[ccp4bb] bioNMR research scientist position available

[Dirk Bussiere]

Dear colleagues,

I realize that this is peripheral to CCP4, but we are looking for a research 
scientist in biological NMR spectroscopy to join our large multi-disciplinary 
Molecular Pharmacology department. It's a great opportunity to work with 
dedicated, innovative scientists focusing on pharmaceutical discovery.   Please 
see the job description below.

https://careers.lilly.com/job/indianapolis/research-scientist-biomolecular-nmr-spectroscopy/410/8126932368

If you have any questions, please don't hesitate to contact me.

-Dirk

Dirksen Bussiere, Ph.D., M.B.A.
Sr. Director/Head, Molecular Pharmacology (Quantitative and Structural Biology)
Lilly Research Laboratories
Eli Lilly and Company
Lilly Biotechnology Center Phone: 510-759-7013
10290 Campus Point Dr.   E-mail: 
bussiere_dirk...@lilly.com
San Diego, CA 92121





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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
>
> > 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 > 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 > CMAIL.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 
> 

Re: [ccp4bb] Analysis of NMR ensembles

[Jon Cooper]

A bit late, I know, but a bit more googling gave me this site which I don't 
think has been mentioned so far:

http://old.protein.bio.unipd.it/mobi/

Given the pdb code, it is a one click job to get a pdb file with the "B-factors 
changed to averaged Scaled Distance x 100" and the resulting picture (attached) 
looks about right, I think/hope.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with ProtonMail Secure Email.

‐‐‐ Original Message ‐‐‐
On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB 
 wrote:

 Hi Jon

 The RMSD data (also NOEs, chemical shifts, etc) are not in the original 
PDB so I would have to calculate them - which takes me to my original question!

 Harry

  On 26 May 2021, at 17:22, Jon Cooper jon.b.coo...@protonmail.com 
wrote:
  Hello Harry,
  Looking at:
  http://www.mcgnmr.mcgill.ca/ProtSkin/
  It says: "If your input is a plain file containing your scalar data 
to map, such as heteronuclear NOE or chemical shift differences, ensure the 
first column in your file contains residue numbers and the second column 
contains the values to map, then click the Browse button to retrieve this file 
and select "Plain list of scores"
  If you can get the residue number and rmsd data into columns in a 
file, it should map them onto a pdb file for one monomer as pseudo-B-factors.
  HTH, Jon.C.
  Sent from ProtonMail mobile
   Original Message 
  On 26 May 2021, 16:51, Harry Powell - CCP4BB  
hrp-ccp...@virginmedia.com wrote:
  Yes, Jon, but I was hoping I wasn’t the first person to ever want 
this…
  Harry
 
   On 26 May 2021, at 16:34, Jon Cooper 
488a26d62010-dmarc-requ...@jiscmail.ac.uk wrote:
   The hard bit is to get the rmsd's into the B-factor column, but 
it shouldn't stretch you too much, Harry ;-
   There is ProtSkin on the web which does something similar with 
sequence alignments.
   Sent from ProtonMail mobile
    Original Message 
   On 26 May 2021, 16:28, Harry Powell - CCP4BB  
193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
   Hi Jurgen
   NMR structures don’t appear to have B_factors, or at least not 
meaningful ones (e.g. in 2kv5 they’re all 0.00…).
   thanks for the response, though
   Harry
  
On 26 May 2021, at 16:21, Jurgen Bosch jxb...@case.edu 
wrote:
How about color by B-factor and look for the cold areas and 
hot areas?
Jürgen
   
 On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
 Hi
 Given that there are plenty of people on this BB who 
are structural biologists rather than “just” crystallographers, I thought 
someone here might be able to help.
 If I have a structure in the PDB (e.g. 2kv5) that is 
an ensemble of structures that fit the NOEs, is there a tool available that 
will give me some idea about the bits of the structure that do not vary much 
(“rigid”) and the bits that are all over the place (“flexible”)?
 Would superpose or gesamt be a good tool for this? 
Ideally I’d like something that could add a figure to the B columns in a PDB 
file so I could see something in QTMG (or PyMol if forced…) or do other useful 
things with the information.
 Harry
 

