Dear Ferrol,
Could you let us know the unit cell parameters for both these crystals ? (did I
miss them somewhere in your previous mails?). I wonder if in fact this is not
the same packing with minor variation.
Sacha
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de ferrol
Dear Vennila,
my guess is that you had a larger number of images in the batch/set starting at
180 degrees (hence the slightly incereased Rmerge for that batch) and that by
the end of that run your crystal had suffered from radiation damage (hence the
large Rmerge for the set starting at
Dear CCP4lers,
We have a staff scientist position (permanent) to fill in the Department
of Biochemistry at University of Bayreuth, Germany
(German language skills required -- see below).
Work in the Dept (Blankenfeldt group and Steegborn group) is focused on
the functional and structural
Dear CCP4ers,
I think this is a very interesting initiative and it could potentially
lead to a discussion within the board.
Best,
Xavier
Mensaje original
Asunto: Could Biological Negative Results be published?
Fecha: Sun, 10 Jul 2011 21:39:52 -0500
De: David
Hi Alenxander,
Thanks for the reply. Here's the details on the unit cell parameters
[image: image.png]
[image: image.png]
[image: image.png]
Thank you. :)
Regards,
Fairolniza
On Mon, Jul 11, 2011 at 2:47 PM, Alexandre OURJOUMTSEV sa...@igbmc.frwrote:
Dear Ferrol,
** **
Could you
http://www.jnrbm.com/
Might this be what you are looking for ?
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
What if the negative results contradict some recent papers in big journals?
Would the PI risk his / her contacts connections? Of course for the PhD
student or postdoc, it matters a lot to get it 'published'..
On Mon, Jul 11, 2011 at 4:27 PM, Bosch, Juergen jubo...@jhsph.edu wrote:
On Mon, Jul 11, 2011 at 04:35:31PM +0530, Partha Chakrabarti wrote:
What if the negative results contradict some recent papers in big journals?
In that case it is certainly not a negative result and I am actually surprised
someone even comes up with the idea of not publishing a result just for
Dear David
In addition to what Partha and Tim have just said, what if the negative
results are simply due to poor experimental skills and/or lack of attention
to detail?. I guess my question is would a journal that publishes negative
results be rapidly populated with junk data?.
Kind
Not if they are properly peer-reviewed as the ones mentioned within this thread
claim to be.
The prevention of junk is IMHO the main reason agains an all-open system as in
arxiv.org
Tim
On Mon, Jul 11, 2011 at 12:55:20PM +0100, Victor Bolanos-Garcia wrote:
Dear David
In addition to
Just a comment: positive results can also be due to poor experimental skills
and/or lack of attention to detail etc.
Peer review should take care of this, at least to some extent. Negative results
can be very valuable.
Bert
From: CCP4 bulletin board
Hmmm...I probably have a bit of experience in this business of 'negative
results'.
Let me just say that it definitely has negative impact on your career when
you criticize colleagues.
It is extremely difficult to cut through the 'defendant's' and editorial
denial. In my experience
a lot of lip
It would be important to recall the most famous null result : the
Michelson-Morley experiment, published in The American Journal of Science,
explained 18 years later.
Fairolniza,
my experience with multiple crystal forms growing from the same drop (I
had 4 that I was able to identify, there could have been more) was that
there were similarities in the way protein molecules packed into
fibers that were subsequently arranged into distinct crystal forms.
You may
Negative results are not necessarily criticisms of colleagues, at least I don't
think it should be perceived as such. And if it is, folks should just grow
up...:-)
It may be (too) idealistic, but one could argue that the most important aspect
of scientific experiments is reproducibility. If
Important: Do *NOT* reply to this e-mail to apply for this position.
Only applications processed through the apply link will be accepted. Any
direct replies to this e-mail will be ignored.
Passionate About Science
We're passionate and rigorous about our science. For more than 30 years,
This brings up a philosophical caveat that one should be very careful about
labeling one set of potential results negative and another positive before
even doing the experiment, because its all too easy to see what you hoped to
see even if it was only marginally there.
The best
There are least two types of negative results
1) Contradiction of previously published results. Negative results of this kind
is either they are wrong, you are wrong or it depends on the differences within
the experimental methods used. An example of the latter case would be SPR vs
ITC. SPR
A RESEARCH ASSOCIATE POSITION is available beginning Aug 1, 2011 in the
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Applicants must possess a Ph.D. in chemistry, biochemistry or biophysics, with
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Dear all,
We are planing to buy a bioreactor (fermentors) for insect and mammalian cell
culture in our lab, current candidates include
WAVE Bioreactor @ GE
CelliGen BLU @ New Brunswick
BIOSTAT CultiBag RM @ sartorius
Our major concern is the size, maintenance easiness, and future
Hi all,
Thanks for all the helpful suggestions. It seems like Phenix LigandFit
requires density for the ligand but unfortunately I only have the
ligand-free model. I've tried blasting the peptide sequence using the
sequence search tool in the PDB but failed to get any hits. I was
wondering how
Wasn't another famous negative result the refutation of the vital
principle which presupposed that substances from living entities were
inherently different from those from non-living?
I guess the essential feature of an important negative result is the
clearly-observed absence of something
Thanks in advance to everyone to everyone who responded to my previous post
about their experiences doing SAXS at home.
Below is a summary of the responses.
Best,
Rebecca
I am using NANOSTAR BRUKER for few years, and the sealed tube is out of
order
now and the intensity dropped significantly
A postdoc in the lab ran into problem creating new project directory in
CCP4i GUI in his computer account. When he tried to add project the
following error popped up:
Can't read array 'CCP4_DATABASE
How to fix this problem? Thanks for your help.
Huiying Li, Ph. D
Department
Does anyone know how many times roughly you can re-use a Streptactin column? I
know that contamination with biotin will destroy the column but the protein
that I am using has gone through both a GST and Nickel purification steps
before seeing the Streptactin column and I think lately that I
Hi Rex,
The protein I'm working on has a defined substrate-binding cleft. I have
a model for the apo form but not the substrate-bound complex. I'd like to
dock a peptide fragment of its binding partner potentailly involved in the
interaction (~8 residues ) to this cleft. My question is what are
Hi Pius,
Thanks for the tip. I've never used that utility in PyMol. It'll give it
go!
From the drop-down menu of the Builder tab, it seems like one could specify
the secondary structure as well.
Have you ever tried that option?
Thanks.
On Mon, Jul 11, 2011 at 12:43 PM, Pius Padayatti
Here are some options:
http://vina.scripps.edu/
http://rosettadock.graylab.jhu.edu/
Jürgen
On Jul 11, 2011, at 8:24 PM, crystal wrote:
Hi Pius,
Thanks for the tip. I've never used that utility in PyMol. It'll give it go!
From the drop-down menu of the Builder tab, it seems like one could
Hi,
Try Autodock from Scripps. It worked beautifully for me. The docked peptide
explained why initial attempts at crystalizing the peptide/protein complex
failed (because of a crystal contact). The crystal structure subsequently
confirmed the calculated structure. My peptide is a 6-mer.
Hi Quixu,
I also used phenix.refine with the reference model ( I have high
resolution model for one domain of the low resolution protein) and
secondary structure restraints, but it seams the same. Any suggestion?
BTW, is that simulator annealing not suitable for low resolution structure?
I
On Jul 8, 2011, at 11:13 AM, Katherine Sippel wrote:
I was shocked to discover that the file with only one questionable solvent
in April now has 173 of them.
One word: Diffusion.
James
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