Amit Sharma,
I second Tim's suggestions.
The first experiment is the following.
Set up several experiments at constantly decreasing precipitant
concentrations.
Streak seed all of them. If in any of those you can get non-clustered
crystals
non matter what size, seeding can solve your problem
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Brisbane, Australia
A post-doctoral position is available in the lab of Jenny Martin, at
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Further information, including the position description and selecti
Hi Tim,
I cannot comment on the installation/hardware problems. But I can give
you a hint on how to 'invert polarisation': Switch the stereo sides. In
pythonic Coot use:
switch_stereo_sides()
For convenience a while back I made a 'zalman stereo toggle' toolbutton
together with a 'switch sid
Dear all,
I am getting protein crystals in clusters. How can I achieve isolated
crystals.
Thanks
Amit Sharma
As Roger writes "One way to separate crystal cluster is to poke them
with a tiny probe". We are often using acupuncture needles as easy
to get and cheap microtools which have very lo
Dear Sudhir,
you have very clear density in the upper right corner of your blob. Just
adding the oxygen and running real-space-refinement in coot should do
the trick.
Best,
Herman
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Sudhi
Hello Sudhir,
In coot, go to the
"Calculate" menu, select "Other Modelling Tools" and in the upcoming window
choose "add OXT to residue"
Tim
On Tue, Apr 13, 2010 at 04:03:27PM +0900, Sudhir Kumar wrote:
> hi all,
> I'm refining a structure in which cysteine is bound to the active site as a
> li
A post-doctoral position is available in the Structural Motility Team
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Our research project includes structural studies of molecular motors in
close collaboration with functional studies.
Our goal is to understand how the
Dear colleagues,
please be informed that the registration slot for the
8th International NCCR Symposium on New Trends in Structural Biology
2 + 3 September 2010, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland
is now open. Online registration is possible directly from the symposium
website
Dear all,
How can i show electron density map for my ligand in pymol, which is bound in
the active site.
i uploaded map as .xplor extension to the map file..
thank u
Hussain
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MiTeGen has a set of soft plastic microtools that are inteded for this
kind of stuff, and I have had suscess using them to break out single
crystals from clumps or fused crystals. You can either load in a
pencil or mount in a base.Also nylon loops. You might need to
have one tool in each hand
I know this is a disputed topic, but is there any reference where
anyone has systematically tested different res cut offs for refinement?
Eleanor
Hussain,
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html
which is the top hit when you google "pymol electron density". Using
google (and not to appear biased, other available search engines) is the
most valuable advice (per word) that you may possible get.
On Tue, 2010-04-13 at
Dear Hussain,
in the electron density example of this tutorial, the parameter
"carve=1.6" is used, which means that density is only shown within a
radius of 1.6 A around atoms. This is usually done for clarity, but may
give an unrealistic impression of the density quality. Here, you should
ca
On Tue, Apr 13, 2010 at 09:24:13AM -0400, Nathaniel Clark wrote:
> [...] If you don't want to buy those tools just try 2 nylon loops, and lots
> of patience.
Or use cats whiskers which you can fix into a Pasteur pipette with wax, nail
varnish, plasticine, etc.
I find them to have just the right s
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Chester Beatty Laboratories
Chelsea, London
Postdoctoral Training Fellow
Structure-Based Development of Tankyrase Inhibitors
The Institute of Cancer Research (a College of the University of London)
is a world-class cancer research o
Probably the only phasing stat that I pay any attention to these days is
the Figure of Merit (FOM). This is because, the _definition_ of FOM is
that it is the cosine of the phase error (or at least your best estimate
of it). FOM=1 is perfect phases and FOM=0 is random phases, and a
reasonable
This is an interesting thread, and perhaps I should not dive in on such
a heady topic, BUT, I do want to point out my own particular bias
regarding FOM that is not entirely consistent with James' point of view.
In my experience, the FOM obtained after density modification runs are
almost always ext
Hello,
If you have crystals that you would like to screen or collect data on, there is
time available starting April 15 on the X6A beam line at the NSLS,
http://protein.nsls.bnl.gov
If you have visited the beam line before you can take advantage of the
ProteinXpress program
(http://protein.n
Dear Crystallographic Community,
Dr. Holton made a comment today that got me thinking on the issue
of modeling. This has been a hotly debated topic in our own lab
but I would like to hear the current opinions of the community as
a whole. It is a question of two parts.
First, what do you thin
Dear K,
I do think there is much of a hornet's nest to be stirred up by your
questions.
I hate to advertise it, but chapter 12 of BMC has a thorough discussion of
the
subject.
Ad riding: ADDING riding hydrogens is not exactly the same as MODELLING
some stuff one has no clue about (like parts with
I should add a comment here about density that might or might not be there :-)
Graphent - trying is believing
Jürgen
On Apr 13, 2010, at 9:29 PM, Bernhard Rupp wrote:
> Dear K,
>
> I do think there is much of a hornet's nest to be stirred up by your
> questions.
> I hate to advertise it, but ch
Hi all,
I'm currently trying to crystallise a two domain protein which
contains several structurally important disulfides. We have a high
resolution structure of one domain (~1.4 A resolution), which reveals
quite a few solvent-exposed lysines, some of which are involved in
crystal-contac
Interesting remark in fact given what maximum entropy methods can
accomplish
in classical image reconstruction, I am not sure why they are not more used
in
crystallography suppose the GlobalPhasing fellows may comment
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Dear Oliver,
In our lab, reductive methylation using dimethylaminoborane is regularly
performed, and nearly everything we work on have native disulfides.
Among five or six reactions I've performed on molecules with disulfides,
I have not had a case where solubility or stability was affected.
Staff scientist position is available in the research group of Kristina
Djinovic-Carugo in the Department for Structural and Computational
Biology, Max. F. Perutz Laboratories at the University of Vienna,
Austria. Areas of the group research include structural biology of
F-actin based cytoske
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