Dear colleagues,
I realize that this is peripheral to CCP4, but we are looking for a research
scientist in biological NMR spectroscopy to join our large multi-disciplinary
Molecular Pharmacology department. It's a great opportunity to work with
dedicated, innovative scientists focusing on
Sorry abt. the result with the imaginary (-1^0.5) Landrover salesperson.
I recall in the '60s that small-molecule (in the '60s that is all there were)
would convert the B to r.m.s deviation, but it didn't stick.
Bob
From: CCP4 bulletin board on behalf of Hughes,
A bit late, I know, but a bit more googling gave me this site which I don't
think has been mentioned so far:
http://old.protein.bio.unipd.it/mobi/
Given the pdb code, it is a one click job to get a pdb file with the "B-factors
changed to averaged Scaled Distance x 100" and the resulting
hey gerald,
yes, and surely it would be better than a u³ -based parameter (if it's the
dimensionality arising from a symmetric covariance matrix that's the problem).
actually, the guy on the beach was a greek-australian ex-cell biologist who now
works for a bank helping it to rake in money from
Dear Jonathan,
You are right of course, as e.g. the standard deviations are in the same
unit as the measurements (or averages) themselves. The dynamic ranges are
also more manageable.
I couldn't help wanting to find something to say as a diversion to yet
another day marked by a stiff dose of
Dear Jonathan,
In 1D sd may be intuitive, but in 3D it is not so much. The square root of a
symmetric covariance matrix is not universally defined and it is not intuitive
to me.
Best wishes,
Gergely
Gergely Katona, Professor, Chairman of the Chemistry Program Council
Department of Chemistry
hi gerard,
yes, but that's like saying that the height of a human being is 1.8 m +/- 0.04
m². and if (thanks to robert!*)
"B = 8π2 where u is the r.m.s. displacement of a scattering center, and
<...> denotes time averaging"
it would seem to me that we would be able to interpret things MUCH
Dear Jonathan,
Isn't it six of one and sqrt(36) of the other ?
Best wishes,
Gerard.
--
On Thu, May 27, 2021 at 04:52:39PM +, Hughes, Jonathan wrote:
> hey!
> thank y'all for the informative (and swift!) answers! but, if the B factor
> (as defined) appears in a mathematical formulation,
hey!
thank y'all for the informative (and swift!) answers! but, if the B factor (as
defined) appears in a mathematical formulation, that doesn't make it an
"appropriate" parameter for mobility/uncertainty. wouldn't √B be better, in the
same way that, for humans, standard deviation (RMSD) is a
Hi Jonathan
It's historical, it's simply how it appears in the expression for the
Debye-Waller factor, i.e. exp(-B sin^2(theta)/lambda^2). So it must have
the same units as lambda^2.
Cheers
-- Ian
On Thu, 27 May 2021 at 13:25, Hughes, Jonathan <
jon.hug...@bot3.bio.uni-giessen.de> wrote:
>
Dear all,
We are looking for experienced Crystallographers to join the Discovery
Biology department at Exscientia.
The Discovery Biology team in Exscientia is responsible for enabling
small-molecule therapeutic projects and integrates with the Artificial
Intelligence (AI) driven drug discovery
A post-doctoral position is available at the Laboratory of Prof. Chris Ulens,
KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of
Structural Neurobiology is aimed at understanding the molecular mechanism of
ligand-gated ion channels. Our methods rely on X-ray
Hello Jon,
Wikipedia has plenty of information on the Debye-Waller factor:
https://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor
Best,
Tim
On Thu, 27 May 2021 12:25:06 + "Hughes, Jonathan"
wrote:
> o yes! but maybe the crystal people could explain to me why the B
> factor is the
o yes! but maybe the crystal people could explain to me why the B factor is the
variance (with units of Ų) rather than the standard deviation (i.e. RMS, with
units of Å) when, to my simple mind, the latter would seem be the more
appropriate description of variability in space?
cheers
jon
Von:
Hello everyone,
While this is not exactly a crystallography question, I do think that most
of you are well versed in structural analysis.
The problem: I have a very large number of ligands (>100.000) resulting
from blind docking against a certain receptor. Due to the large number,
this can not be
If you want something comparable to B-factors don’t forget to put the MSF in
the B-factor column, not the RMSF. Will change the scaling of the tube radius
considerably!
Nick
On 27 May 2021, at 11:16, Harry Powell - CCP4BB
Dear Dale,
It is more complex than just 'flexibility', but then it is always more
complicated. Here are the main possibilities for undetermined regions:
-1- fast, free movement - signals are easy to see, have 'random-coil'
chemical shifts, often overlap, and there are no NOEs
-2-
Cool…
Purely for visualisation this does look like the approved CCP4 way -
Harry
> On 27 May 2021, at 10:01, Stuart McNicholas
> <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Drawing style (right menu in display table) -> Worm scaled by -> Worm
> scaled by NMR variability
>
>
Drawing style (right menu in display table) -> Worm scaled by -> Worm
scaled by NMR variability
in ccp4mg?
This changes the size of the worm but not the colour.
On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Anyway, thanks to all
Anyway, thanks to all those who answered my original question - especially
Tristan: Chimerax (+ his attached script)
Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
Rasmus CYRANGE
For the NMR structure ensemble, you could calculate root mean square
fluctuations (RMSFs) and put them into the B factor column. This is a fairly
common analysis within molecular dynamics software. You could also use the
ProDy Python API to do this.
ProDy also has command line apps including
Hi
This is why I put “rigid” and “flexible” in quotes in my original post - to
allow people to put whatever interpretation on them that they chose (within
limits)!
Of course, it’s always best to try to use the correct terms in a scientific
discussion, but we all use shorthand; e.g., in
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