Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Ethan A Merritt]

ices, analogously how MD 
> trajectories can be described as average structures and covariance matrices.  
> I think the assumption of independent variations per atoms is too strong in 
> many cases and does not give an accurate picture of uncertainty.
> 
> 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  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 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 least seems useful), but 
> Ų (i.e. the B factor) seems neither logical nor helpful in this context, 
> irrespective of its utility elsewhere. 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".
> cheers
> j
> 
> Von: Ian Tickle mailto:ianj...@gmail.com>>
> Gesendet: Freitag, 28. Mai 2021 12:10
> An: Hughes, Jonathan 
> mailto:jon.hug...@bot3.bio.uni-giessen.de>>
> Cc: CCP4BB@JISCMAIL.AC.UK<mailto: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 
> mailto: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_ 
> displacement which of course is constantly changing (on a timescale of the 
> order of femtoseconds) and cannot be measured.  So u2 is the squared 
> instantaneous displacement,   is the mean-squared displacement, and so 
> the root-mean-squared displacement (which of course is amenable to 
> measurement) is sqrt(), not the same thing at all as u.
> 
> Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
> Debye-Waller factor expression I mentioned earlier.
> 
> Also for crystals at least, the averaging is not only over time, it's over 
> all unit cells, i.e. the displacements are not only thermal in origin but 
> also due to spatial static disorder (instantaneous differences between unit 
> cells).
> 
> 
> it would seem to me that we would be able to interpret things MUCH more 
> easily with u rather than anything derived from u².
> So then I think what you mean is sqrt() rather than , which seems not 
> unreasonable.
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] (R)MS

[Philippe BENAS]

Dear CCP4bbers,

As Zbyszek and some others wrote, the explanation of B factors is linked to the 
mathematical expression of structure factors: the X-ray crystallographer 
primary data are projections of the reciprocal space. And it's probably better 
to keep this primary info in PDB files rather than RMS displacements on one 
hand and to try to make the story short on the other hand: 50 emails on the 
subject seem to be enough, don't they ?

All the best and have a nice weekend,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Conrad Roentgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:  https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/

 

Le samedi 29 mai 2021 à 03:12:39 UTC+2, zbyszek  a 
écrit :  
 
 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 lattice orientation definition. B-factors are the measure of 
this uncertainty (variance) in somewhat unusual units (Angstrom squared 
/ (8*pi*pi)). The fact that you can directly measure uncertainty by 
observing the width of the profile of the atomic distribution (shape of 
the uncertainty function) does not negate that this function represents 
uncertainty of atomic position relative to the crystal lattice.

As a comment: uncertainty of the centroid of the uncertainty 
distribution is a second order or recursive uncertainty. As this 
centroid is deposited as atomic coordinates in pdb files, its 
uncertainty is a separate subject from the uncertainty (variation) of 
the atom position in the crystal lattice. Unfortunately theories of 
uncertainty estimates of uncertainty estimates is more complex and for 
this reason crystallographers rarely deal productively with uncertainty 
of the x,y,z coordinates deposited.

A second comment: the B-factor really represents the sum of two 
uncertainties. One is the uncertainty of atom positions in the crystal 
lattice. The second is our experimental uncertainty about the knowledge 
of atom position. The first one has a physical interpretation. The 
second represents our data and analysis, e.g. phasing.

For these reasons, saying that the B-factor represents uncertainty 
estimates is very productive because it is all about uncertainty. 
Independent uncertainties are convolved with each other to produce a 
final uncertainty function. In terms of the width squared of that 
function, it represents the sum of the widths squared of the 
contributors. In fact this observation is behind the Central Limit 
Theorem.

Zbyszek

On 2021-05-28 19:05, James Holton wrote:
> 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  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 
>> Gesendet: Donnerstag, 27. Mai 2021 18:32
>> An: Hughes, Jonathan 
>> Cc: CCP4BB@JISCMAIL.AC.UK
>&

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Gergely Katona]

