MX-beamtime at BESSY-Berlin period: January/2008 - December/2008
Next MX-proposal application deadline: August 15th 2007
See:
http://www.bessy.de/boat/www/
We kindly request MX-proposals for beamtime applications for the next
beamtime period: January/2008 - December/2008.
In order to app
It could be a hardware problem or it could be a mis-configuration. The card
you list DOES support stereo viewing in all crystallographic applications, I am
sure, because we have the same hardware (except our computers are 64 bit and we
run CentOS operating system, but otherwise identical).
As
Are you using the NVidia drivers and if so, how have you configured your
xorg.conf file? It may be a hardware or a configuration issue. A fellow lab
here was having a problem with no OpenGL programs running properly and odd
resolution issues after installing the NVidia drivers, turned out the
Dear all,
I think our earlier posting is not clear. So we would like to
draw to your attention regarding our stereo viewing problem. As Dr. Paul
Emsley suggested it seems to be a harware problem, we are experiencing the
same problem not only using coot but other programs too. We will
Hello venkadesan krishnan,
On Mon, 2007-07-16 at 15:57 -0500, venkadesan krishnan wrote:
> Hello everyone,
> We have bought a new Dell Precision Workstation
> 690 (32-bit) and installed Fedora core 6. We are having problem while
> viewing molecules in harware stereo mode usin
Dear all,
We are happy to announce the release of ARP/wARP version 7.0
Please visit http://www.arp-warp.org for details and software download.
The major improvements are:
• A new module for ultra-fast low resolution tracing of helical and
beta-stranded fragments at resolution down to 4.5 A.
•
Hello everyone,
We have bought a new Dell Precision Workstation 690
(32-bit) and installed Fedora core 6. We are having problem while viewing
molecules in harware stereo mode using programs coot, pymol, etc.
The graphics card came with system is, 256MB PClex16 nVidia Quadro Fx
I am forwarding an answer I sent previously in response to a similar
question. We used refmac5 to refine a number of acyl-enzyme structures:
Radisky ES, Lee JM, Lu CJ, Koshland DE Jr.
Insights into the serine protease mechanism from atomic resolution
structures of
trypsin reaction intermediates.
Dear all,
I am trying to refine a serine protease crystal structure using REFMAC5.
The density at the protease active site clearly indicates an acyl-enzyme
intermediate as a result of nucleophilic attack on P1 substrate residue by
the active site serine.
The model thus should display serine Og
Moleman2 can do that. You can get it from Uppsala Software Factory.
-Original Message-
From: fang sheng [mailto:[EMAIL PROTECTED]
Sent: Mon 2007-7-16 14:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] calculate B-factor of individual parts
Dear all,
The refmac output lists B-factor of
Dear all,
The refmac output lists B-factor of each individual atom. But how can I get
the B-factor of each set of group, say, protein, ligand A, B, and all 300
waters?
suzi
_
http://liveearth.msn.com
That's interesting. I was not aware that procheck paid any attention
to anisotropic ADPs.
Try feeding your PDB file to the Parvati web server.
It will look for problems with your anisotropic model.
http://skuld.bmsc.washington.edu/parvati
On Friday 13 July 2007 01:15, Jiamu Du wrote:
>
Hi,
You can try the following to improve your protein-DNA complex crystals:
1) Try HPLC purified oligos. You can get that from IDTDNA instead of the
standard desalting form. Alternatively, if you have access to a reverse phase
HPLC/column, if you order DNA with Trityl group on, run it on th
Dear all,
We have an opportunity for a highly motivated crystallography
scientist to join the protein structure group at Genentech. The
successful candidate will participate actively in our structure-based
drug discovery programs and engage in the structural elucidation of
proteins and pr
Hi Kumar,
1) While you contemplate other ideas, have you tried the following already?
- microseeding or macroseeding with the tiny crystals you have?
- crystallization using sitting drop vapour diffusion under oil? Often, one
gets a burst of
nucleation with several tiny crystals. Not sure if thi
On Jul 16, 2007, at 12:01 PM, bputcha wrote:
I am trying to crystallize a protein-DNA complex. I purify the
protein finally
using gel filtration. I purchase
single stranded complementary oligos (desalting from idtdna.com),
mix them up
How can I purify the duplex DNA further?
in my exper
Following up on Prof. Rice's suggestions about trying different ends and
reading the literature, you might have a look at
Crystallization of the yeast MATalpha2/MCM1/DNA ternary complex: general
methods and principles for protein/DNA cocrystallization.
J Mol Biol. 2000 Apr 7;297(4):947-59.
PMID: 1
Kumar and Joe-
I'm not sure if this helps but I always purified my oligos prior to
crystallization. Originally, I would order them with the trityl-group on
and purify then on a reverse phase HPLC column and used TFA to cleave on
column. Although towards the end of the project, I just ordered the
Dear Kumar,
One often has to try duplexes with many different
ends before getting decent crystals (e.g. 18 for
one project in my lab, even more for others).
Depending on your Kd, you might find that your
complex falls apart during gel filtration.
How long are your oligos? Gel purification
som
Hi Kumar,
I also have the same issue. If you get any helpful response, could you
forward me a copy? Thank you.
P.S. Could anyone who has any comments or suggestions on this issue also
forward the response to ccp4bb? Thank you in advance.
Best,
Joe
On 7/16/07, bputcha <[EMAIL PROTECTED]>
Hi,
I am trying to crystallize a protein-DNA complex. I purify the protein finally
using gel filtration. I purchase
single stranded complementary oligos (desalting from idtdna.com), mix them up
and make DNA duplex by
heating to 95 degree C and cooling to room temperature. I mix protein and DNA,
Dear crystallography colleagues,
I very much hope that you have or will send in your comments on the
NIH Protein Structure Initiative. You can send in comments until this
Friday. I've listed below a few accomplishments of the PSI you may
want to mention. I've also added a brief analysis showi
Dear all,
Could you let me know where I can get or calculate the standard
accessible area of residues?
I want to determine if a residue is a solvent accessible one or buried
one by calculating the ratio of solvent accessible area to standard
accessible area.
I managed to calculate the solvent ac
Do you mean you only have experimental data to 2.3A - if that is the
case I am afraid you cant force REFMAC to work to higher resolution.
Do you mean you just want SFS calculated to 2.2A ?
Eleanor
JOE CRYSTAL wrote:
Dear all,
I am refining a structure in Refmac at 2.3 A and I set resolution
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