Re: [ccp4bb] (R)MS

2021-05-29 Thread 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] (R)MS

2021-05-28 Thread 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

2021-05-28 Thread 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

Re: [ccp4bb] (R)MS

2021-05-27 Thread 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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Re: [ccp4bb] (R)MS

2021-05-27 Thread 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:
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>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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Re: [ccp4bb] (R)MS

2021-05-27 Thread 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
> 
> 
> 
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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

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