t 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 On Behalf Of Hughes,
> Jonathan
>
t;> 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 On Behalf Of
>> H
On Behalf Of Hughes, Jonathan
Sent: 28 May, 2021 14:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
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
Web: http://katonalab.eu, Email: gergely.kat...@gu.se
From: CCP4 bulletin board 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 ma
rg, 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 *On Behalf Of
*Hughes, Jonathan
*Sent:* 27 May, 2021 18:53
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] AW: [ccp4bb] (R)MS
hey!
t
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:
xaggerated – which is another word for
"misrepresented".
cheers
j
Von: Ian Tickle
Gesendet: Freitag, 28. Mai 2021 12:10
An: Hughes, Jonathan
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
Hi Jonathan
On Thu, 27 May 2021 at 18:34, Hughes, Jonathan
ma
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_
, Jonathan
Sent: Thursday, May 27, 2021 3:03:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
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
being what they are. they were a nice
couple though.
cheers
j
-Ursprüngliche Nachricht-
Von: Gerard Bricogne
Gesendet: Donnerstag, 27. Mai 2021 20:19
An: Hughes, Jonathan
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] (R)MS
Dear Jonathan,
You are right of course, as e.g
ardinia.
>
>
>
> -Ursprüngliche Nachricht-
> Von: Gerard Bricogne
> Gesendet: Donnerstag, 27. Mai 2021 19:05
> An: Hughes, Jonathan
> Cc: CCP4BB@jiscmail.ac.uk
> Betreff: Re: [ccp4bb] AW: [ccp4bb] (R)MS
>
>
>
> Dear Jonathan,
>
>
>
&g
@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
each in sardinia.
-Ursprüngliche Nachricht-
Von: Gerard Bricogne
Gesendet: Donnerstag, 27. Mai 2021 19:05
An: Hughes, Jonathan
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] (R)MS
Dear Jonathan,
Isn't it six of one and sqrt(36) of the other ?
Best wishes,
Gerar
j
>
> Von: Ian Tickle
> Gesendet: Donnerstag, 27. Mai 2021 18:32
> An: Hughes, Jonathan
> Cc: 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 fa
tion (RMSD) is a more appropriate
parameter of variability than variance? or am i missing something?
cheers
j
Von: Ian Tickle
Gesendet: Donnerstag, 27. Mai 2021 18:32
An: Hughes, Jonathan
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] (R)MS
Hi Jonathan
It's historical, it's simply how
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:
>
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:
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