Dear Dr. Ross,
Thanks very much for your suggestion. I was thinking that there must be
people who have used both the systems. But, i see that its nearly
impossible to find.
Oxford system people have agreed to take our crystals by cryo-shipper
and try them out in their machine.
sincerely
s
Dear Pat and friends,
Our lab has a ultraX18 5.4kw x-ray generator, and the lifetime of the
filament is more than 1000 hours before rigaku recalled and changed the
vacuum pump. I noticed that the lifetime is really related with the the
vacuum. Ideally it is below 0.1mpa and the lifetime can be lon
Dear Anagha,
just a guess...
I'm not sure I understood you properly, but you are only trying to
make a model of a solved protein which will lack 3-4 amino acids in a
loop... therefore, why not using a modeling soft, such as Coot,
remove the amino acids, and do one run of "Regularize Zone"?
Hello Balaji,
You may try the following:
1) Try different detergents
2) Use a 100 kDa concentrator after protein purification if possible, to
eliminate as much of empty detergent micelles as possible. You probably
have a lot of these since the CMC value of LDAO is ~0.023% and mol. wt.
of
Dear TriNgo,
Firstly, the fact that you can see your His-tag via Western blot does not
mean that it's attached to the majority of the protein molecules in
solution - strong Western signals may be observed for as little as 1% of
the protein that is *supposed* to be His-tagged. So one of the causes
Hello All,
We are trying to crystallize a membrane protein but cannot get the xtals to
grow bigger. Presently we have only thin needles (diffracting to about 8A).
Thus far we have tried to change protein concentration, LDAO concentration, PEG
screen as well as temperature. Have tried macro and m
Have you tried Modeller ?
-Sid.
On 2/28/07, anagha gupta <[EMAIL PROTECTED]> wrote:
Hi CCP4 community!
I have constructed a homology model of a deletion variant of a protein whose
structure has already been solved. These deletions are 3-4 amino acid in
length and are in a loop that connects tw
Before loading the Ni-NTA column you should exchange the medium
buffer (some media have histidine which will compete with your
protein) to a more suitable buffer, like your loading buffer (Buffer
A is 50mM phosphate buffer pH 7.5 and 300mM NaCl is OK).
If your His-tag is not accessible, then
Dear all,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.1, I found out that NAG is
actually N-acetyl-glucose, which is much less common, I believe. I
downloaded the high-resolution structure of N-acetyl-glucosamine from
HIC-UP an
Hi,
I would try to include up to 1 to 2 M NaCl in your lysis buffer and
during purification you can then decrease your salt concentration
in your elution buffer ...
Good Luck
Sabrina Biarrotte-Sorin
Quoting Ngo Duc Tri <[EMAIL PROTECTED]>:
Dear CCP4 users,
I'm purifying a kind of pro
Dear all,
please ignore this email that contains a video. THIS IS A VIRUS on my email.
Prezados,
Por favor desconsiderem qualquer mensagem minha contendo video, pois se
trata de virus no meu email.
On 2/28/07, Emmanuel Prata <[EMAIL PROTECTED]> wrote:
video zueras do tooby
video de pessoas
On Wednesday 28 February 2007 11:39, you wrote:
> Not sure what R-free error is either, I am trying to deposit a pdb and there
> is a blank to fill in "R-free error" located in the highest res refinement
> section.
> It filled in all the other values automatically from my mmfic except that
>
Hi Everyone,
For anyone that is interested in structure based fragment screening-
ActiveSight has created a fragment library kit optimized for
crystallography. The library consists of 384 small molecules and shape
diverse mixtures, dissolved and ready to use for fragment screening agai
sometimes the insect cell medium intereferes (for whatever reasons)
with nta purifications when they ar employed as a first step in the
purification scheme. i experienced that occasionally. this can easily
be circumvented by doing an ion exchange step beforehand!
alternatively you might want
- Original Message -
From: "Juergen Bosch" <[EMAIL PROTECTED]>
To:
Sent: Wednesday, 28 February, 2007 8:18 PM
Subject: Re: [ccp4bb] Cannot running NTA to purify the protein having
His-tag?
Ngo Duc Tri wrote:
Dear CCP4 users,
I'm purifying a kind of protease having His-tag. The pro
Hi CCP4 community!
I have constructed a homology model of a deletion variant of a protein whose
structure has already been solved. These deletions are 3-4 amino acid in
length and are in a loop that connects two helices. The model structures
look good with respect to bond lengths in the aforeme
--- Marius Schmidt <[EMAIL PROTECTED]>
escreveu:
> Dear colleagues,
> I was wondering whether someone of you has
> reported/published
> new or improved crystallographic software somewhere
> else than Acta Cryst. It would be nice if you could
> share your experience with me. Topics might be:
> - qu
On Wednesday 28 February 2007 11:08, John Bruning wrote:
> When using Refmac how does one find/calculate R-free error in the highest
> resolution bin?
R and Rfree by shell are in the data-harvesting output file
What is "R-free error"?
--
Ethan A MerrittCourier Deliveries: 1959 NE
When using Refmac how does one find/calculate R-free error in the highest
resolution bin?
Ngo Duc Tri wrote:
Dear CCP4 users,
I'm purifying a kind of protease having His-tag. The protein is
expressed in insect cells and broken by sonication.
I used NTA resin to purify this protein.
Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl. Buffer B is
50mM phosphate buffer pH 7.5,
Well since Jim answered I must do also!! Bruker, together with Incoatec,
has on the market a new Incoatec Microfocus Source with novel QUAZAR
multilayer optics which in my understanding is significantly brighter
than the other systems referred to. This source is very interesting as
it is air cooled
Sankar
We had an Oxford Diffraction PX system, with the same goniometer and
detector as the Nova, for 3 years until last Fall when we upgraded to
the Nova. We also have 3 other Xcalibur instruments with the same
goniometer and control systems. All four diffractometers have
performed reliably
Dear CCP4 users,
I'm purifying a kind of protease having His-tag. The protein is expressed in
insect cells and broken by sonication.
I used NTA resin to purify this protein.
Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl. Buffer B is 50mM
phosphate buffer pH 7.5, 300 mM NaCl and 300 mM I
Hi,
I've managed to do a pretty good job of confusing myself in my latest
attempt to understand the likelihood stuff, and was hoping that I could
get some pointers as to what I'm misunderstanding.
1. How does one determine the amplitude and phase to use from a given
likelihood surface? Some of t
Of course, the Rigaku system would be the best.
Jim
On Wed, 28 Feb 2007, Sankar Narayanan Manicka wrote:
Hi,
Our lab is planning to buy an X-ray machine for protein crystallography.
Which system would be best for home source, Oxford diffraction system
Xcalibur Nova or a MSC/Rigaku MicroMax-
Hi all,
Thanks for those who replied so far. I can see that the
solubility issue is not that problematic for the crystallization work
(as Kendall mentioned).
I recall that some people on the board reported in a different
thread that they tried the solid powder in the crystallization dro
hahaha! brazilian humour - always cracks me up!
for those of you whose portuguese is a bit rusty, let me provide a quick and
dirty translation:
video de pessoas famosas em cada situa?ao!!!
"videos of famous pessaries in situation comedy"
clika o lik p/ ver o video se nao der disite
why don't you just send all your images to the ccp4bb, then we'll
process them, solve the structure and publish it for you.
And we might put you in the acknowledgements, if you are lucky.
Mark
On 28 Feb 2007, at 16:35, Jonathan Grimes wrote:
Anastassis Perrakis wrote:
On Feb 28, 2007, at 14:3
Hi Ibrahim,
I think solubility is overrated.
We routinely obtain structures from protein solutions with a big pellet of
ligand in the bottom of the tube. For co-crystallizations we add 1mM
compound to a 0.3mM solution of the protein and incubate overnight. Many of
the compounds are only soluble t
Dear all,
I have a small library of In-silico screened compounds to test for
activity and for crystallization trials with our protein of interest.
We only have about 10 mg/ml of each compound. As there is no
available experimental information about solubility of these
compounds, I have n
>On Feb 28, 2007, at 14:37, shivesh kumar wrote:
>
>Dear all,
>I have a data set at 2.2A, of the selenomethionene labelled
>protein.How should I process the data.
Some hopefully useful remarks (fairly random and not complete and
exhaustive):
1. make sure to mask out the backstop and beamstop hol
video zueras do tooby
video de pessoas famosas em cada situaçao!!!
clika o lik p/ ver o video se nao der disite a url em outra janela
-->http://h1.ripway.com/videozueras/52609-videozueiras.rar
Anastassis Perrakis wrote:
On Feb 28, 2007, at 14:37, shivesh kumar wrote:
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.How should I process the data.
Carefully !
Thanx for the help.
Shivesh
Tassos
i am sure what tassos really meant was "Very Careful
> Dear all,
> I have a data set at 2.2A, of the selenomethionene labelled
> protein.How should I process the
> data.
Properly
On Feb 28, 2007, at 14:37, shivesh kumar wrote:
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.How should I process the data.
Carefully !
Thanx for the help.
Shivesh
Tassos
Dear Pat,
I too am shocked by the extra-long lifetimes the current batch of MM
filaments have. I've had filaments in both our instruments (a M007 and
an M007 hf) since August and they are still going strong.
Not long ago I would replace a filament before it blew if I knew there
was an importan
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.Howshould I process the
data.Thanx for the help.
Shivesh
CONTACT from the CCP4 suite can do this - have a look at the documentation
and examples.
Tadeusz
"mathias" <[EMAIL PROTECTED]>
Sent by: "CCP4 bulletin board"
27-Feb-2007 18:43
Please respond to "mathias" <[EMAIL PROTECTED]>
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
[ccp4bb] software to calcul
Dear Colleagues,
During more than three years of operation, I have recorded considerable
difference in filament lifetimes on my Micromax007: roughly in the range
500-2000hrs. Some of this may be accounted for by poor manufacture and Rigaku
have, in the past, noticed this problem and replaced so
Hi Mattias,
CCP4mg will list contact areas in the form of the attached file.
This is evaluating the buried area (ie difference is solvent accessible area
with and without the ligand bound).
It ought to be possible to run a script if you have a significant number of
structures - contact me for
Two postdoctoral positions in
membrane protein crystallography at the
Stockholm Center for Biomembrane Research
The Center for Biomembrane Research (CBR), located at Stockholm
University, is a newly formed strategic research center funded by the
Swedish Foundation for Strategic Research and head
Well,
cp solve.com test.inp
would be your starting point. You should now be able to run it.
Next you might want to use your favourite editor (say gedit on Linux,
which is a bit like notepad on Windows) to make some changes to it, if
it doesn't do exactly what you want. To do that, you will hav
Hi, All,
If I have a solve script named solve.com and I can use command
./solve.com
to run it, now I want to write a script named test.inp and use command
./test.inp
to run it, how should I write it?
Thanks
Li Yang
43 matches
Mail list logo
