Hi Markus,
I had a brief look at the structure fragment that you had included in your
mail, and I don't think that you really observe these two conformations.
Stereochemistry of the A conformation looks fine, but the sugar in the
alternate B conformation is not an NAG but an NDG (i.e. it has
Dear Markus,
I just did a test: I generated in Coot an alternative conformation for an ASN
with attached NAG, wrote out the coordinates and manually adapted the LINK
record, read it back in in Coot and hit the Refmac button (version 5.7.0029).
Except for some green difference density because I
I should be most grateful if you could point your most able students who
might be considering a PhD to one of the following links.
http://www2.le.ac.uk/departments/biochemistry/postgraduate-study/Three-year%20PhD%20programme.doc
or
Postdoc position in protein structural modeling and EM image data analysis
We have an opening for a Postdoc position in the Computational Structural
Biology Group
(www.schroderlab.org) at the Forschungszentrum Jülich, Germany.
Our group is working on modeling and refinement of protein
Dear Markus,
You could also try the inse keyword, which will tell refmac two mutually
exclude two atoms occupying the same position but we occupancy for example of
0.6 and 0.4, stopping them from repelling each other.
Here is an example in the case of an Fe site which was contaminated by Mn in
Dear all
In Britain there is a free newspaper that you can pick up on buses called the
Metro. My colleague Geoff Ford pointed out this short feature on the history
X-ray crystallography in last Monday's Metro newspaper. I think it's rather
good.
Following on from that - readers may be interested in Stephen Curry's
post in the Guardian, regarding the Crystallography exhibit at the
London Science Museum.
http://www.guardian.co.uk/science/occams-corner/2013/apr/19/1
regards,
Dave
David C. Briggs PhD
Another of my colleagues, Jeremy Craven, is an NMR spectroscopist and
bioinformatician. He is in referee mode at present and comments:
From: Jeremy Craven c.j.cra...@sheffield.ac.uk
Date: 19 April 2013 10:05:18 GMT+01:00
To: Peter Artymiuk p.artym...@sheffield.ac.uk
Subject: Re: Fwd:
Dear Pet,
On the contrary, far as I know, nature seems to require most solids we see
around us to be crystalline. And much of the rest is either gaseous or plasma.
Hence, by the reasoning proposed, we are led to suspect a different conclusion:
that it's studies dealing with the remaining state
Hi all,
we are looking for a new swingout centrifuge to spin down drops in case
our nanodispensing is not perfectly centered.
Ideally it should have small footprint and low price. The simple
PCR-centrifuges (2 slots, vertical) don't work, at least in our hands.
The standard swingout
Dear users,
The native structure for a protein is available and there is a
ligand bound data. The crystallisation condition has anomalous
scattering metal ions (Cd). Both the data are scaled by separating
anomalous pairs. So while refining a ligand bound data with a
solution obtained using
Sir,
Thank you Sir. I tried this once at the end in order to
check the refinement statistics, R, Rfree and FOM showed
improvement. but I encountered one problem. One of the a
nomalous scatters which had double occupancies (which was
confirmed by anomalous peak search) after the refinement
of
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Dear Kavya,
one reason could be an incorrect script for running refmac, or a bug
in refmac, or, if the distance allows, that the two peaks really are
two different fully occupied atoms with a lesser anomalous signal than
expected.
Best,
Tim
On
Just to clarify, Jeremy was not being serious, but imagining what an awkward /
obnoxious grant reviewer might have said in 1913. But your points would be
valuable in rebutting such a view
Pete
On 19 Apr 2013, at 11:28, Navdeep Sidhu wrote:
Dear Pet,
On the contrary, far as I know,
Dear Sir,
Thank you. I run refmac using GUI so most
Probably there are two different atoms.
Regards
Kavya
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Dear Kavya,
one reason could be an incorrect script for running refmac, or a bug
in refmac, or, if the distance allows, that the two
However, a reviewer could reject the method on theoretical grounds - the
explanation of X-ray diffraction as a multi-photon process is not
correct
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter
Artymiuk
Sent: Friday, April 19, 2013
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Hello Bernhard,
could you explain this? A photon is the exchange particle of the
electromagnetic force, i.e. as soon as you have more than two charged
particles interacting there is more than one photon - why is it
incorrect to use the term
Because there is never more than one photon in flight at any given
time. Even at 1 photon/s, we still eventually get spots.
Atoms also don't emit synchrotron radiation, despite there being charged
particles accelerating around their little orbits in there.
But yes, in 1913, people were
Simply on grounds that even a single photon can get diffracted (remember the
photon counting multiwire detectors?). The phenomenon might be best
described as something like a annihilation-creation process a la Feynman.
Much of this has been discussed on board before. Mini-summary:
'Multiphoton'
Imperial College London
Department of Life Sciences
Faculty of Natural Sciences
Research Associate
Salary range: £32,100 - £40,720 per annum
We wish to recruit a Research Associate to work in the research group of
Professor Paul Freemont (www.msf.bio.ic.ac.uk), in the Department of Life
James
In 1915, I thought Debye and Scherrer were testing for interference between the
electrons in different orbits within atoms. This was in order to test the Bohr
model. They got rings but they were powder diffraction rings. The method never
did identify planetary type orbitals. However
I would like to add/support James comments. Once it used to bother me the fact
that diffraction was observed from the crystal even though the beam does not
possess a space-time coherence (or even worse in the case of in-house
diffractometers). This is because in text books they always
Problem Solved - Short Summary
---
Dear all,
First of all, a big thank you to everyone who devoted their precious time to
help figure this out!
Good news, Refmac (tested with v.5.7.0032) does handle alternate sugar
conformations correctly.
As Thomas Lütteke
It was the observation that atoms have size.
Rutherford's alpha-particle experiment had shown that the nucleus was
incredibly small, very much smaller than the distances between atoms,
bringing about the solar system idea, which right away came into question
because such atoms would produce
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