Hi,

It is enough to have Ų as unit to express uncertainty in 3D, but one can 
express it with a single number only in a very specific case when the atom is 
isotropic. Few atoms have a naturally isotropic distribution around their mean 
position in very high resolution protein crystal structures. The anisotropic 
atoms can be described by a 3x3 matrix, where each row and column is associated 
with the uncertainty in a specific spatial direction. The matrix elements are 
the product of the uncertainty in these directions. The diagonal elements will 
be the square of uncertainty in the same direction and they should be always 
positive, the off-diagonal combination of directions are covariances (+,0 or 
-). In the end, every element will have a unit distance*distance and the matrix 
will be symmetric. We cannot just take the square root of the matrix elements 
and expect something meaningful, if for no other reason the problem with 
negative covariances. To calculate the square root on the matrix itself one has 
to diagonalize it first. The height of a person in your example  sounds easy to 
define, but the mathematical formalism will not decide that for me. I can also 
define height as the longest cord of a person or the maximum elevation of a car 
mechanic under a car.  Through diagonalization one can at least extract some 
interesting, intuitive, principal directions. The final product, the 
sqrt(matrix), is not more intuitive to me. To convert it to something intuitive 
I would have to diagonalize square rooted matrix again. So shall we make an 
exception for the special, isotropic description? Or use general principles for 
isotropic and anisotropic treatments?

About what B-factors are, I like to think about them as necessary model 
parameters. Computational biologists also use them for benchmarking their 
molecular dynamics models. They are also reproducible to the extent that one 
can identify specific atoms just based on their anisotropic tensor from 
independent structure determinations in the same crystal form. They are of 
course not immune to errors and variation.

I also wonder how we can represent model parameter variation in the best way. I 
admire NMR spectroscopists’ approach to deposit multiple samples from a 
structural distribution. One could reproduce their conclusions without assuming 
any sort of error model from these samples. In crystallography, we have more 
and more distributions to deal with because we are swimming in data. It is easy 
to sample/resample data sets from the same or different crystals (SFX for 
example). Which can lead to many replicates of structural models. I cannot 
really motivate to create multiple PDB entries for these replicates, it is not 
good for to reader to try to understand which PDB codes belong to which group 
of samples. Maybe it works for up to 10 structures, but how about a 100? Is it 
possible to deposit crystal structures as a chain of model/data pairs under the 
same entry? It is possible to just make a tarball and deposit in alternative 
services such as Zenodo, but it would be a pity to completely bypass the PDB. I 
can think of more compact description of structural distributions, for example 
mean positions and mean B-factors of atoms with their associated covariance 
matrices, analogously how MD trajectories can be described as average 
structures and covariance matrices.  I think the assumption of independent 
variations per atoms is too strong in many cases and does not give an accurate 
picture of uncertainty.

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  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 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 least seems useful), but 
Ų (i.e. the B factor) seems neither logical nor helpful in this context, 
irrespective of its utility elsewhere. 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".
cheers
j

Von: Ian Tickle mailto:ianj...@gmail.com>>
Gesendet: Freitag, 28. Mai 2021 12:10
An: Hughes, Jonathan 
mailto:jon.hug...@bot3.bio.uni-giessen.de>>
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS


Hi Jonathan

Re: [ccp4bb] (R)MS

[zbyszek]

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 lattice orientation definition. B-factors are the measure of 
this uncertainty (variance) in somewhat unusual units (Angstrom squared 
/ (8*pi*pi)). The fact that you can directly measure uncertainty by 
observing the width of the profile of the atomic distribution (shape of 
the uncertainty function) does not negate that this function represents 
uncertainty of atomic position relative to the crystal lattice.


As a comment: uncertainty of the centroid of the uncertainty 
distribution is a second order or recursive uncertainty. As this 
centroid is deposited as atomic coordinates in pdb files, its 
uncertainty is a separate subject from the uncertainty (variation) of 
the atom position in the crystal lattice. Unfortunately theories of 
uncertainty estimates of uncertainty estimates is more complex and for 
this reason crystallographers rarely deal productively with uncertainty 
of the x,y,z coordinates deposited.


A second comment: the B-factor really represents the sum of two 
uncertainties. One is the uncertainty of atom positions in the crystal 
lattice. The second is our experimental uncertainty about the knowledge 
of atom position. The first one has a physical interpretation. The 
second represents our data and analysis, e.g. phasing.


For these reasons, saying that the B-factor represents uncertainty 
estimates is very productive because it is all about uncertainty. 
Independent uncertainties are convolved with each other to produce a 
final uncertainty function. In terms of the width squared of that 
function, it represents the sum of the widths squared of the 
contributors. In fact this observation is behind the Central Limit 
Theorem.


