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 com
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 (Insect-XP
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. Yo
> 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 6
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 t
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, Gerard
ehind the error estimation.
> ..In short, I/σ is the preferred way of assessing the quality of
> diffraction data because it derives its validity from the χ2 (likelihood)
> analysis. "
>
> credits to Otwinowski et al.
>
> end of story, i believe. so R-merge died long b
, 2012, at 2:55 PM, Ian Tickle wrote:
> Hi Alex
>
> On 3 June 2012 07:00, aaleshin 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 r
lling 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
it's been 15 years since this was pointed out in no less than
> Nature group 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-
minal resolution is a single number indicating the quality of
> a structure, but this has never been true, irrespective of the cutoff method.
> Apart from the considerable problem of anisotropy, we all need to note the
> wisdom of Ethan Merritt
>
>> "We should also encourage
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 estimatio
> 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 p
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
> I wouldn't claim 99.99% are honest reviewers (that would only be one black
> sheep out of 1 crystallographers).
Similarly to sexual orientation, honesty is not a two-state phenomenon, but the
one that varies from 0 to 100%. So, it is likely that a higher percentage of
referees (than 0.01%)
> Biology is obsessed with high impact, and I argue science is ill served by
> this preoccupation.
When two equally good scientists apply for a job, which one will be selected,
the one with N-C-S publications or the one with J-B-C publications?
Alex
On Apr 19, 2012, at 9:42 AM, Patrick Loll wro
> - 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 t
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 shoul
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, the
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
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, on
p/1Y13
>
> Jürgen
>
> On Apr 5, 2012, at 11:46 PM, aaleshin wrote:
>
>> 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 (
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...
> Agree
ts. No one has time or
> resources to check everything, so 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
&g
ers at:-
>> http://forums.iucr.org/
>> Within this Forum you can find for example the ICSU convened Strategic
>> Coordinating Committee on Information and Data fairly recent report;
>> within this we learn of many other areas of science efforts on data
>> archiving and e
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
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 monst
Moreover, PDB does not need even to store the raw data, just validate their
consistency with the scaled structural factors and then trash them.
On Apr 3, 2012, at 10:44 AM, aaleshin wrote:
> Hi James,
> My previous message on this matter remains unnoticed, but I also suggested a
> ve
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 peo
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
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?
http://www
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 anisotropi
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. Y
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 o
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 d
st time I looked 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 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)?
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 re
racy.
>
> Cuvettes will give a better accuracy 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 wrote:
> I also like our Nanodrop, but I do not recommend using
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 issue
> 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 foi
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
before 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 s
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 propos
I've already got the answer from Warren DeLano. It is easy indeed.
You just create a set of scenes with different objects and then add
them (append) to the list using the Scene menu. Then you chose a
proper scene at each point of the time line...
On Oct 22, 2009, at 9:57 AM, aaleshin
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
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
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