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 expl
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 expe
RhrCSCQ2UlIzAfbrxxY%3D&reserved=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
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 ma
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).
Alex
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 progra
not sure if there is anything that can handle a
> few ml volume.
>
> Ray
>
> Lieh Yoon Low
>
>> On Aug 20, 2014, at 6:38 PM, Alexander Aleshin
>> wrote:
>>
>> I agree with Alex and Roger.
>> But my mentioning of plates number for a concentrator
, 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
mailto:aales
www.khayatlab.org<http://www.khayatlab.org>
Original message
Date: Wed, 20 Aug 2014 18:57:07 +
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
(on behalf of Alexander Aleshin
mailto:aales...@sanfordburnham.org>>)
Subject: Re: [ccp4bb] Removing PEG335
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 u
ith
large hard to express proteins.
Best of luck,
Remie
On Aug 19, 2014, at 10:45 AM, Alexander Aleshin
mailto:aales...@sanfordburnham.org>> wrote:
Remie,
Actually, concentrating of a protein solution is not the best approach to
removing low MW impurities, gel filtration chromatography
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 work
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 Al
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
;s screen. 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
> de
nk, even if your set 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
mailto:aales...@sanfordburnham.org>>
To: CCP4BB mailto:CCP4BB@JISCMAIL.AC
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
ally. Can
> anyone suggest us other 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 structures
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