Dear All,
I read the announcement of André’s passing with great sadness and yet with
undeniable joy of fond memories. I knew André very well and we spent many
hours working together at the 19ID beamline of Structural Biology Center,
the Advanced Photon Source, Argonne National Lab.
André indeed w
Hi Marco,
I wonder what is the highest concentration of the protein you've tried.
Once I worked with a protein which would crystallize only if it was
concentrated into a jell...
Good luck!
Nukri
On Thu, Jan 9, 2025 at 7:01 PM Marco Bravo <
d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> wrote:
> H
Hi All,
There is a bit of information in the crystallization conditions that I
would like to comment on.
Crystals grow in a variety of conditions, including one that contains
Na-Cacodylate buffer (#3 in the list).
When this is the case, the cacodylate-containing conditions should be
dropped from fu
Hi, What size are these crystals? Chances are, you could take them as they
are (with cryo-protection and cryo-cooling, of course) to a synchrotron
beamline with a small beam.
Also, what is the PI of the protein? If crystals grow at both pH 5.5 and
8.5, perhaps you could set up a grid with pH in one
s the most comprehensive, although this one too is missing Günter Blobel
.
It appears that the number to be quoted would be highly contextual.
Best wishes,
Nukri
On Mon, Jul 22, 2024 at 1:41 PM Nukri Sanishvili wrote:
> Dear All,
> Does anyone know the number of Nobel Prizes
Dear All,
Does anyone know the number of Nobel Prizes awarded for macromolecular
structures?
This would be a very effective way to explain the importance of structural
biology to the uninitiated.
I suppose I could look at the whole list of laureates and figure out what
was given for what, but if so
Hi James,
The elevator pitch has to be 90 degrees, no? Otherwise it would travel
horizontally as well.
Or, perhaps, we should petition these types of elevators to be added to
building codes for large, multi-entrance buildings?
Best,
Nukri
On Mon, Apr 1, 2024 at 10:08 AM James Holton wrote:
> For
Excellent idea, Mark!
I think the solution to your dilemma is rather straightforward: we
introduce a Winter Standard Room Temperature (WSRT) and a Summer Standard
Room Temperature (SSRT). This way, the folks from locales closer to the
equator can always use SSRT, while those from more temperate cli
The workshop website at https://seacoast.kmutt.ac.th/2024/
On Mon, Dec 4, 2023 at 8:21 PM Nukri Sanishvili wrote:
> Dear potential applicants,
>
> This is a friendly reminder that the deadline for application to the
> crystallographic workshop in Bangkok, Thailand, is fast approa
*
For
*the application form, the program, and all other details, please visit the
workshop website:*
On Sun, Oct 15, 2023 at 10:29 PM Nukri Sanishvili
wrote:
> Dear All,
>
> We are very excited to let everyone know that after a Covid19-induced
> pause, we are renewing our macromolecular c
Dear All,
We are very excited to let everyone know that after a Covid19-induced
pause, we are renewing our macromolecular crystallographic school “*South-East
Asian Crystallographic Overview And Systematic Training”* *(SEA COAST)**,
organized jointly by King Mongkut’s University of Technology, Tho
Hi Elspeth,
You are right on the political correctness topic. However, the modern term
would be Garthem, not Garperson...
:)
Best,
Nukri
On Wed, May 24, 2023 at 5:14 AM Elspeth Garman <
elspeth.gar...@bioch.ox.ac.uk> wrote:
> Thanks a lot Harry! Unfortunately there is only one of me so it should
Sad news indeed for so many of us, those who knew Alexei personally and
those who benefited professionally from his selfless dedication to
computational crystallography.
A wise man once said something along the lines of anyone successful today
standing on the shoulders of giants of the past. Unfort
eople to your
> meeting from two different domains, well, I guess you will end up having
> two bubbles of people clustered by their field of interest.
>
> Same disclaimer goes here as yours -- no offence to any one, just thinking
> out loud...
>
> All the best!
> Pavel
&g
Hi James,
This meeting has indeed been one of the best ones by its format, content,
and atmosphere. Many thanks to all the organizers and attendees of the
past. Nevertheless, it is not surprising that it was cancelled, given the
trends in structural biology research. Straightforward evolutionary
pr
Hi Carmien,
It appears to me that the dewars in your first link are those made by
Taylor Wharton. You can do a search with that name and hopefully find less
expensive options. We've used them for many years and they are good.
Another one, you could try, is VME https://mvebio.com/aluminum-dewars/
We
Hi Jessica,
Your subject being membrane proteins, I might ask a question if your
conclusions and claims are commensurate with the data quality but as
Eleanor says, it really depends on what you are actually claiming and what
kind of data you have.
Cheers,
Nukri
On Tue, Jun 14, 2022 at 10:59 AM Jes
Hi Frank, CCP4bb-ers,
While the progress in the digital world in 2021 over the 90s is undeniable
(which, unfortunately cannot be said about the analog world), we should
keep in mind that some institutional accounts may filter out the
"suspiciously" large emails.
