you saying only 2% of structures are deposited in that journal ?
Jü
Just to add in the controversy, with a somewhat related issue:
Current crystallographic ethic presumes that a structure is deposited just
before
the submission of the paper. In a survey we did, we found that while
in one journal only 2% of structures are deposited after the paper submission
date
since you have already identified the correct beam position through the ice
rings I would fix that beam position. My assumption is that the drifting of
your predicted spots is due to "shifts" in the beam position. Also you should
probably fix the detector distance at that resolution.
Jürgen
On
Hi everyone,
I recently switched from HKL2000 to imosflm to get rid of ice rings.
The group space and cell unit of the data set are known and perfectly
recognized by HKL2000. The predictions are also correct.
In imosflm, the unit cell and space group are recognized. However the
predictions are ter
Randy Read just pointed out to me that in their case-controlled analysis
paper
http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html
when considering lower resolution and other factors, the vanity journals
seem to come out
no worse than the rest.
In any case I suspect any retractions a
I think that the jump between "fraud" and "other quality indicators" is
a bit too steep for me. Poor quality indicators may suggest poor data
that the xtal was willing to diffract, a concept that to me is very
orthogonal to fraud.
Fred
[32m*
My two cents: the R-squared for figure 3A is < 9%, therefore only a minor
proportion of the variation (or random noise) in the data was explained by
the fitted model, taking a log scale may reduce that random scatter look
but the fit is essentially the same.
On Thu, Oct 18, 2012 at 12:10 PM, Ethan
As much fun as it is to bash Nature, Science and Cell, the evidence that they
publish poorer quality structures doesn't actually hold up well. Gerard
Kleywegt (cited below) and I tried to use that supposition as the basis of a
"positive control" for our case-controlled validation paper in Acta
One might include independent prior evidence (Kleywegt, Brown @ Ramaswami)
showing that in general most other quality indicators are worse for high
impact journals.
So, as a frequentist I agree that his correlation is significantly weak, as
a Bayesian I say it is reasonably probable.
Cheers, BR
On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote:
>
> Le Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)"
> a écrit:
>
> I had a look to this PNAS paper by Fang et al.
> I am a bit surprised by their interpretation of their Fig. 3:
> they claim that
The fit seems to be driven by the high number of points in the area of the
graph where many points overlap. The points that catch your eye and establish
the visible balance probably do not contribute much.
Maybe this one should have been plotted as log in the abscissa for appearances.
James
Le Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)"
a écrit:
I had a look to this PNAS paper by Fang et al.
I am a bit surprised by their interpretation of their Fig. 3: they claim that
here exists a highly signficant correlation between Impact factor and number of
retr
Dear CCP4 followers,
Maybe you are already aware of this interesting study in PNAS regarding the
prevalence of fraud vs. 'real' error in paper retractions:
Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the
majority of retracted scientific publications. Proc Natl Acad Sci U S A
I say (of course I would!) why not try co-crystallization with random
microseeding using the crystals with the original ligand?
It usually allows you to control the number of crystals per drop too
On 18 October 2012 15:59, Dmitry Rodionov wrote:
> Hi Sabine,
>
> Glutaraldehyde crosslinking wor
Hi Sabine,
I also have good experience with crosslinking crystals with
glutaraldehyde to stabilise them for soaks with ligands that were only
soluble in DMSO (http://dx.doi.org/10.1016/j.jmb.2006.06.007). More
often than not it destroys the crystals, I think, but it's worth a try.
If you can
Hi Sabine,
Glutaraldehyde crosslinking worked pretty good for various soaks in my
experience.
J. Appl. Cryst. (1999). 32, 106-112[ doi:10.1107/S002188989801053X ]
A gentle vapor-diffusion technique for cross-linking of protein crystals for
cryocrystallography
C. J. Lusty
Best regards,
Please find details below details of software development posts at Diamond.
Full details on these posts and others can be found on the web site
http://www.diamond.ac.uk/Home/Jobs/Current.html.
MX and BioSAXS Automation
-
Job Title: Software Engineer
Post Type: Full Time
Thanks a lot for all the excellent suggestions!
Lots more things to try now!
Cheers,
Sabine
On 10/18/2012 12:18 PM, Boaz Shaanan wrote:
Hi Sabine,
On top of the excellent suggestions of Herman, I was just wondering. Do you
have a structure of the ligand-bound protein? If you do and the lig
Hi Sabine,
On top of the excellent suggestions of Herman, I was just wondering. Do you
have a structure of the ligand-bound protein? If you do and the ligand bound at
crystal contact with another molecule, I would think that it would be hard to
get it out without harming the crystals (althoug
Hello,
Two positions available in my lab at EMBL Grenoble:
1. Post doc position via the BioStruct-X Joint Research Activity (JRA)
workpackage "Mammalian cell toolbox for structural biology" (collab. with
Oxford University).
2. Research technician position.
Details pasted below. Furthe
Thanks ! I got it !
Sandra
On Mon, Oct 15, 2012 at 7:23 PM, Das, Debanu wrote:
> Hi Sandra,
>
> Yes, there are several ways of getting this information.
>
> Go to PDB website Advanced Search section. In the Query Type pull down,
> select All and then select "Remove Similar Sequences at 30% iden
Hi Sabine,
The easy experiment to start with, is to take your best conditions (nice
looking crystals, no diffraction) and instead of overnight wait 4-8 weeks.
Sometimes ligand exchange is slow, or the ligand induces a conformational
change which takes a long time to complete in the crystals. Th
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