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[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
> 
> > 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 > 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 > CMAIL.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>>
> >  wrote:
> 
> >
> 
> > Cool…
> 
> >
> 
> > Purely for visualisation this does look like the approved CCP4 way -
> 
> >
> 
> > 
> 
> >
> 
> > 

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
> 
> > 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>
> 
> > 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 

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
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
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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[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

> 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>

> 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 

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
> 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/
> 
> 
> 
> 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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[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
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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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/
>
>
> 
>
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>
>
>
>
> --
>
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[ccp4bb] Crystallography positions at Exscientia

[Simone Culurgioni]

Dear all,

We are looking for experienced Crystallographers to join the Discovery
Biology department at Exscientia.
The Discovery Biology team in Exscientia is responsible for enabling
small-molecule therapeutic projects and integrates with the Artificial
Intelligence (AI) driven drug discovery platform.

The ideal candidates should have a strong experience in structural biology
with a focus on crystallography.

Please apply through the link:
https://jobs.lever.co/exscientia/3264b5a0-10be-489a-8394-a8f2db392424
or
https://www.exscientia.ai/careers


Best wishes,

Simone


-- 
Dr Simone Culurgioni
Head of Crystallography
Exscientia Ltd.
The Schrödinger Building
Heatley Road
The Oxford Science Park
Oxford
OX4 4GE

Tel. 07892 715263



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Re: [ccp4bb] post-doc position at KU Leuven, ligand-gated ion channels

[Chris Ulens]

A post-doctoral position is available at the Laboratory of Prof. Chris Ulens, 
KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of 
Structural Neurobiology is aimed at understanding the molecular mechanism of 
ligand-gated ion channels. Our methods rely on X-ray crystallography and 
cryo-EM in combination with electrophysiological recordings and 
fluorescence-based techniques. Our laboratory hosts an integrated 
macromolecular crystallization facility with a Mosquito crystallization robot 
and two RockImagers. We have access to a 200 kV Glacios microscope on campus as 
well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current 
projects are situated at the crossroads of structural elucidation and drug 
discovery of different pentameric ligand-gated ion channels.

 We would like to recruit a post-doc with prior experience in cryo-EM or X-ray 
crystallography of membrane proteins.
 
The successful candidate:

- easily communicates in an open verbal manner and has a team player spirit
- has an ambitious work ethic
- critically contributes to writing of manuscripts and grant proposals
- makes efforts to obtain independent funding
- meets intermediate deadlines and brings projects to a successful end
- fuels internal discussions of recent publications in the field
- sets an example to younger PhD students in the lab
- identifies directions for future scientific research

 
The position is open immediately and applications will be accepted until the 
position is filled. Applicants are requested to submit a CV with publication 
list and two references. E-mail to chris.ul...@kuleuven.be

 
Selection of recent publications:

 
A lipid site shapes the agonist response of a pentameric ligand-gated ion 
channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch 
J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan 
G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 
2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4.

 
Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 
receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, 
Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, 
Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511.

 
The structural basis for an on-off switch controlling Gβγ-mediated inhibition 
of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous 
PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, 
Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc 
Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117.


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Description: S/MIME cryptographic signature

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
> 
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> 
> 
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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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[ccp4bb] clustering large number of ligands by position relative to the receptor

[Sorin Draga]

Hello everyone,

While this is not exactly a crystallography question, I do think that most
of you are well versed in structural analysis.
The problem: I have a very large number of ligands (>100.000) resulting
from blind docking against a certain receptor. Due to the large number,
this can not be done visually.
Is there a way to cluster these ligands based on their positions, so that
we can observe potential binding sites?

Any insight would be greatly appreciated!

Cheers!