Zbyszek

On 2021-05-28 19:05, James Holton wrote:

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  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 
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 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
 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  Im Auftrag von
Pearce, N.M. (Nick)
Gesendet: Donnerstag, 27. Mai 2021 12:38
An: 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 RMSF. Will change the
scaling of the tube radius considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

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 b

Re: [ccp4bb] (R)MS

[James Holton]

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  *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 mailto:ianj...@gmail.com>>
*Gesendet:* Donnerstag, 27. Mai 2021 18:32
*An:* Hughes, Jonathan <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 
<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 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
<193323b1e616-dmarc-requ...@jiscmail.ac.uk
<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>> wrote:

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
<mailto:19a0c5f649e5-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
<193323b1e616-dmarc-requ...@jiscmail.ac.uk
<mailto:193323b1e616-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 Su

[ccp4bb] (R)MS

[David A Case]

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:

1. Crystallographers have a half-century of experience in "seeing the B
factor as a number", and many have a good intuitive feeling for how these
numbers are affected by secondary structure, resolution, and so on.

2. B-factors are really refinement parameters, and can serve to account for
errors or uncertainties in other parts of data processing or refinement.
Stated in another way: the simple atomic model of xyz coordinates + ADPs
is generally not sufficient to represent what is really going on at the
atomic level.  The connection to  is a rough one: especially for large
B-factors (relative to the average) using the simple formula to estimate
 often underestimates the atomic fluctuations that are actually present.

dac



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[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Hughes, Jonathan]

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 least seems useful), but 
Ų (i.e. the B factor) seems neither logical nor helpful in this context, 
irrespective of its utility elsewhere. 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".
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 
mailto: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_ 
displacement which of course is constantly changing (on a timescale of the 
order of femtoseconds) and cannot be measured.  So u2 is the squared 
instantaneous displacement,   is the mean-squared displacement, and so the 
root-mean-squared displacement (which of course is amenable to measurement) is 
sqrt(), not the same thing at all as u.

Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
Debye-Waller factor expression I mentioned earlier.

Also for crystals at least, the averaging is not only over time, it's over all 
unit cells, i.e. the displacements are not only thermal in origin but also due 
to spatial static disorder (instantaneous differences between unit cells).


it would seem to me that we would be able to interpret things MUCH more easily 
with u rather than anything derived from u².
So then I think what you mean is sqrt() rather than , which seems not 
unreasonable.

Cheers

-- Ian







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Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] (R)MS

[Randy John Read]

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 mean-squared value by 
3 to get the variance in any particular direction.  This is a source of 
considerable confusion in crystallography textbooks!

Best wishes,

Randy Read

> On 28 May 2021, at 11:09, Ian Tickle  wrote:
> 
> 
> Hi Jonathan
> 
> On Thu, 27 May 2021 at 18:34, Hughes, Jonathan 
>  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_ 
> displacement which of course is constantly changing (on a timescale of the 
> order of femtoseconds) and cannot be measured.  So u2 is the squared 
> instantaneous displacement,   is the mean-squared displacement, and so 
> the root-mean-squared displacement (which of course is amenable to 
> measurement) is sqrt(), not the same thing at all as u.
> 
> Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
> Debye-Waller factor expression I mentioned earlier.
> 
> Also for crystals at least, the averaging is not only over time, it's over 
> all unit cells, i.e. the displacements are not only thermal in origin but 
> also due to spatial static disorder (instantaneous differences between unit 
> cells).
> 
> it would seem to me that we would be able to interpret things MUCH more 
> easily with u rather than anything derived from u².
> 
> So then I think what you mean is sqrt() rather than , which seems not 
> unreasonable.
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Ian Tickle]

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_ displacement which of course is constantly changing (on a
timescale of the order of femtoseconds) and cannot be measured.  So u2 is
the squared instantaneous displacement,   is the mean-squared
displacement, and so the root-mean-squared displacement (which of course is
amenable to measurement) is sqrt(), not the same thing at all as u.

Incidentally, the 8π2 constant factor comes from Fourier-transforming the
Debye-Waller factor expression I mentioned earlier.

Also for crystals at least, the averaging is not only over time, it's over
all unit cells, i.e. the displacements are not only thermal in origin but
also due to spatial static disorder (instantaneous differences between unit
cells).

it would seem to me that we would be able to interpret things MUCH more
> easily with u rather than anything derived from u².
>
So then I think what you mean is sqrt() rather than , which seems
not unreasonable.

