Dear All:
Only by using CCP4, how to perform anneal refinement ?
Thanks
--
Jiamu Du
Key Laboratory of Proteomics
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
Hi Sam:
You need to index in P222 and find out the axis that does not have
systematic absence (not screwed) in P21212, then rationalize yourself how
to switch this axis to c while keeping the same handness.
But since you already know the correct index a = 96.54 b = 121.95 c =
75.33 and yours a'
I usually buy my IMAGE clones from Geneservice in the UK
(http://www.geneservice.co.uk/products/image/index.jsp), if you buy more
than 75 clones the price per is GBP 33.75 which is CAD76.62 according to the
google exchange rate...
Flip
-Original Message-
From: CCP4 bulletin board [mailto
It depends on scale. With some synthetic DNA companies if you order many
at once, you can get a huge discout, down to maybe 35-45 cents per base.
Alternatively, if you have free labor (students) then you can
multiparallel your PCR, but $100 per clone is going to be hard to beat
given the fact that
Sorry a little offtopic...
We'r trying to clones a number of putative human proteins for
crystallization. Besides IMAGE clones from OpenBiosystem, is there any
the cheaper way of obtaining human cDNA clones? OpenBiosystem
is okish, ~$100Cdn for each clone, but does get abit expensive when you
I am writing on behalf Zbyszek Otwinowski.
This problem was supposedly corrected in later versions of
the program but in any case is benign unless number of such
lines is very large (thousands).
You can simply ignore it.
Dominika
Nalam, Madhavi wrote:
Hello:
I am posting this question on beh
Do you have any data to support the implication that Acta F will have
a lower citation factor than Acta D?
Checked a web of sciences "Citation report" for a search with the year
2005 and "source titles":
ACTA CRYSTALLOGRAPHICA SECTION F STRUCTURAL BIOLOGY "AND"
CRYSTALLIZATION COMMUNICATI
On Monday 19 February 2007 11:39, Jon Wright wrote:
> Acta D is likely to improve again following the creation of Acta F in 2005.
Do you have any data to support the implication that Acta F will have
a lower citation factor than Acta D?
FWIW, the impact factor of Acta D was down in 2005 relative
Hi,
The point is to check where you have the non helicoidal 2fold axis (no
extinction). I guess, it will be the 2-fold axis along your a parameter.
Then, you have to reindex, because the convention is to choose the 2
fold axis along c.
Goood luck,
Claudine
U Sam wrote:
Hi
I crystallized a
Kevin Cowtan wrote:
Acta D has for some reason a rather poor impact rating, and J. Appl.
Cryst. a rather better one.
There is no outlier rejection in the calculations for journal citation
reports (eg: impact factors).
Congratulations to: Spek AL, "Single-crystal structure validation with
t
Hi, Sam,
I think you have the same crystal form as that which was reported. The
screw axes are not assigned when you index and integrate your data.
HKL2000 will assign the unit cell edges from shortest to longest for a, b,
and c. You'll assign the screw axes when you scale the data. It looks
Hi
I crystallized a protein in different condition than reported before and
structure had been already reported by other group. In both cases space
group is P21 21 2
Right now I am not interested in solving the structure, but to look for some
other properties.
I see a difference in cell dimens
Hi Emmanuel,
try MZ protocol (MZ = multi-zone) in phenix.refine. It does the smart
rigid body refinement starting from a few low resolution reflections and
ending up with using all data. In-between it does the maximum-likelihood
bulk-solvent modeling and scaling. All together it results in a V
As co-editor of J Appl Cryst, handling teaching/education and computer
software mainly, J Appl Cryst is the appropriate journal in the IUCr
series for publishing new software, improved software, tutorials, etc.
We would strongly encourage you to submit such manuscripts to J Appl
Cryst, both 'biolog
On Mon, 19 Feb 2007, Patrick Loll wrote:
Matlab
octave is the free software answer to Matlab:
www.octave.org
i heard it can take matlab scripts.
-bryan
> The mathcad image processing module is too expensive for my taste.
My university has a campus- wide license for Matlab, so it's *free* for me...
I have no idea of what it would cost to purchase.
[reminder: never compare "educational licensing" with giving drugs to
schoolchildren.]
For so
Dear all,
I apologize for the non-ccp4 related question.
However, I am trying to crystallize a (very pure) protein, but
according to the mass-spectrometry data, it's able to form dimers and
even trimers..
I was told that adding DTT (dithiothreitol) to the crystallization
conditions could p
I would take a well-ordered helix out of your
allegedly-correctly-placed model (BEFORE doing any refinement other
than rigid body), phase a 2Fo-Fc and an Fo-Fc map with it, and see if
the helix shows up. If it does, there is some reality in your
solution. If it doesn't, start over from scratc
Hello,
This is another off-topic question.
We are trying to purify a putative ATP-binding protein. What kind of
beads or column would work best in this situation?
Jena Biosciences sells a kit of four different ATP-Sepharose beads
with different attachment points of the ATP to the solid matrix.