S



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Re: [ccp4bb] Analysis of NMR ensembles

[Pearce, N.M. (Nick)]

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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Re: [ccp4bb] Analysis of NMR ensembles

[Rasmus Fogh]

Dear Dale,

It is more complex than just 'flexibility', but then it is always more 
complicated. Here are the main possibilities for undetermined regions:


-1- fast, free movement - signals are easy to see, have 'random-coil' 
chemical shifts, often overlap, and there are no  NOEs
-2-  intermediate-range exchange between several different 
conformations, free/bound etc. Signals are broadened and harder to 
observe, NOEs even more so.
-3-  The molecule is too big and slow-moving - you might be able to 
observe a domain linked by a flexible linker to a huge and invisible 
protein (or virus, ...)

-4- Proximity to lanthanides or other kinds of unpaired electrons.
-5- Missing observations, due to overlapped signals combined with barely 
adequate S/N ratio.


Arguably 1) and 2) are both movement, just in different time scales - 1) 
can be identified from relaxation measurements and/or chemical shifts, 
which should be pretty routine.

3) and 4) you would know about.
5) you could check by looking at, essentially, completeness.

Yours,
Rasmus

On 26/05/2021 22:06, Dale Tronrud wrote:

Dear Boaz,

   We are likely in agreement. "Deficient NOE's for some regions (e.g. 
loops) arise from their flexibility, ..."  This makes it sound like you 
agree that these deficiencies in other regions may be caused by 
properties other than flexibility.


   As an extreme example, the N-terminal region of a protein may have a 
broad distribution in the ensemble model either because this region 
experiences many conformations in solution, or because this peptide was 
cleaved from the protein at some earlier time and its absence was not 
recognized by the experimentalist.


Dale Tronrud

On 5/26/2021 1:06 PM, Boaz Shaanan wrote:

Hi Dale and Cecil,

This is quite a circular argument, isn't it? Deficient NOE's for some 
regions (e.g. loops) arise from their flexibility, hence they are not 
as well resolved as other (e.g. internal ) regions for which the 
number of NOE is large. So they are flexible by all accounts and, not 
surprisingly, align usually with high B-factor regions in the 
corresponding crystal structures. In cases where such flexible regions 
are held by crystal contacts the situations would likely be different.


Cheers,

                Boaz


/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/

/

*From:* CCP4 bulletin board  on behalf of Dale 
Tronrud 

*Sent:* Wednesday, May 26, 2021 10:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Analysis of NMR ensembles
 I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation.  The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation.  There are many reasons
why these data are be absent and high mobility is only one.

Dale Tronrud

On 5/26/2021 8:45 AM, Cécile Breyton wrote:

Hello,

In my understanding of NMR, the loops and terminii that adopt very 
different conformations in the structure ensemble rather reflect the 
fact that for those residues, the number of constraints is lower, 
thus the number of structures that fulfil the constraints is 
larger A dynamics study of the protein will be much more 
informative.


Cécile

Le 26/05/2021 à 17:29, S. Mohanty a écrit :

Hi Harry,

The superpose/overlay of all the structures in PyMol should inform 
you the rigid part of the protein as well as the flexible part. The 
rigid part would have very low backbone RMSD or overlay tightly and 
the flexible part (loops, N-term and C-term etc.) would not 
superpose tightly. If you check literature, the dynamics of the 
protein may have been studied through NMR relaxation.


Smita


On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:



Hi

Given that there are plenty of people on this BB who are structural 
biologists rather than “just” crystallographers, I thought someone 
here might be able to help.


If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
structures that fit the NOEs, is there a tool available that will 
give me some idea about the bits of the structure that do not vary 
much (“rigid”) and the bits that are all over the place (“flexible”)?


Would superpose or gesamt be a good tool for this? Ideally I’d like 
something that could add a figure to the B columns in a PDB file so 
I could see something in QTMG (or PyMol if forced…) or do 
otheruseful things with the information.