Cheers

-- Ian



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Re: [ccp4bb] AW: [ccp4bb] (R)MS

[Sweet, Robert]

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, 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).
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 fast trading and also plays a 
mean saxophone. but actually i was more interested in his girlfriend who, 
before she moved to the west end to run a restau, used to sell landrovers in 
poland, apparently. well, i'd have bought a dozen from her on the spot, but she 
didn't accept credit cards, beaches 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. 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 virtual meetings - all highly productive and 
absolutely necessary, but somehow lacking in jokes ... .

Best wishes,

Gerard.

--
On Thu, May 27, 2021 at 05:34:18PM +, Hughes, Jonathan wrote:
> 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 more 
> easily with u rather than anything derived from u².
>
> best
>
> jon
>
>
>
> *nice presentation, by the way, not that i know what a complex number is, 
> unfortunately, although i did once see someone trying to explain it to his 
> girlfriend with the help of a graph drawn in the sand on a beach 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,
>
>
>
> 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, 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 mailto:ianj...@gmail.com>>
>
> > Gesendet: Donnerstag, 27. Mai 2021 18:32
>
> > An: Hughes, Jonathan
> > mailto:jon.hug...@bot3.bio.uni-g
> > iessen.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 
> > mailto:jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de%3cmailto: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
>
> > mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JI
> > SCMAIL.AC.UK%3cmailto:CCP4BB@JISCM

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Hughes, Jonathan]

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 fast trading and also plays a 
mean saxophone. but actually i was more interested in his girlfriend who, 
before she moved to the west end to run a restau, used to sell landrovers in 
poland, apparently. well, i'd have bought a dozen from her on the spot, but she 
didn't accept credit cards, beaches 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. 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 virtual meetings - all highly productive and 
absolutely necessary, but somehow lacking in jokes ... .

Best wishes,

Gerard.

--
On Thu, May 27, 2021 at 05:34:18PM +, Hughes, Jonathan wrote:
> 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 more 
> easily with u rather than anything derived from u².
> 
> best
> 
> jon
> 
> 
> 
> *nice presentation, by the way, not that i know what a complex number is, 
> unfortunately, although i did once see someone trying to explain it to his 
> girlfriend with the help of a graph drawn in the sand on a beach 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,
> 
> 
> 
> 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, 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 mailto:ianj...@gmail.com>>
> 
> > Gesendet: Donnerstag, 27. Mai 2021 18:32
> 
> > An: Hughes, Jonathan 
> > mailto:jon.hug...@bot3.bio.uni-g
> > iessen.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 
> > mailto:jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de%3cmailto: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
> 
> > mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JI
> > SCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>>> Im Auftrag von
> 
> > Pearce, N.M. (Nick)
> 
> > Gesendet: Donnerstag, 27. Mai 2021 12:38
> 
> > An: 
> > CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JIS
> > CMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>>
> 
> > Betreff: Re: [ccp4bb] Analy

Re: [ccp4bb] AW: [ccp4bb] (R)MS

[Gerard Bricogne]

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 virtual meetings - all highly
productive and absolutely necessary, but somehow lacking in jokes ... .

Best wishes,

Gerard.

--
On Thu, May 27, 2021 at 05:34:18PM +, Hughes, Jonathan wrote:
> 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 more 
> easily with u rather than anything derived from u².
> 
> best
> 
> jon
> 
> 
> 
> *nice presentation, by the way, not that i know what a complex number is, 
> unfortunately, although i did once see someone trying to explain it to his 
> girlfriend with the help of a graph drawn in the sand on a beach 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,
> 
> 
> 
> 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, 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 mailto:ianj...@gmail.com>>
> 
> > Gesendet: Donnerstag, 27. Mai 2021 18:32
> 
> > An: Hughes, Jonathan 
> > 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 
> > mailto:jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de%3cmailto: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
> 
> > mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>>>
> >  Im Auftrag von
> 
> > Pearce, N.M. (Nick)
> 
> > Gesendet: Donnerstag, 27. Mai 2021 12:38
> 
> > An: 
> > CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK%3cmailto: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 RMSF. Will change the scaling of the tube 
> > radius considerably!
> 
> >
> 
> > Nick
> 
> >
> 
> > On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
> > <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk%3cmailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>>
> >  wrote:
> 
> >
> 
> > Cool…
> 
> >
> 
> > Purely for visualisation this does look like the approved CCP4 way -
> 
> >
> 
> > 
> 
> >
> 
> > Harry
> 
> >
> 
> > On 27 May 2021, at 10:01, Stuart McNicholas 
&g

