Hi James,
My previous message on this matter remains unnoticed, but I also suggested a
very simple solution to the data fraud: the crystallographers should submit to
PDB partially processed data, like unmerged partial reflections. These files
are much smaller than the images, and only a few
People who raise their voices for a prolonged storage of raw images miss a
simple fact that the volume of collected data increases proportionally if not
faster than the cost of storage space drops. I just had an opportunity to
collect data with the PILATUS detector at SSRL and say you that
Dear John,
Thank you for a very informative letter about the IUCr activities towards
archiving the experimental data. I feel that I did not explain myself properly.
I do not object archiving the raw data, I just believe that current methodology
of validating data at PDB is insufficiently robust
science is based on trust. There are
efforts underway outside crystallographic circles to address this larger
threat to all science, and we should be participating in those discussions
as much as possible.
Ron
On Thu, 5 Apr 2012, aaleshin wrote:
Dear John,Thank you for a very informative
Alright, if the image deposition is the only way out, then I am for it, but
please make sure that synchrotrons will do it for me...
On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
Ojweh
c) Discarding your primary data is generally considered bad form...
Agreed,
the corresponding
images which led to a structure solution somewhere. And as others mentioned
bad data or good data can always serve for educational purposes.
Just as an example
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/1Y13
Jürgen
On Apr 5, 2012, at 11:46 PM, aaleshin wrote
Since I was the person who started a public outcry to do something, I shell
explain myself to my critics. Similarly to all of you, I do not care much about
those few instances of structure fabrication. I might put too much emphases on
them to initiate the discussion, but they are, indeed, only
of every A^3
counts. It is not clear to me how to report the resolution of data when it is
3A in one direction, 3.5A in another and 5A in the third.
Alex
On Apr 9, 2012, at 4:51 AM, Phil Evans wrote:
On 8 Apr 2012, at 21:18, aaleshin wrote:
What I suggested with respect to the PDB data
It is a wonderful server indeed, but its default setting cuts the resolution at
3 sigma (if I remember correctly). It is too stringent in my opinion. Also, it
is not clear to me whether to submit all data to the highest resolution point,
or the data that come from the server? But then again,
Hi Pavel,
Reporting the table that you suggested would create more red flags for the
reviewers and readers than explaining how to understand the resolution of my
data. We need more studies into this issue (correlation between the resolution
of anisotropic data and model quality). And there
- Find a dinosaur from my generation who can suck one into a capillary and
check diffraction at room T.
- Try to find conditions where the crystals don't start to redissolve while
you mount them
As a matter of fact, people begin to forget that capillaries are good not only
for checking the
Back in Iowa State University we used Waters HPLC for protein purification
during many years without noticeable damage to the stainless steel tubings. But
Dan was right about the pumps, someone in the lab forgot to flush the high salt
pump with water after its use and damaged the pump...
Alex
There are things you can expect to learn from a
2Å structure that you are unlikely to learn from a 5Å structure, even
if equal care has been given to both experiments, so it makes sense
for the title to give the potential reader an idea which of the two
cases is presented. But for this
Please excuse my ignorance, but I cannot understand why Rmerge is unreliable
for estimation of the resolution?
I mean, from a theoretical point of view, 1/sigma is indeed a better
criterion, but it is not obvious from a practical point of view.
1/sigma depends on a method for sigma estimation,
the considerable problem of anisotropy, we all need to note the
wisdom of Ethan Merritt
We should also encourage people not to confuse the quality of
the data with the quality of the model.
Phil
On 1 Jun 2012, at 18:59, aaleshin wrote:
Please excuse my ignorance, but I cannot understand
magazine, and we still hear that Rmerge should decide
resolution cutoff, chances are increasingly slim that I will personally
see the dethroning of that other major oppressor, R-value.
On Fri, 2012-06-01 at 10:59 -0700, aaleshin wrote:
Please excuse my ignorance, but I cannot understand why
them with different names: I am not a
methods developer and my language is fool with working-class jargons...
Alex
On Jun 2, 2012, at 11:00 PM, aaleshin wrote:
Could you please give me a reference to the K D paper? Without reading
it, I do not see a problem with Rmerge going to infinity
On Jun 3, 2012, at 2:55 PM, Ian Tickle wrote:
Hi Alex
On 3 June 2012 07:00, aaleshin aales...@burnham.org wrote:
I was also taught that under normal conditions this would occur when the
data are collected up to the shell, in which Rmerge = 0.5.
Do you have a reference for that? I have
its validity from the χ2 (likelihood)
analysis.
credits to Otwinowski et al.
end of story, i believe. so R-merge died long back.
-tommi
On Jun 4, 2012, at 9:00 AM, aaleshin wrote:
Wow, it is quite a lecture here! It is very appreciated.
I admit some (most?) of my
I wonder if anyone attempted to write a historic book on development of
crystallography. That generation of crystallographers is leaving this world and
soon nobody will be able to say how the protein and non-protein structures were
solved in those days.
Alex
On Jun 6, 2012, at 8:48 AM,
I and Victor Lamzin solved our first protein structure (3A resolution) in 80-s
using pure MIR and a home made (Russian) diffractometer...
Alex
On Jun 6, 2012, at 1:42 PM, Boaz Shaanan wrote:
So if get the gist of the thread right, am I correct in assuming that the
last protein structures to
it is not cheap - probably $500
When we purchased the pump, it was below $300 (a year ago). Replacement took ~4
hours, but you must like doing it. You'll have to disassemble almost entire
pump module, so make pictures of each step and mark tubings ends with labels.