Harry

 



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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

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 
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Re: [ccp4bb] Analysis of NMR ensembles

[Stuart McNicholas]

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 
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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

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] CCP4BB Digest - 25 May 2021 to 26 May 2021 (#2021-147)

[James Krieger]

For the NMR structure ensemble, you could calculate root mean square 
fluctuations (RMSFs) and put them into the B factor column. This is a fairly 
common analysis within molecular dynamics software. You could also use the 
ProDy Python API to do this.

ProDy also has command line apps including one for writing out biomol 
assemblies, which could be added to the growing list too.

Best wishes 
James 

> On May 27, 2021, at 00:03, CCP4BB automatic digest system 
>  wrote:
> 
> There are 40 messages totaling 21155 lines in this issue.
> 
> Topics of the day:
> 
>  1. writing coordinates of full biomol into one (PDB) file (4)
>  2. Postdoctoral position in structural biology of comammox in Vienna
>  3. PhD position, University of Konstanz
>  4. Fwd: Abstract submission deadline extended to 2 June - PSB Symposium
> "Frontiers in Bioimaging", 1-2 July 2021
>  5. Unmodeled density (12)
>  6. External: Re: [ccp4bb] Unmodeled density
>  7. Analysis of NMR ensembles (19)
>  8. Fully-funded PhD at the University of Liverpool
> 
> 
> 
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> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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> Date:Tue, 25 May 2021 16:58:49 -0700
> From:Pavel Afonine 
> Subject: Re: writing coordinates of full biomol into one (PDB) file
> 
> Hi Frank,
> 
> phenix.pdb.biomt_reconstruction command should do it.
> 
> Pavel
> 
>> On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
>> frank.vonde...@cmd.ox.ac.uk> wrote:
>> 
>> Hello all - this presumably has a really simple solution:
>> 
>> For a PDB file with a (correct) biomolecular assembly record (REMARK
>> 350), what program do I use to generate and write out the coordinates of
>> the biomolecular assembly (or one of them).
>> 
>> Thanks
>> Frank
>> 
>> 
>> 
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> Date:Wed, 26 May 2021 07:05:26 +0200
> From:Kristina Djinovic Carugo 
> Subject: Postdoctoral position in structural biology of comammox in Vienna
> 
> *Postdoctoral position in structural biology of comammox in Vienna*
> 
> For 120 years, microbiologists had strongly assumed that nitrification 
> must be performed by two distinct groups of microorganisms 
> (‘nitrifiers’) in cooperation: the ammonia oxidizers and the nitrite 
> oxidizers, respectively. This scientific dogma broke in 2016, when 
> ‘complete ammonia oxidizers’ were discovered (1). In collaboration with 
> the research lab (Daims/Wagner) who discovered the comammox bacterium 
> Djinovic lab plans to structurally and biochemically characterize 
> selected enzymes of the comammox, with the aim to decipher the catalytic 
> mechanism and to identify those structural determinants of the substrate 
> affinity and specificity.
> 
> *Qualifications and experience: *The applicants should hold a recent PhD 
> degree in a relevant field with a structural biology experience. Strong 
> background in molecular cloning, expression, and purification of protein 
> complexes is essential. Prior knowledge of crystallography and/or 
> single-particle electron microscopy is needed. Excellent spoken and 
> written English are required.
> 
> Applications are accepted through *Vienna International Postdoctoral 
> Program (VIP^2 )*, details on the program which offers excellent 
> research environment,tructured training and career development program 
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> 
> https://training.vbc.ac.at/post-docs/vip2-post-doc-program/ 
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> 
> *Deadline*: 15^th June 2021
> 
> For details in the project contact please contact: Kristina Djinovic 
> Carugo kristina.djino...@univie.ac.at 
> 
> 
> 1.Daims, H., Lebedeva, E. V., Pjevac, P., Han, P., Herbold, C., 
> Albertsen, M., Jehmlich, N., Palatinszky, 

Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi

This is why I put “rigid” and “flexible” in quotes in my original post - to 
allow people to put whatever interpretation on them that they chose (within 
limits)! 