I would not be surprised if some of
Hi Rob,
There is no information provided to think what might be the problem with
indexing. How confident are you in the direct beam coordinates?
Are any of the cell lengths long-ish?
It may not be enough but at a minimum, two images 90 degrees apart might be
helpful.
Preferably, they would be taken
Dear Saurab,
It's a shame these crystals do not diffract well - they look so good!
I assume the diffraction you saw was recorded at cryo temperatures? If so,
it is possible that you may be damaging the crystals during cryo-pretection
and cryo-cooling. Before you go too deep into changing the crysta
Sorry, in my previous email I was oblivious to the fact that there was Fe.
Iron is almost certainly oxidized. So, if you started collecting data with
reduced iron, but it got oxidized during data collection, you are probably
using the parametrization for the reduced rather than oxidized one in the
Is the oxidation state of the coordinated atom, or the identity of that
atom correct?
If there was a very slightly bigger atom, it would take care of the
positive residual density and would push out the His side chains a little
bit, which in turn could take care of the negative ones.
Or, the same e
Hi John,
I think I know what might have happened:
Many of the MX beamlines at the APS use some sort of filler in the
containers where the LN2 is dumped. If I remember correctly, one of the
beamlines is using fine gravel for this purpose. Also, it is required that
before shipping, the dewars are emp
Hi John,
These look like real pebbles. If so, they would not word as an absorbent.
It looks more like a bad joke. Was the FedEx driver expecting some kind of
Thanksgiving gift from you? Wait till Christmas time then to see the real
surprises...
Best,
Nukri
On Fri, Dec 4, 2020 at 10:05 AM Tanner, J
Hi All,
Adding some more details to what's been said already. Only because I've
seen too many times the polarizers being used incorrectly.
First, you need two polarization filters which are typically called
polarizer and analyzer. First one (the polarizer) lets through only the
light waves of a ce
Hi Robert,
In addition to the great suggestions you already have received, maybe you
should also consider SIMBAD or similar programs? The behavior you are
describing is typical of, albeit not exclusive to, having crystallized a
contaminant protein.
Good luck!
Nukri
On Thu, Jun 18, 2020, 08:01 Rob
Hi Jessica,
You do not say how well is the rest of the structure refined.
First, you should refine the structure best you can, without placing
anything in the unclear blob of your interest so to obtain the best
possible phases and hopefully improve the blob density as well.
Then you should let the
Dear Colleagues,
This is a friendly reminder that we will be organizing a second
crystallographic school in Bangkok, Thailand, January 21-29, 2020.
The school will cover all aspects of macromolecular crystallography and *a
big part will be dedicated to the practical problem-solving sessions where
t
both SAD and MAD with peak 12661 (0.9793 Å) and inflection
> 12658 (0.9795 Å)
>
> Thanks again,
> Lindsey
>
>
> On Aug 26, 2019, at 6:54 PM, Nukri Sanishvili wrote:
>
> Hi Lindsey,
> Obviously, one would need a lot more information to properly diagnose the
> problem a
Hi Lindsey,
Obviously, one would need a lot more information to properly diagnose the
problem and I am sure much smarter people them me will ask you for that.
But just to move the task by couple of steps, I want to point out couple of
things.
1. Trivial question: did you have the anomalous option t
I know it is going to hijack the original topic but I could not help...
“The reports of death of (macromolecular) crystallography are greatly
exaggerated.
If we believed the prognosticators, it has been dead since the 80s when
some folks made the claim that the only relevant structures were those
Hi Jakob,
If there is radiation damage, for every "new" positive density there should
be a negative density in the original position. From the pictures we've
seen, it seems unlikely.
Best,
Nukri
On Wed, Jul 10, 2019 at 10:21 AM Keller, Jacob
wrote:
> How about radiation-damaged/smashed Sulphur?
Dear Scott,
For the grant application, better question might be how many structural
biologists are out there, because "a crystallographer" may be interpreted
differently depending who is reading the grant application: are these the
people who know crystallography, or people who solve structures us
Hi Aleix,
Can you describe how you did the fluorescence scan, or share the plot
itself? I am asking this because you say you could discard Fe, Zn and As/Se
but you don't say anything about Cu which is in between these elements.
If you tried but could not discard Cu, then it could be your "Culprit".
Hi Ethan,
I am not a linguist of Greek or even of English but I would assume that
the term "cryo-cooling" is advocated not by DRD but by the people who
want to distinguish between cooling down to *cryogenic* temperatures and
say, cooling from 25 C to 4 C.
Cheers,
N.
On 11/15/2012 12:45 PM,
s: An alternative way to avoid the argument and discussion all together
is to use "cryo-cooled".
Tim: You go to a restaurant, spend all that time and money and order a
fruitcake?
Cheers,
N.
On 11/15/2012 11:59 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear s,
I have
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