On 10/19/2012 10:37 PM, Acoot Brett wrote:
Will you please explain to me why the protein salt bridge can still
exist in the high salt concentration as used in the crystallization
condition?
You are saying it as if there is some fundamental law of nature that
says that salt bridges cannot be
Dear All,
A lot of 3-D crystal structures highlight the salt bridges in the structure,
although some structures of them are got at high salt concentrations.
Will you please explain to me why the protein salt bridge can still exist in
the high salt concentration as used in the crystallization
Hi,
For those starters on python programming, I strongly recommend Hanns Petter
Langtangen's book "A primer on scientific programming with python". It
specifically targets the scientific programming, which we care about the
most. The only thing I am not sure is that this book was written using
pyth
One of the hardest things for an author, and a handling Editor, is making sure
that the references list of a submitted article is complete, but is an easier
task now with our e-tools than in the days of the penicillin discovery. Another
case is that of Einstein's special theory article of 1905 w
Hello all,
Considering that many biologists come to the field with no background in
programming (like me) and want to learn a scripting language, I thought that
many young members of the community might find this useful.
There's an ongoing FREE online course "An Introduction to Interactive
Pr
On Fri, Oct 19, 2012 at 2:20 PM, Jrh wrote:
> Dear Colleagues,
> A different type of, post publication, fraud is the case of the discovery
> of streptomycin. See :-
>
> http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext
>
I can't resist posting this quite interes
CCP4-
intetesting topic and many off-target topics veing discussed.
John Ionnandis' work, who is an epidemiologist and statistician, addresses
issues in the design and interpretation of GWAS studies for SNPs and disease
associations in one hand and clinical studies, especially Phase III
inte
I think the real point here is that a difference exits between divergent
interpretation of legitimate evidence - which is normal scientific
epistemology - or whether the presented 'evidence' is in some fashion
tampered with. The former is healthy procedure and (I hope) not subject of
disagreement -
Dear Colleagues,
A different type of, post publication, fraud is the case of the discovery of
streptomycin. See :-
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext
I am just returned from the ICSTI Conference on Science, Law and Ethics in
Washington DC represent
This gets us more into the philosophy of science but I've always felt authors
had a right to speculate in the discussion sections of their papers on what it
all means. And speculate even past the information in the actual data (see for
example the wonderfully prescient final lines of the Watson
On Friday, October 19, 2012 10:12:44 am Colin Nave wrote:
> This is worth looking at as well. Suggests most papers should be retracted!
> http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124
A paper claiming that all papers are false, by someone named Ioannidis?
I wonder i
This is worth looking at as well. Suggests most papers should be retracted!
http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124
Colin
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter,
Charlie
Sent: 19 October 2012 17:55
To: ccp4bb
Subject: Re: [cc
Dom,
You've opened a pandora's box here, which I won't try to contain. The short
answer is both of the above.
I feel it is becoming increasingly difficult as a referee to be on top of every
paper I review, and as an editor it is becoming increasingly difficult to find
willing referees. Both ph
Hi Phillippe,
If looking only at the figs. 3A,B,C in the PNAS paper alone, yes, I would
agree with you that the proposed correlation is quite weak. Without the help
of the trend lines, I would probably conclude that there is no correlation
between the IF and number of retractions by a simple l
Dear Charlie,
Do you mean that small doses of fraud should be accepted as a form of natural
evolution? Or perhaps you were suggesting that genuine errors/mistakes are
acceptable in 1/1 due to the high costs of spotting them?
D
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Be
On Oct 18, 2012, at 3:39 PM, Kip Guja wrote:
>
> 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 /Applications/ccp4-6.3.0/bin/ccp4.setup-csh & ccp4i
You need to replace "&" wi
Begin forwarded message:
Date: October 19, 2012 4:40:35 AM EDT
To: Randy Read mailto:rj...@cam.ac.uk>>
Subject: Re: [ccp4bb] PNAS on fraud
This thread has been quite interesting to me. I've had a long interest in
scientific fraud, which I've generally held to be victimless. While that view
is
The HZB MX-team is seeking a beamline scientist to support the operations of
the three MX-beamlines at BESSY-II. The initial contract will run over a period
of three years. Payment will be on the basis of germans TVöD-Bund salary scheme.
HZB-MX is offering state-of-the-art MX-beamlines to the int
Well, the first thing I note is that P6(3) is a polar space group.
Hence what I would do myself is the following:
take your crystal 'number 1' (as a reference);
take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it;
try to see which of the original XDS_ASCII or the reinde
Just a few additional ideas on the significance of the presented values
of the correlation coefficient.
For samples of size N from a bivariate normal with correlation r, its
standard deviation is approximately
StDev(R) = (1 - R^2)/sqrt(N – 1) - note that it depends on the number of
points used
Hello everybody,
I collected datasets with a resolution to 2.8A from 3 crystal grown in the
same condition. The space group seems to be P63. Statistic of XSCALE.LP
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS
Hi
This was indeed the issue - on this beamline (I think it's 19-ID-D at APS, but
I'm waiting on confirmation of this) the phi axis rotates the opposite way to
"usual", so Mosflm needs to be told.
(As an aside, in the most recent release we automatically check the serial
number of the detector
Hello,
I am afraid that you aren't saying (writing) enough to describe the
problem(s) you are facing...
Twin fraction ? How many crystals were used to collect the diffraction
data (remember that there are polar space groups, where c going "up" is
different from c going "down") etc etc. Witho
The HZB MX-team is seeking a beamline scientist to support the operations of
the three MX-beamlines at BESSY-II. The initial contract will run over a period
of three years. Payment will be on the basis of germans TVöD-Bund salary scheme.
HZB-MX is offering state-of-the-art MX-beamlines to the int
Hello everybody,
I collected data to 2.8A with the space group P63 but they seems to be twinned.
I tried phenix refinement with the twin law I got from Xtriage but the model
looks quiet weird...
Hope that somebody can help me with this problem.
Kind regards,
Iris
_
Also, saying that you have
a. 4.0 data without defining the beam line
b. plates without defining the dimensions
is of limited use to get feedback, in my view.
If you got 4.0 data at home, and your plates are at least a couple of micron
thick,
one of the few modern micro crystal beam lines is
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