Of course, it’s always best to try to use the correct terms in a scientific 
discussion, but we all use shorthand; e.g., in crystallography we’re (mostly) 
happy to talk about “reflections” (even Lawrence Bragg did, but spelt it with 
an “x” not “ct”) when we all know that they aren’t specular reflections, which 
is what most people (including physicists) mean by the word…

Harry

> On 26 May 2021, at 22:06, Dale Tronrud  wrote:
> 
> Dear Boaz,
> 
>   We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) 
> arise from their flexibility, ..."  This makes it sound like you agree that 
> these deficiencies in other regions may be caused by properties other than 
> flexibility.
> 
>   As an extreme example, the N-terminal region of a protein may have a broad 
> distribution in the ensemble model either because this region experiences 
> many conformations in solution, or because this peptide was cleaved from the 
> protein at some earlier time and its absence was not recognized by the 
> experimentalist.
> 
> Dale Tronrud
> 
> On 5/26/2021 1:06 PM, Boaz Shaanan wrote:
>> Hi Dale and Cecil,
>> This is quite a circular argument, isn't it? Deficient NOE's for some 
>> regions (e.g. loops) arise from their flexibility, hence they are not as 
>> well resolved as other (e.g. internal ) regions for which the number of NOE 
>> is large. So they are flexible by all accounts and, not surprisingly, align 
>> usually with high B-factor regions in the corresponding crystal structures. 
>> In cases where such flexible regions are held by crystal contacts the 
>> situations would likely be different.
>> Cheers,
>>Boaz
>> /Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben-Gurion University of the Negev
>> Beer-Sheva 84105
>> Israel
>> E-mail: bshaa...@bgu.ac.il
>> Phone: 972-8-647-2220
>> Fax:   972-8-647-2992 or 972-8-646-1710 /
>> //
>> //
>> /
>> /
>> 
>> *From:* CCP4 bulletin board  on behalf of Dale 
>> Tronrud 
>> *Sent:* Wednesday, May 26, 2021 10:46 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK 
>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles
>> I agree with Dr Breyton. The variability in an NMR ensemble does not
>> reflect "mobility" but simply "uncertainty" in conformation.  The spread
>> in coordinates in some regions simply reflects the lack of experimental
>> data which could define a single conformation.  There are many reasons
>> why these data are be absent and high mobility is only one.
>> Dale Tronrud
>> On 5/26/2021 8:45 AM, Cécile Breyton wrote:
>>> Hello,
>>> In my understanding of NMR, the loops and terminii that adopt very 
>>> different conformations in the structure ensemble rather reflect the fact 
>>> that for those residues, the number of constraints is lower, thus the 
>>> number of structures that fulfil the constraints is larger A dynamics 
>>> study of the protein will be much more informative.
>>> Cécile
>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit :
 Hi Harry,
 
 The superpose/overlay of all the structures in PyMol should inform you the 
 rigid part of the protein as well as the flexible part. The rigid part 
 would have very low backbone RMSD or overlay tightly and the flexible part 
 (loops, N-term and C-term etc.) would not superpose tightly. If you check 
 literature, the dynamics of the protein may have been studied through NMR 
 relaxation.
 
 Smita
 
 
 On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
 <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
 
 
 Hi
 
 Given that there are plenty of people on this BB who are structural 
 biologists rather than “just” crystallographers, I thought someone here 
 might be able to help.
 
 If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
 structures that fit the NOEs, is there a tool available that will give me 
 some idea about the bits of the structure that do not vary much (“rigid”) 
 and the bits that are all over the place (“flexible”)?
 
 Would superpose or gesamt be a good tool for this? Ideally I’d like 
 something that could add a figure to the B columns in a PDB file so I 
 could see something in QTMG (or PyMol if forced…) or do other useful 
 things with the information.
 
 Harry
 
 
 
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>> 
 >