Hello all
I have refined and built model a dataset of 3.0A resolution dataset. This
model is assocaied with a ligand. After final refinement and model building
i found a big blob of Fo-Fc density of around 4sigma level at the
N-terminal of the fianl model. My protein doesnot carry any tag at the
Hi Vanessa
It is better to get rid of traces of residual acrylamide that may
contaminate your final purified and refolded RNA.
It is usual to have contaminations with monomeric acrylamide. NMR
spectroscopists studying RNA can usually detect its presence on their
spectra.
If you can dialyze your pur
Sadly, it is no joke:
Silicon Graphics timeline - San Jose Mercury News:
http://www.mercurynews.com/businessheadlines/ci_12049125
Hi.
I am trying to optimize a commercial crystallization condition that
contains glycerol. So far, I have not been able to even reproduce the
results from the initial screen, and I thought that this may be due to
poor quality glycerol (among other possibilities). I believe that the
glycerol that
Are you talking about chunks of acrylamide? Or perhaps trace molecules?
As for chunks, we normally pass it through a 0.2 um filter before
setting up trays.
FR
On Apr 1, 2009, at 4:48 PM, vanessa delfosse wrote:
Dear all,
I'm currently trying to crystallize a 70 nt RNA and I would like to
Dear all,
I'm currently trying to crystallize a 70 nt RNA and I would like to know if
the presence of acrylamide, some traces from the purification step, may
interfere with crystallization of nucleic acids ?
Thanks in advance,
Vanessa.
--
Vanessa Delfosse - PhD
U
I am experimenting with GLRF and am having trouble calculating the
locked self rotation function for a protein of known structure. The
protein has a 3 fold NCS axis that is not parallel to a
crystallographic axis. I'm at the step of specifying the local
symmetry elements for the locked sel
On Wednesday 01 April 2009 07:21:16 Thomas Womack wrote:
> A perusal of the PDB reveals that the game of Periodic Table bingo still
> has eleven rounds to run:
>
> scandium, titanium, germanium, zirconium, niobium, neodymium,
> dysprosium, thulium, hafnium, bismuth and thorium remain absent from P
Dear Peter,
some time ago I have written the program Twister
to analyze the geometry of coiled coils (Strelkov SV and Burkhard P
(2002) J. Struct. Biol.)
It will calculate the curvature of each individual a-helix in a coiled
coil,
among other things. But in fact you can ask it to analyze an iso
Sorry 'bout that. I don't know if this one is black, but it's definitely an
A-hole...
LOL
Cheers,
Michael
- Original Message -
From: "Marius Schmidt"
To:
Sent: Wednesday, April 01, 2009 1:48 PM
Subject: Re: [ccp4bb] NCBHT: severe warning
Interesting, isn't it? :-), nice person.
Not nice either to air the address of someone who wrote you privately.
Miguel
Le 1 avr. 09 à 22:48, Marius Schmidt a écrit :
Interesting, isn't it? :-), nice person.
F*** Off.. it might be 1st April but most people are not interested
about
your shit sense of humour.. send them to your frie
Posting private emails on a public email list is rarely considered good
form, in fact on some email lists it would get you thrown off fairly
quickly, especially considering your intended purpose.
(Who is the list admin here ?)
If you're going to post semi-humorous way off-topic posts, you shou
Interesting, isn't it? :-), nice person.
> F*** Off.. it might be 1st April but most people are not interested
> about
> your shit sense of humour.. send them to your friends..
>
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email:
On 21:12 Wed 01 Apr , John Badger wrote:
> We are examining alternatives for water-picking that workable in the
> context of automated refinement and are not aware of any other
> incompatibilities at this time.
No doubt you're already aware of findwaters, which comes with coot and
looks lik
The automated cocrystal solution pipeline and refinement applications in
MIFit8 ( http://code.google.com/p/mifit/ ) employs arp_waters for water-
picking and some automated error detection. However, arp_waters is
deprecated in CCP4 6.1.1.
For now, one solution (Linux or Windows) is simply to co
Hello all
I would like to calculate the curvature of a curved helix. Is any method or
program exists, which can calculate the cuvature of a curved helix? I would
appreciate the suggestions.
Thanks in advance
Hi,
I cannot really answer what the lowest resolution for MR is but I have
been successful with 4 A data for a protein-DNA complex and so I
encourage you to try your 3.6 A data set. Of course, it also depends on
the quality of your data, in particular how well/how many low resolution
reflections we
Just because it is not in the PDB does not mean that noone has ever
tried it. I think I can attest to seeing pretty much all the
Lanthanides tried at my beamline. Indeed, Hampton sells a Lanthanide
kit, and I recommend using it as every Lanthanide has a slightly
different ionic radius. For e
Are you talking about the respective ligand with progesterone or estrogen
receptor ligand binding domains? That has been done many times. Larger
pieces of the receptor have proven more difficult.
Adding 10uM compound in the fermentation media is the traditional route,
because a significant porti
Unless you want a ligand free molecule it might be a good idea to add the
substance already to the growing Ecoli (?) culture. That has proven to be
successful for such molecules.
