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 mean variation squared? I expect it is because it
is supposed to be proportional to temperature. Hence the name
"temperature factor".
-James Holton
MAD Scientist
On 5/27/2021 11:09 AM, Gergely Katona wrote:
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 and Molecular Biology, University of Gothenburg
Box 462, 40530 Göteborg, Sweden
Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
Web: http://katonalab.eu, Email: gergely.kat...@gu.se
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of
*Hughes, Jonathan
*Sent:* 27 May, 2021 18:53
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] AW: [ccp4bb] (R)MS
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 more appropriate parameter of variability than
variance? or am i missing something?
cheers
j
*Von:*Ian Tickle <ianj...@gmail.com <mailto:ianj...@gmail.com>>
*Gesendet:* Donnerstag, 27. Mai 2021 18:32
*An:* Hughes, Jonathan <jon.hug...@bot3.bio.uni-giessen.de
<mailto:jon.hug...@bot3.bio.uni-giessen.de>>
*Cc:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* Re: [ccp4bb] (R)MS
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
<mailto:jon.hug...@bot3.bio.uni-giessen.de>> wrote:
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:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *Pearce, N.M. (Nick)
*Gesendet:* Donnerstag, 27. Mai 2021 12:38
*A**n:*CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* Re: [ccp4bb] Analysis of NMR ensembles
If you want something comparable to B-factors don’t forget to put
the MSF in the B-factor column, not the _R_MSF. Will change the
scaling of the tube radius considerably!
Nick
On 27 May 2021, at 11:16, Harry Powell - CCP4BB
<0000193323b1e616-dmarc-requ...@jiscmail.ac.uk
<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk>> wrote:
Cool…
Purely for visualisation this does look like the approved CCP4
way -
<Screen Shot 2021-05-27 at 10.13.59.png>
Harry
On 27 May 2021, at 10:01, Stuart McNicholas
<000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk
<mailto:000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>> wrote:
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
<0000193323b1e616-dmarc-requ...@jiscmail.ac.uk
<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk>> wrote:
Anyway, thanks to all those who answered my original
question - especially
Tristan: Chimerax (+ his attached script)
Michal, Scott: Theseus
(https://theobald.brandeis.edu/theseus/
<https://theobald.brandeis.edu/theseus/>)
Bernhard: Molmol
(https://pubmed.ncbi.nlm.nih.gov/8744573/
<https://pubmed.ncbi.nlm.nih.gov/8744573/>)
Rasmus CYRANGE
(http://www.bpc.uni-frankfurt.de/cyrange.html
<http://www.bpc.uni-frankfurt.de/cyrange.html>) and
https://www.ccpn.ac.uk/ <https://www.ccpn.ac.uk/>(of
course…)
Andrew (uwmn - not sure if this is buildable on
a modern box)
Smita: PyMol (not sure if I’m allowed to say
that on ccp4bb…)
or I could script it and use Gesamt or Superpose for
the superposition if I wanted to stay in the ccp4
universe and had the time to spare ;-)
Harry
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