Ethan,
Thank you for describing existence of two types of polarizers. I use two
crystal imagers/incubators, a smaller machine is easy to adjust to compensate
for birefringence of plastic plates/covers, another is more capricious and the
compensation is uneven over a plate. Company engineers
Hi Monika,
Philippe is right, ITC can detect only binding with -dH > ~0.3 kcal/mole
(depends on instrument). If the binding is Entropy driven, i.e. TdS >> -dH,
than Kd might be quite low, like 20 uM, but ITC would still not detect it (this
often happens in mutants). You can try to optimize
AfbrxxY%3Dreserved=0
Thomas
> On Mar 2, 2020, at 7:12 PM, Alexander Aleshin
wrote:
>
> Dear Dale,
> You raised a very important issue that has been overly ignored by the
crystallographic community. The riding hydrogens are just a tip of an iceberg.
It is absolutel
Dear Dale,
You raised a very important issue that has been overly ignored by the
crystallographic community. The riding hydrogens are just a tip of an iceberg.
It is absolutely unclear even to an experienced crystallographer how to treat
poorly ordered side chains or even whole residues. As a
because the Depositor refinement
statistics would differ from that calculated from the submitted structure
missing the hydrogens.
Regards,
Alex
From: Diana Tomchick
Date: Friday, February 28, 2020 at 12:34 PM
To: Alexander Aleshin
Cc: CCP4
Subject: Re: [ccp4bb] Hydrogens in PDB File
[EXTERNAL
Dipankar,
It is possible that the peptide was cleaved by other proteases present in the
soaking solution as impurities. The crystallized protein simply selected that
fragment that binds the best. You can try soaking with a lower amount of the
peptide (use a smaller drop and concentration).
Could anyone remind me how to calculate anomalous difference Fourier maps
using model-calculated phases? I was doing it by
(1) calculating PHcalc from a pdb file using Sfall, then
(2) merging PHcalc with Dano of experimental SFs, then
(3) calculating a map with Dano and PHcalc using FFT
with
large hard to express proteins.
Best of luck,
Remie
On Aug 19, 2014, at 10:45 AM, Alexander Aleshin
aales...@sanfordburnham.orgmailto:aales...@sanfordburnham.org wrote:
Remie,
Actually, concentrating of a protein solution is not the best approach to
removing low MW impurities, gel filtration
I meant application of GF as an ion exchange column.
Oh, my goodness! Ion exchange is something else!
It should read buffer-exchange = desalting column.
On Aug 20, 2014, at 11:48 AM, Alexander Aleshin wrote:
Dear Remie,
I meant application of GF as an ion exchange column. You can use special ion
://www.khayatlab.org
Original message
Date: Wed, 20 Aug 2014 18:57:07 +
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
(on behalf of Alexander Aleshin
aales...@sanfordburnham.orgmailto:aales...@sanfordburnham.org)
Subject: Re: [ccp4bb] Removing PEG3350
To: CCP4BB
, efficiency of molecules separation by a
concentrator is hard to describe quantitatively.
On Aug 20, 2014, at 3:04 PM, Lieh Yoon Low wrote:
I agree with Alex and Roger. Just a matter of choosing the right SEC column.
Ray
Lieh Yoon Low
On Aug 20, 2014, at 4:56 PM, Alexander Aleshin
aales
that can handle a
few ml volume.
Ray
Lieh Yoon Low
On Aug 20, 2014, at 6:38 PM, Alexander Aleshin aales...@sanfordburnham.org
wrote:
I agree with Alex and Roger.
But my mentioning of plates number for a concentrator was an act of
stupidity! I bet it is possible to introduce
Remie,
Actually, concentrating of a protein solution is not the best approach to
removing low MW impurities, gel filtration chromatography is more reliable and
... faster.
Regards,
Alex
On Aug 19, 2014, at 7:03 AM, Remie Fawaz-Touma wrote:
Hi Reza, I had to do this before.
This protocol
crystal which weighted between 0.5 - 1.0 kg.
It grew suspend on a mountain boots shoelace of the read colour.
Sounds like a crystallographic legend, beautiful but never achievable…
Happy Halloween!
Alexander Aleshin
Sanford-Burnham Medical Research Institute
La Jolla, California
On Oct 25
Sorry for a provocative question, but I am surprised why nobody
comments/congratulations laureates with regard to recently awarded Nobel
prizes? However, one of laureates in chemistry contributed to a popular method
in computational crystallography.
CHARMM - XPLOR - CNS - PHENIX-…
Alex
Thanks to everyone responded!
I tried the advices of Pierre Aller (command xrandr -s 18 in the remote machine
terminal) and Scott Classen (control+option+0 in the remote machine window).
Both approaches worked.
Regards,
Alexander Aleshin
Staff scientist
Sanford-Burnham Medical Research
. As a result I can see
only a half of it. Does anybody know how to fix this problem?
Alexander Aleshin
But the amount of time spent on turning a protein into a publishable structural
data is pretty much same, if not larger. There are no low hanging fruits any
more.
On Mar 27, 2013, at 11:50 AM, Frank von Delft wrote:
Is it too much to dream that Tom has set a trail-blazing precedent and
On Mar 13, 2013, at 1:36 PM, Ed Pozharski wrote:
But what if I only have one measurement worth of sample?
Is it proper to use statistical analysis for a single measurement? I thought
statistics, by definition, means multiple measurements.
Alex
of observation
is too small to say for sure, with n=1 being the ultimate too small. (Maybe not
ultimate, n=0 is really too small.)
Mark
-Original Message-
From: Alexander Aleshin
aales...@sanfordburnham.orgmailto:aales...@sanfordburnham.org
To: CCP4BB CCP4BB
crystallization robots out in the market that
are good? Thanks in advance,
Regards,
Madhavi
Alexander Aleshin, PhD
The Burnham Institute
San Diego, CA
I do not think the small molecule approach proposed by George Sheldrick
is sufficient for validation of protein structures, as misrepresentation
of experimental statistics/resolution is hard to detect with it, and
these factors appear to play crucial role in defining the fate of many
hot
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