A Post-doctoral position in chromatin structural biology is available in my
group. My lab aims to characterize proteins and protein/DNA or RNA complexes
by
X-ray crystallography in combination with other biochemical and biophysical
techniques.
Applicants should have a Ph.D. in structural b
On Dec 20, 2010, at 1:16 PM, jlliu liu wrote:
> it is also within hydrogen bonding distance to the main
> chain N of another protein residue.
This also strongly suggests it is not Mg2+, which prefers hard ligands such as
charged oxygen, rather than softer ligands like uncharged backbone nitroge
I am very sorry for trouble by sending picture,and won't do it again
Hi,
I saw the same thing once and the cause was that the crystal had been
hideously over-exposed during data collection. As a result, essentially
all the spots at lower than 2.5A resolution were overloaded. The Wilson
plot was thus more or less flat at medium to high resolution and
accordingly the
Hi Jim,
If I remember correctly the delay volume from the pumps to the top of the
column is roughly 8 ml for Äkta Purifier, Explorer and also Prime. The actual
volume from the bottom of the column to the fractionator, or more important
from the UV cell to the fractionator depends on the tubing
The Lawrence Berkeley National Laboratory has an opportunity for a
Computational Biologist Postdoctoral Fellow as part of a project that
will involve writing the software to process X-ray diffraction
patterns from protein crystals analyzed on the free-electron laser at
Linac Coherent Light Source.
Hello all,
Does anyone have a rough estimate (or has anyone actually determined) an
average dead/delay volume between buffers run on an AKTA Prime FPLC? We are
attempting to overexpress/isolate a smaller His-tagged transmembrane protein,
and require running several detergent buffers in success
Another option would be to collect data at the Mn K edge (1.89A) - at this
wavelength Mg has a weak anomalous signal that you should still be able to
detect. I've used Mn K edge to successfully distinguish between Mg, Mn and
Ca ions as well as identify them as ions and not waters by looking at pea
Hi,
I'm not sure if it has been mentioned yet, but you could take an
experimental approach if you still have crystals. You could soak them with
EDTA/EGTA and if the density disappears that is good evidence it was Mg (or
other divalent cation), if not then putatively water. You could also soak
wi
I agree. It is very unlikely to be Magnesium ion; may be an ordered water!
I'd recommend to have a look at the following paper which discusses the
different properties of Mg2+, Mn2+, and Zn2+.
Charles W. Bock, Amy Kaufman Katz, George D. Markham, and Jenny P.
Glusker. Manganese as a replaceme
Using different web servers on your refined structure is good thing to
do. But for distinguishing metal ion, specifically Mg, from water was
done unambiguously before these programs existed. The simple rule is two
fold: 1. distance; 2. coordination. For Mg ion distances are between 2
and 2.2 A and
Yes the BV method relies on summing up the 'bond valence'
contributions for each ligand co-ordinated to the metal, and comparing
the result with the formal charge on the metal ion (e.g. +2 for Mg).
This means that even if say one water that is present in the crystal
is omitted from the calculation
You might also like to look at the paper "Is the bond-valence method able
to identify metal ions in protein structures", Acta Cryst. D59 (2003)
32-37. In retrospect, the BV method is very good for identifying Mg2+
because it is almost always tightly octahedrally coordinated by oxygen
atoms. For
I think it would be a lot easier to understand what's going on if you
posted your actual scripts.
Cheers
-- Ian
On Mon, Dec 20, 2010 at 6:11 PM, wrote:
> Thanks Ian, but I was using the output from 2a for 2b running. Results are
> still different between 2 and 1. More curious is more second qu
Note that the original Nayal & Di Cera algorithm uses an older and
less preferred version of the bond valence model and its associated
parameters than current implementations of BV.
The original WASP uses this formula:
bond valence = (Rij/R0)^(-N)
The most up-to-date BV parameter set
(http://www
Dear CCP4 users,
I would like to draw your attention to the topic "If it is a new
structure?", which is one more case, when new community members were
welcomed, and were "gently" explained about the rules of files sharing,
as it is an evidence, that the rules about files sharing are not well
[christmas flame]
The 'hiding' only applies to Windows, and that's your own fault then...
and your responsibility to look after it. And since attachments are deprecated
on this list it further imposes no real problem at all.
[/christmas flame]
;-> Tim
On Tue, Dec 21, 2010 at 11:08:27AM +0100, V
James Stroud wrote:
On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote:
what is the .odp file extension?
http://tinyurl.com/mjokqs
A .odp file is an "open document presentation". It is the open version
of a power point presentation.
http://en.wikipedia.org/wiki/OpenDocument
An .odp fi
On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote:
> what is the .odp file extension?
http://tinyurl.com/mjokqs
A .odp file is an "open document presentation". It is the open version of a
power point presentation.
http://en.wikipedia.org/wiki/OpenDocument
An .odp file is an ISO standard--
Hello,
as to the WASP server: We found it to be very useful in the past, but the link
is no longer functional!
Is there any other address for accessing this server?
Oliver
PD Dr. Oliver H. Weiergräber
Institut für Strukturbiologie und Biophysik
You could also try the original WASP here (also for coloured Indo-dutch
catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use
the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's
algorithm.
Cheers,
Robbie
> Date: Mon, 20 Dec 2010 22:59:53 +00
21 matches
Mail list logo