Re: [ccp4bb] (R)MS

[Gergely Katona]

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  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 mailto:ianj...@gmail.com>>
Gesendet: Donnerstag, 27. Mai 2021 18:32
An: Hughes, Jonathan 
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 
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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Pearce, N.M. (Nick)
Gesendet: Donnerstag, 27. Mai 2021 12:38
An: 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 RMSF. Will change the scaling of the tube radius 
considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

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<mailto:19a0c5f649e5-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
<193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-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/)
   Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
   Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
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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[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Hughes, Jonathan]

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 more easily 
with u rather than anything derived from u².

best

jon



*nice presentation, by the way, not that i know what a complex number is, 
unfortunately, although i did once see someone trying to explain it to his 
girlfriend with the help of a graph drawn in the sand on a beach 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,



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, 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 mailto:ianj...@gmail.com>>

> Gesendet: Donnerstag, 27. Mai 2021 18:32

> An: Hughes, Jonathan 
> 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 
> mailto:jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de%3cmailto: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

> mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>>>
>  Im Auftrag von

> Pearce, N.M. (Nick)

> Gesendet: Donnerstag, 27. Mai 2021 12:38

> An: 
> CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK%3cmailto: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 RMSF. Will change the scaling of the tube radius 
> considerably!

>

> Nick

>

> On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk%3cmailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>>
>  wrote:

>

> 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<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk%3cmailto:19a0c5f649e5-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

> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk%3cmailto:193323b1e616-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/)

>Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )

>Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
> 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 al

Re: [ccp4bb] AW: [ccp4bb] (R)MS

[Gerard Bricogne]

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, 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 
> 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 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 
> 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 
> mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Pearce, 
> N.M. (Nick)
> Gesendet: Donnerstag, 27. Mai 2021 12:38
> An: 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 RMSF. Will change the scaling of the tube radius 
> considerably!
> 
> Nick
> 
> On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
>  wrote:
> 
> 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<mailto:19a0c5f649e5-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
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-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/)
>Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
>Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
> 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
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of 
> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list 
> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions 
> are available at https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of 
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> are available at https://www.jiscmail.ac.uk/policyandsecurity/
> 
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> 
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[ccp4bb] AW: [ccp4bb] (R)MS

[Hughes, Jonathan]

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 
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 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 
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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Pearce, N.M. (Nick)
Gesendet: Donnerstag, 27. Mai 2021 12:38
An: 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 RMSF. Will change the scaling of the tube radius 
considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

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<mailto:19a0c5f649e5-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
<193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-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/)
   Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
   Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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Re: [ccp4bb] (R)MS

[Ian Tickle]

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:

> 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  *Im Auftrag von *Pearce,
> N.M. (Nick)
> *Gesendet:* Donnerstag, 27. Mai 2021 12:38
> *A**n:* 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 <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
>
> 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
>
> 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 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 (http://www.bpc.uni-frankfurt.de/cyrange.html) and
> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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> --
>
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Re: [ccp4bb] (R)MS

[Tim Gruene]

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 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  Im Auftrag von
> Pearce, N.M. (Nick) Gesendet: Donnerstag, 27. Mai 2021 12:38
> An: 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 RMSF. Will change the scaling of
> the tube radius considerably!
> 
> Nick
> 
> 
> On 27 May 2021, at 11:16, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> wrote:
> 
> 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
> 
> 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 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 (http://www.bpc.uni-frankfurt.de/cyrange.html)
> and 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
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of
> www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk,
> terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
> 
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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpDnh2b0PHz1.pgp
Description: OpenPGP digital signature

[ccp4bb] (R)MS

[Hughes, Jonathan]

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  Im Auftrag von Pearce, N.M. 
(Nick)
Gesendet: Donnerstag, 27. Mai 2021 12:38
An: 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 RMSF. Will change the scaling of the tube radius 
considerably!

Nick


On 27 May 2021, at 11:16, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:

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

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 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 (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
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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