Bernhard,
I've used Matlab to calculate 2D FTs (eg, a Cowtan-esque FT of a
cat). I'm sure you could come up with a way to do the phase
coloring without too much sweat--the degree of flexibility available
to you in this program is quite large. My university has a campus-
wide license for
-- Forwarded message --
From: Daniel Adams <[EMAIL PROTECTED]>
Date: Feb 16, 2007 12:29 PM
Subject: Re: [ccp4bb] pseudotranslation and dyads in NCS
To: [EMAIL PROTECTED]
My apology for not mentioning unit cell,
The P1 unit cell is 74 91 116 109 105 90
Any suggestions or comments
Dear Bernhard,
Have a look at the Java applet "Diffraction and Fourier Transform"
located here: http://lcr.epfl.ch/page37304.html
You can draw an image, periodic or not periodic, the application will
compute the FFT. You can then select either phases or magnitudes or
Re/Im components and com
Hi,
You may want to have a look at ShaFFT:
http://www.ibg.uu.se/static/exjobb/00/5.pdf (the undergraduate
project write-up)
You can download the program from ftp://xray.bmc.uu.se/pub/alwyn
(file is shafft_export.tar)
Cheers,
Martin
On Feb 19, 2007, at 4:35 AM, Bernhard Rupp wrote:
[posted on behalf of Lydia Tabernero]
UNIVERSITY OF MANCHESTER
FACULTY OF LIFE SCIENCES
POST DOCTORAL RESEARCH ASSOCIATE
This post offers an excellent opportunity to join a dynamic research
team in the Structural Biology group o
Interestingly enough (or not as the case maybe), the CCP4 study
weekend now goes out as the January issue of Acta D in order to try
and raise the impact rating. Something to do with the scoring
working on a calendar year.
Charles
On 19 Feb 2007, at 10:50, Kevin Cowtan wrote:
J. Appl. Cr
J. Appl. Cryst.
I have used it for things which I think need publishing, but are of more
abstract subjects and less direct interest to the biological
crystallography.
However, politics and finances may dictate otherwise. Acta D has for
some reason a rather poor impact rating, and J. Appl. Cr
Just an aside to this - I have had R factors > 55% which then refine..
It is when they dont refine you are in trouble ..
Eleanor
Jiamu Du wrote:
*Dear Prata:*
First, I think you'd better check your subgroups. Maybe you got
opposite hand of the data.
Or change a model. When the Rfactor is ab
Dear All:
I am trying to make FFTs of images of assemblies of
spheres and other shapes to explain diffraction, the
usual thing. So far I do this through cumbersome
cludges, and I bet there are better ways, and I
am looking for free or cheap software to do this.
I load the image into basic math
Hi,
I dare say with an R-factor of 0.64, your MR solution is simply wrong.
Just into the blue, you could
1) try various MR-programs (phaser, molrep, amore...)
2) try a different search model
3) try your best model but start with subdomains or chop off possibly
flexible parts
4) have a look at
Dear All,
I appreciate the feed back from my question. I refined anisotropically without
hydrogens and when I was satisfied with the model I added hydrogens with zero
refinement cycles in REFMAC5. This worked equally well as adding hydrogens
earlier in the refinement stage and keeping them pr
*Dear Prata:*
First, I think you'd better check your subgroups. Maybe you got opposite
hand of the data.
Or change a model. When the Rfactor is above 0.55 after MR, I think it means
nothing.
On 2/16/07, Emmanuel Prata <[EMAIL PROTECTED]> wrote:
Dear all,
I have a data set of a protein soake
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:
- quality of the journal
- rapid publication
- literate peers
- ...
On 2/8/07, Justin Schmitz <[EMAIL PROTECTED]> wrote:
Morning every body!
Does anybody know a board for NMR releated questions which has a quality
like this?
Both the NMRPipe and ARIA lists have some decent general NMR discussion in
the style of CCP4BB, in addition to the discussion related
However, be warned that your structure needs to be very sexy to get
into Cosmo, and then there might be better choices. If it is not,
but has a few stacked beta sheets, you may be able to color the
figures in plaid designs and get into American Rifleman (I assume
there is no European Rifl
Hey Emmanuel
Typical R-factor for random structure will be above
57% and for initial MR model it will be somewhere
between 40-50%. In your case, High R-factor might be
due to many reasons.
So check the data for any twining and also again check
the Space group. Because sometime you will end up
Cheers,
Many thanks to all of you who sent in the (mostly positive) helpful
replies. A lot of folks asked why do we have to place the structure on
hold - since this is a pretty typical example of how industrial
crystallographers have to operate sometimes, I will attempt to explain.
We have a choi
To understand this one at least needs the P1 unit cell..
Operators 3 4 and 5 are almost the same rotation.. It is unlikely that
they are all 2 folds?
Eleanor
Daniel Adams wrote:
Hi bb,
I am working on P1 dataset, SAD phasing resolution is 3.5 and trying
to build model. However I am facing d
I think Martha Stewart's magazine has fairly liberal data deposition
policies as well.
_
Eric A. Toth, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
Marlene and Stewart Greenebaum Cancer Center
University of Maryland
Hello:
I am posting this question on behalf of my colleague.
Thanks,
Madhavi
-Original Message-
From: Romano, Keith
Sent: Friday, February 16, 2007 10:43 AM
To: Nalam, Madhavi
Subject: FW: scaling question
I am in the process of scaling synchrotron data with scalepack, and I
am havi
If you publish the paper a year from now, with no hold,
will everyone be happy?
-Original Message-
From: CCP4 bulletin board on behalf of [EMAIL PROTECTED]
Sent: Fri 2/16/2007 6:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] journals with on-hold policy
Dear CCP4ers,
This is a new qu
Registration is now open for the
EMBO Workshop on
THE CHEMISTRY AND BIOCHEMISTRY OF CATALYSIS BY BIOLOGICAL SYSTEMS
20 - 22 June 2007, EMBL Hamburg
http://www.embl-hamburg.de/workshops/2007/catalysis/
Registration deadline: 31st March 2007
Workshop aims:
With the continuously emerging ne
If the work is funded by the NIH, you must deposit and release
coordinates upon publication regardless of the journal's policy.
http://grants.nih.gov/grants/guide/notice-files/not99-010.html
Joe Becker
Merck Research Labs
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From: CCP4 bulletin board [mailto:[EMAIL PROTEC
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