Alex
On Jul 12, 2012, at
I did not replace the entire pump, only a motor. Sorry for a confusion.
On Jul 12, 2012, at 9:28 PM, aaleshin wrote:
it is not cheap - probably $500
When we purchased the pump, it was below $300 (a year ago). Replacement took
~4 hours, but you must like doing it. You'll have to disassemble
Sorry for an off-topic question.
We began experiencing a sudden reduction in stability of baculovirus stock
stored at 4C, like the titer drops more than 5 fold in 3-5 month. The only
difference compared with previous preparations is a switch from Gibco SF900-II
to a media from Lonza
Chita,
I disagree that the age limitation for an entry level job does anything good to
a society. It gives a clear advantage to graduates from a few prestigious
universities, because less fortunate students would need more time to develop
their careers, no matter how talented they are. So, a
Doesn't natural selection act like a Reverse Translatase? Which is
quite an elegant implementation of the idea...
On Sep 7, 2010, at 6:29 PM, Artem Evdokimov wrote:
Regardless of whether a system like this exists in Nature or not -
it's fun to imagine!
On a microscopic scale one could
the
introduction of the immune system.
Alex
On Sep 7, 2010, at 7:26 PM, aaleshin wrote:
Doesn't natural selection act like a Reverse Translatase? Which is
quite an elegant implementation of the idea...
On Sep 7, 2010, at 6:29 PM, Artem Evdokimov wrote:
Regardless of whether a system like
Hi Michael,
It worked for me with one viral enzyme but did not work with 2 others. In the
successful case, I used Takara's chaperone plasmids to screen for the best
composition of chaperones. The GroEL-GroES improved the yield of the soluble
enzyme, but I got same activity (per 1L of media) as
I'm surprised that a better re-sealing system has not been invented to
prevent evaporation from the blocks when they are stored.
Companies that produce these screen want us to buy their screens as often as
possible...
We use transparent plastic seals from Hampton Research. The aluminum foil
I also like our Nanodrop, but I do not recommend using it for Bradford
measurements.
The 25% accuracy mentioned by Flip is pretty good for biological samples.
Using 50 ul cuvette in a traditional spectrophotometer will not give this
accuracy because cleanness of the cuvette will be a big
provided you clean them properly. Just
some water or EtOH is *not* enough...
Filip Van Petegem
On Thu, Jun 16, 2011 at 12:52 PM, aaleshin aales...@burnham.org wrote:
I also like our Nanodrop, but I do not recommend using it for Bradford
measurements.
The 25% accuracy mentioned by Flip
Mischa,
You intrigued me. What is the experimental technique for the Extinction
Coefficient measurement (which requires knowledge of protein concentration)?
Let me guess, Bradford? Protein evaporation and weighing?
Alex
On Jun 16, 2011, at 4:22 PM, Machius, Mischa Christian wrote:
With
Sorry for misprint, I meant evaporating water from a protein solution...
On Jun 16, 2011, at 4:45 PM, aaleshin wrote:
Mischa,
You intrigued me. What is the experimental technique for the Extinction
Coefficient measurement (which requires knowledge of protein concentration)?
Let me guess
into this, the consensus
was that the Edelhoch method is the most accurate method for protein
concentration determination; more accurate than dry-weighing plus N-terminal
sequencing, etc.
MM
On Jun 16, 2011, at 7:51 PM, aaleshin wrote:
Sorry for misprint, I meant evaporating water from
The concentration of a protein in a crystal [Po] and the volume of a crystal V
are needed only to calculate the total amount of a ligand [Lo] required for
soaking.
[Lo] [Po]*V
The occupancy of the active sites in a crystal will depend only on the ligand
concentration in solution and Kd. It
Jacob,
In case if the hint that I sent yesterday was not clear, below is the solution
for the equation
Kd=[P][L]/[PL]
in terms of ligand occupancy:
O=[ PL]/[Po]= 1/(Kd/L+1)
You see, it does not depend on [Po]
Alex
On Jun 26, 2011, at 10:05 AM, aaleshin wrote:
The concentration
Jacob,
In the formula:
Kd=[P][L]/[PL]
[P] and [L] are concentrations of UNBOUND protein and ligand, and [PL] is that
in the complex.
Since the occupancy of the ligand in the crystal is
[ PL]/[Po]= 1/(Kd/L+1),
varying [L] around Kd like from 0.1Kd to 10Kd will make the titration of
occupancy.
Careina,
I recommend to compare the quality of your data (Rmerge) to that of an average
data set of same resolution. Do you have meaningful data to 2.3A resolution?
Another possibility is the anisotropicity of your data. Try this server
http://services.mbi.ucla.edu/anisoscale/, if the
I never used pET20b, but I found on the Internet that it expresses inserts
constitutively. Since the cloned protease should be toxic to cells, its
constitutive expression might prevent the formation of colonies. But there
might be millions of other reasons. Why did you use pET20b?
Dear James,
With all due respect, you have left out a key component to successful data
fabrication in the modern age: THE MOLECULAR REPLACEMENT.
Since almost all new structures have more or less close homologues in PDB, a
smart fabricator should use their experimental data as a template. It will
Are the salaries compared in orders of magnitude?
Or you mean other pays?
On Sep 30, 2009, at 8:30 PM, William Scott wrote:
I always Look on the Bright Side of Life, so I take a certain solace
in
the fact that while this may be true, most postdoc positions pay
about as
well as my job, if
Sorry for the off-topic question.
I am trying to make a complex animation using new movie-making
features of MacPymol 1.2. The video tutorials that are available to
power users explain how to use the timeline, however, they do not
tell how to switch objects during the animation. Is it
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