B-factors are definitely a measure of uncertainty in variance (square)
units. The crystal lattice has multiple occurrence of the atoms that are
equivalent by crystal symmetry. They will have the same fractional
coordinates within the uncertainty of their position relative to the
crystal
I feel I should point out here that B-factors are NOT a measure of
uncertainty. They are a width. This width itself may be uncertain, as
may be the position of the center of the peak, but just because your
peak is broad doesn't mean you don't know where the middle of it is.
As for why leave
The Structural Molecular Biology (SMB) Division at the Stanford Synchrotron
Radiation Lightsource (SSRL) is seeking a Research Associate with a strong
background in X-ray diffraction data processing and/or software
development. A successful candidate will work with an interdisciplinary
group of
Dear Rasmus,
Thankyou for your very useful summary of NMR being “more complex than
flexibility”.
The complementary roles of NMR and crystallography are important and I very
recently provided a resume in section 2.3 of my Acta Cryst A article
Dear CCP4 community,
We currently have a crystallographer position open in our structural biology
team, with strong focus on RNA crystallography.
If you are interested, please apply using this link:
On Fri, May 28, 2021, Hughes, Jonathan wrote:
if you just see the B factor as a number, ok, you can do the √ in your
head, but if it's visualized as in pymol/putty larger uncertainties become
exaggerated – which is another word for "misrepresented".
Two points that haven't yet been raised:
hi ian,
yes, that aspect was in my mind, a bit, but i wanted to keep it simple. my
point wasn't really how the "uncertainty" parameter is derived but rather its
units. i can imagine that uncertainty in 3D could be expressed in ų (without
helping the naïve user much) or in Å (which to me at
It’s also important to keep in mind that, in this equation, u is the component
of the displacement *in the direction of the diffraction vector*. If you
assume isotropic displacements and you know the mean-squared value of the
overall xyz vector displacement, you have to divide that
Hi Jonathan
On Thu, 27 May 2021 at 18:34, Hughes, Jonathan <
jon.hug...@bot3.bio.uni-giessen.de> wrote:
"B = 8π2 where u is the r.m.s. displacement of a scattering center,
and <...> denotes time averaging"
Neither of those statements is necessarily correct: u is the
_instantaneous_
Hi Joern,
Yes, these values are all stored in a file called data.json that each entry
has. The keys that are most relevant are:
BLTBEST (geometric restraint weight)
BBEST (B-factor restraint weight)
BREFTYPE (B-factor model)
DOTLS (Whether or not TLS refinement is used)
ISTWIN (Whether or not
We are currently advertising two positions at the BioMAX beamline: a beamline
scientist (see https://lu.varbi.com/en/what:job/jobID:404484/) and a postdoc
(https://lu.varbi.com/en/what:job/jobID:40/ )
BioMAX is the first macromolecular crystallography beamline at MAX IV. It
started user
This even seems to have a”batch” mode (similar to the well-known homology
modelling server Phyre2) that might accept a zip file containing multiple PDBs.
If it does, and if it will take my ~700 PDBs, then that would save me a little
bit of scripting.
Harry
> On 27 May 2021, at 22:03, Jon
Dear all,
I want to do the following: I want to download several structures from
PDB-REDO and pipe them into Refmac5 for re-refinement, replacing the
restraints dictionary of a certain ligand with a customized one. The
refinement settings I want to keep otherwise unchanged. We are talking
Uncovering protein dynamics: developing statistical crystallography
Postdoctoral Position
Center for Free Electron Laser Science (CFEL), Hamburg, Germany [DESY Campus]
Protein motion is at the heart of life, but remains challenging to witness
firsthand. Proteins move to reading and copying DNA,
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