Memmert?
http://www.memmert.com/en/products/product-range/peltier-cooled-incubators/overview/
- J. -
Michael Hothorn wrote:
Dear all,
sorry for the off-topic question. I am looking for an affordable+small
crystallisation incubator (16-21 deg Celsius). Ideally, it would fit
neatly under my
Hi everyone,
I'd like to bring to the attention of anyone looking for a postdoc position
in structural biology that I currently have two vacancies in my lab., which
is based in Norwich in the UK.
These projects are focussed on structure/function studies of 'effector'
proteins from microbial patho
Dear ccp4 Users,
I would like to say thank you to all of your valuable advices to optimize
the needle crystal and related problems when dealing with membrane protein.
Here I report the summary of your advices to help other students who got the
same problem:
1. Additive screening from Hampton Rese
You must be asking for a MAP to be calculated - see near the top of the
GUI. click off this radio button and the warning should go away.
Eleanor
Chavas Leo wrote:
Dear Sajid --
Thanks for your suggestions to run revise. Suggestions
from Mike Latchem helped me to overcome the problem.
I have
I think you get this problem whether or not you have selected to write a
map. I find that you need to open up the dialogue for maps set to
temp.map and temp1.map and then the gui remembers that going forward
whether or not you deselect the option to generate a map. It also means
you cannot ru
You might have to test if it is salt/detergent or protein crystal first. If
it is really protein crystal, never give up and for needle crystal,
generally it is difficult to optimze, however in most cases, the diffraction
is well enough. If it is protein crystal, as some researcher has mentioned,
fi
Hi,
I can confirm what Bert Van Den Berg wrote about the round shaped
"crystals". It seems to appear often with DDM (in my case too, even
sometimes in several drops per screen) and first looks like phase
separation. Then it starts to be hard and is looking like a small CD
under the microscope
Hi,
it could be really useful in refining low resolution structure (with
poor electron density map) to have a refinement program that can
restrain phi and psi angles to follow Ramachandran plot. Does anyone
know if such program exist?
Thank you,
mario
Mario Milani, PhD
University of Milan
Another possible, and easy, way to optimize initial hits is to take your hit
condition in the reservoir and add small volumes (say 10% or so) of other
screen solutions. In this way you get small deviations from the initial hit
condition that may lead to better crystals or at least gives you hint
Hi Mario
Maintaining the secondary structure of your protein when refining against weak
data can be really challenging.
There are some options, but in the end you might have to accept a fairly large
number of Ramachandran plot outliers.
Try phenix.refine with the keyword "discard_psi_phi=Fals
Remember that phi-psi angels are excellent for validation purposes,
but only when they are unrestrained, so if you restrain them you
lose this option.
The above is a very important point!
Having now said that, restraining alpha-helices hydrogen bonding, and
beta-sheet cross-strand hydrog
After many warning messages, I think I have to clarify the meaning of
my question. After careful refining, in a low resolution structure
often many residues (mainly in loop regions) can still adopt
different dihedral conformations which are equally compatible with a
low resolution electron
Don't be afraid of trying to shoot needles. You'll have to improve yours but
it was possible for me.
I managed to increase the size of some needles to the point where I could (with
great difficulty) pick them up with a loop and shoot them. The key was
changing the cation from Na to Zn2 . Tr
I co-crystalise a protein with insoluble ligands fairly frequently and
normally dissolve the ligand (about 1mg) in 50ul DMSO and then add
450ul buffer. The solution is often rather cloudy so I set up one set
of hanging drops with the cloudy solution, then spin out the
precipitate and set up
Dear All:
Is there a simple graphical way to generate atoms that lie on a surface
(and wite out a pdb file) for modeling surface docking experiments?
Thanks a lot
Subbu
I am looking for Cerius2 type but any code will be fine
I have recently installed QNIFFT on an SGI machine and
am trying to use it to calculate the electrostatic
surface potential of an RNA structure.
The installation went fine and I am able to run the
program, but I keep getting this message- "error
reading the radius file".
The radius file I am usin
Dear All,
I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook Pro
(Core Duo model).
I would like to install coot using fink, but am getting stuck when it
comes to installing ruby. Has anyone else experienced this problem?
Also, are there any alternative solutions to installi
On 17 Apr 2008, at 6:07 PM, Buz Barstow wrote:
I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook
Pro (Core Duo model).
I would like to install coot using fink, but am getting stuck when
it comes to installing ruby. Has anyone else experienced this problem?
I've spent the a
Dear bb members,
I just installed the most current version of refmac5 for Mac OSX.
When I attempt to run it, however, it fails with an error message:
The program run with command: refmac5
... (lists input and output files)
has failed with error message
error in dsyev_mo
Dear Chris et al,
My guess is something needs ruby built as a build-time dependency, but
coot doesn't require it. In any case, I've got the latest version of
ruby built and anyone who needs it can download it from one of my
servers as described on this page:
http://tinyurl.com/h2lzq
That
Hi,
Does anyone have experience with molecular replacement at low
resolution? I have a 6Å dataset with probably 3-4 monomers per ASU.
Phaser doesn't seem to give me clear results. Can I get some advice?
Any comment will be appreciated.
Thanks a lot,
Junyu
===
Hi Bill,
Thanks for your advice! Ruby now installs on my machine, as does Coot
(which is what I really wanted).
Unfortunately, coot is unhappy with my X11 install. When I run coot, I
get the following error:
dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib
Referenced from:
Hi Buz:
You need to upgrade to the current (three day old) X11, available from
here:
http://trac.macosforge.org/projects/xquartz
It fixes a lot of bugs, so the pain you are being subjected to now
will be worth it.
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Hi Bill,
Thanks a lot for your advice. Coot now installs and runs, however, I
do get some warnings;
** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/coot/
pixmaps/connect-to-ccp4.svg
** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/coot/
pixmaps/connect-to-
I have
i librsvg22.9.5-11SAX-based render library for
SVG files
i librsvg2-gtk2.9.5-11Enable GTK to use SVG data
i librsvg2-shlibs 2.9.5-11SAX-based render library for
SVG files
Do you have all of those installed? If not, the package i
Hi Bill
Up until a moment ago, my installed fink packages (matching librsvg2)
were;
librsvg2 2.9.5-11 SAX-based render library
for SVG files
librsvg2-bin 2.9.5-11 SAX-based render library
for SVG files
i librsvg2-gtk 2.9.5-11
Dear Buz:
Not sure why you have to install ruby. But if you describe the
problem, I might be able to help.
Meanwhile you can use what I pre-compiled:
http://tinyurl.com/h2lzq
This will speed things up by a few orders of magnitude.
Bill
On Apr 17, 2008, at 10:07 AM, Buz Barstow wrote:
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