In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D.,
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser-
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.
Perhaps,
I think the results from AlphaFold2, although exciting and a breakthrough are
being exaggerated just a bit. We know that all the information required for
the 3D structure is in the sequence. The protein folding problem is simply how
to go from a sequence to the 3D structure. This is not a compl
We store raw data for two main reasons:
a) We currently use only a fraction of the information actually contained in
raw images and extraction of that fraction can be improved. Destroying the data
means
- we lose the extra information, and make future research in some areas either
impossible o
Every dataset costs money to produce. Is it more cost effective to expect that
those wishing to use the data repeat the expenditures by repeating the
experiments? To exaggerate the point, imagine a world without published
research articles, would it be more expensive to do science or less? We s
Your 64bit system does not have the 32bit LSB libraries installed. Install the
packages "redhat-lsb.i686" and "redhat-lsb-graphics.i686" using yum as follows:
yum install redhat-lsb.i686 redhat-lsb-graphics.i686
>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.U
Very interesting
"Response to Detection and analysis of unusual features in the structural model
and structure-factor data of a birch pollen allergen"
doi:10.1107/S1744309112008433
a quote from the response:
"Author Schwarzenbacher admits to the allegations of data fabrication and
deeply apol
It is available online at
http://www.stat.ucla.edu/history/essay.pdf
Michel Fodje
Staff Scientist
Canadian Macromolecular Crystallography Facility
Canadian Light Source
Tel: 306 657 3758
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk
The preferred method to get NVIDIA drivers for Fedora is to use the RPM Fusion
repositories (http://rpmfusion.org/Howto/nVidia).
Drivers installed this way will be automatically updated with the kernel as
required.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.
f the number of frames.
I hope this helps.
Michel Fodje,
Canadian Macromolecular Crystallography Facility,
Canadian Light Source
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank
Murphy
Sent: April-19-11 6:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Su
The opinionator piece is misleading about the meaning of probability,
especially as it implies that you could reformulate every problem into one
about frequencies. As was pointed out a long time ago by Harold Jeffreys and
repeated by Ed Jaynes,
"The essence of the present theory is that no pro
You are probably referring to the following works:
Caliandro et al, Acta Cryst. D61 (2005) 556-565
and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087
in which they used density modification to calculate phases for
unmeasured reflections, and used the phases to extend the resolution by
calculat
On Tue, 2007-07-03 at 10:54 -0700, Ethan Merritt wrote:
> Not at all. Consider all those users of GPL programs running on Windows.
> The developers of cygwin, mplayer, etc have no right to redistribute
> Windows itself.
Programs running under windows are not derivative works of Windows
otherwis
On Tue, 2007-07-03 at 12:34 -0700, Ethan Merritt wrote:
> Yes. That is a more complete statement of rights under the GPL.
> Please note, however, that "the source code" to which you are
> guaranteed access is the source code to the GPL-ed program itself,
> not to pieces of the operating environment
Dear Crystallographers,
Here are a few paradoxes about diffraction I would like to get some
answers about:
1. In every description of Braggs' law I've seen, the in-coming waves
have to be in phase. Why is that? Given that the sources used for
diffraction studies are mostly non-coherent.
2. Trying
> > 1. In every description of Braggs' law I've seen, the in-coming waves
> > have to be in phase. Why is that? Given that the sources used for
> > diffraction studies are mostly non-coherent.
>
> Think of Bragg's Law as explaining what happens to a single photon
> that is probabilistically scatte
> For every direction where there is destructive interference and a
> loss of energy there is a direction where there is constructive
> interference that piles up energy. If you integrate over all
directions
> energy is conserved.
For the total integrated energy to be conserved, energy will have
> You are just using the coherent fraction of the beam.
My point is that Braggs' law as currently understood does not preclude
the diffraction from waves which were non-coherent before hitting the
sample
> It is not clear at all how you arrive to that condition. By definition, if
> two waves are n
Would it be taking it too far to suggest that one could go all the way
and consider that each electron diffracts not as groups in a plane but
as individual electrons and a photon impinging on an electron with with
a specific phase will be diffracted in a specific direction. However the
lattice arra
Povray is just a renderer like the renderer in blender, only in the case
of povray, the input file defines the model. I would think that if it is
possible to generate a povray input file from molecule objects, it
should be possible to generate a VRML file which blender can open. If
I'm not mistaken
I should add that inspecting the average three-dimensional profiles in
INTEGRATE.LP could give you an indication if you have overlaps or not.
The profiles look like slices through a 3D unimodal gaussian. If you
have overlaps it will be revealed by bi-/multi-modal features. However,
these are avera
Dear Crystallographers,
Beamline 08ID-1 (CMCF1) at the Canadian Light Source (CLS) is accepting
user beamtime requests for the period November 6 - December 18, 2008.
Detailed information about the beamline can be found on our web pages
http://www.lightsource.ca/experimental/cmcf.php ,
http://ex.li
On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote:
> 2) Graphics Cards:
> I like the Nvidia cards since they provide linux drivers. ATI also does
> now. I would say the only thing I don't like about them is when you do a
> kernel update you have to remake the driver.
I would just add tha
Hardware: Say I do a lot of screening on Beamline A (many hours used), collect
a low resolution anomalous dataset on Beamline B, which helps me to solve the
structure, then I collect a high resolution native dataset on Beamline C (in
just a few minutes) for refinement and model building. Many pe
Has anyone else noticed a problem with the structure of the N-terminal capsid
domain of HIV-2 PDB 2wlv.
Load it up to in coot and navigate to residue B118.
/Michel.
By the way, you will need to show symmetry atoms to see the problem.
>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>Michel Fodje
>Sent: April-12-13 1:14 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] Puzzling Structure
Just to round up this topic, a bug report was submitted to PDBe concerning
entry 2wlv and the PDB has how responded acknowledging the problem. An updated
entry will be available in one week.
As pointed out by Savvas, it is very likely the CRYST1 record was manually
edited prior to deposition re
That looks like a magnessium hexahydrate.
From: CCP4 bulletin board On Behalf Of Pearce, N.M.
(Nick)
Sent: May 26, 2021 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: Re: [ccp4bb] Unmodeled density
Is it on a symmetry axis? If so it could be the superposition of two molecules
(a molecule
The Canadian Light Source Inc. (CLSI) is the national synchrotron research
facility on the
University of Saskatchewan campus in Saskatoon. This facility serves national
and international users from academia, industry, and government institutions.
The CLS facilitates scientific research aimed at
mline instrumentation, and excellent
communication skills. For more information and to apply online, please visit
the following link:
https://www.northstarats.com/Canadian-Light-Source
Please feel free to share this announcement with anyone who may be interested.
Regards
Michel Fodje
Senior Scientis
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