Best wishes
Kornelius
On Wed, 1 Apr 2009 16:59:05 +
KUMARASWAMI MUTHIAH wrote:
>
> Anybody tried to cocrysta
Anybody tried to cocrystallize the protein-progesterone or estrogen complexes,
if so how do you go about the solubility of these compounds? Progesterone is
only soluble in 50% chloroform or 100% DMSO and the dilution of this stock is
not possible as chloroform falls out of solution. Lots of pap
You know Kevin,
April fools notwithstanding, you idea actually makes good sense in a
tiny-url sort of way. There would of course be collisions, and thus,
need for a global disambiguation registry, but society could do a whole
lot worse than something like:
http://prot.seq.db/3fc28e91d74b39ec/a6
SEVERE BLACK HOLE WARNING ***
The National Center for Black Hole Tracking (NCBHT) is issuing
a black hole warning. During the night shift from March 31st
to April 1st, a black hole formed in the Atlas Detector at the
Large Hadron Collider, Cern/Geneva, Switzerland, although t
Huber's empire in Martinsried had a cabinet with ~500 compounds, many
of them synthesized by himself (occasionally blowing up a lab in the
process...) that in fact contained thorium, hafnium, etc. compounds.
Radioactive compounds were kept in a little lead box. I am not aware
of any success
Dear Colleague,
in case you haven't yet submitted an abstract for the
European Crystallography Meeting (ECM25) scheduled
for August 16 (Sunday) to August 20 (Thursday) in
Istanbul, Turkey, you can still do so until this Friday,
April 3, 2009.
The link to the conference site is:
http://www.ecm25.
Title: Intern - CCP4
Location: Gaithersburg, MD
Req: 01497
Position Summary:
Perform testing, data analysis, and computer based structural modeling
in a biophysical characterization group. Correlate model predictions to
data collected by analytical ultracentrifugation, light scattering, and
other
A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:
scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium, thulium, hafnium, bismuth and thorium remain absent from PDB
entries.
OK, many of these are elements that would rather be re
The impact factor of UAt4 has recently been upgraded from 'huge' to 'all
over the place' after the unfortunate accident at the Miscatonic
university labs which left half the building as glowing multi-colored
glass puddle.
Artem
> What is the impact factor for that? 100 or 1000?
>
> leo
>
> ar...
In a powerful counter-proposal I recommend that human genes be named after
actual people. I think many of us have heard of the star catalogue - for
fifty bucks you can have a star named after you (not sure if they still do
this). So, the same deal applies - only a bit more expensive because
there's
Hi Hongnan
The standard criterion for choosing the optimum weight(s) is to choose the
value(s) that minimise Rfree at convergence of the refinement, i.e. at the
local or global maximum of the likelihood function. Axel Brunger and his group
have published a lot of nice work in this area. Alte
What is the impact factor for that? 100 or 1000?
leo
ar...@xtals.org wrote:
Hey,
This is *the* place to report my experiments with Uranium (IV) Astatide
(UAt4) and Radon for phasing!
Artem
Dear Crystallography Community:
... good stuff ...
Sehl Oediter
Chief Guy in Charge
J
Dear Sehl Oediter,
I am not sure this is the right forum but I cannot resist. While I welcome the
announcement of this new and important journal, as I'm sure all other members
of the community do, I'd like to urge you reconsider for publication the paper
which I submitted to your journal this
Why molecular weight? That's just arbitrary.
There is a simple way of referring to proteins which avoids any
ambiguity - by it's sequence. When referring to a protein, we should use
its sequence as an identifier. No ambiguity.
Now, I understand that some smart people in America are now solvin
I think actually *naming* the proteins would be too extreme. Even the
current alpha-numeric system is overwrought. I liked it better when we
just called proteins "p75" or "p105". For instance, how many proteins
in the human genome are 75 kD, anyway? My guess is not enough to make
the situat
Hey,
This is *the* place to report my experiments with Uranium (IV) Astatide
(UAt4) and Radon for phasing!
Artem
> Dear Crystallography Community:
>
... good stuff ...
> Sehl Oediter
> Chief Guy in Charge
> Journal of Failed Crystallization Trials
> Sell Press
> Boston, MA
>
April Fools Day? I hope so!!
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Frank von Delft
Sent: 01 April 2009 11:16
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] New human genome policy - please read.
H... just saw this. !!!?!??!
--
On Apr 1, 2009, at 4:35, Liew Chong Wai wrote:
Hi,
Good day
I am currently building my structure by using COOT. My protein is a
tetramer protein and I have fit my protein sequence into one of the
monomer of the homologous model. May I know how can I replace other
monomer with the amended
On Apr 1, 2009, at 7:12, conancao wrote:
Dear All:
Hi. I have a question about selecting weighing term during
restrained refinement using Refmac5 of CCP4 packages.
For a 300kDa homodimer protein structure at 2.5A, 91%
complete. I obtain optimal R and Rfree by using NCS tigh
H... just saw this. !!!?!??!
The International Human Genome Organization (HUGO) has announced its intention
to commercialize the naming of human genes. They put it out for public
consultation, and are asking
What's the date today? It must be Christmas I have lots of stuff to
publish. A
Ha ha ha Good Try..Better luck next time !!!... Mr. Sehl Oediter !!!
Sehl Oediter wrote:
Dear Crystallography Community:
I am happy to announce the Journal of Failed Crystallization
Experiments, a bimonthly publication that highlights the exciting
field of failed crystallography projec
Dear Crystallography Community:
I am happy to announce the Journal of Failed Crystallization Experiments, a
bimonthly publication that highlights the exciting field of failed
crystallography projects and trials.
As you are all well aware, most scientific journals have been publishing
crystal stru
David Cobessi wrote:
Liew Chong Wai wrote:
Hi,
Good day
I am currently building my structure by using COOT. My protein is a
tetramer protein and I have fit my protein sequence into one of the
monomer of the homologous model. May I know how can I replace other
monomer with the amended monome
43 matches
Mail list logo
