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 <[email protected]> Gesendet: Donnerstag, 27. Mai 2021 20:19 An: Hughes, Jonathan <[email protected]> Cc: [email protected] 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 +0000, 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<u2> 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 <[email protected]> > Gesendet: Donnerstag, 27. Mai 2021 19:05 > An: Hughes, Jonathan <[email protected]> > Cc: [email protected] > 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 +0000, 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 <[email protected]<mailto:[email protected]>> > > > Gesendet: Donnerstag, 27. Mai 2021 18:32 > > > An: Hughes, Jonathan > > <[email protected]<mailto:[email protected] > > iessen.de>> > > > Cc: [email protected]<mailto:[email protected]> > > > 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 > > <[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>> > > 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 > > > <[email protected]<mailto:[email protected]<mailto:CCP4BB@JI > > SCMAIL.AC.UK%3cmailto:[email protected]>>> Im Auftrag von > > > Pearce, N.M. (Nick) > > > Gesendet: Donnerstag, 27. Mai 2021 12:38 > > > An: > > [email protected]<mailto:[email protected]<mailto:CCP4BB@JIS > > CMAIL.AC.UK%3cmailto:[email protected]>> > > > 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 > > <[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>> > > wrote: > > > > > > Cool… > > > > > > Purely for visualisation this does look like the approved CCP4 way - > > > > > > <Screen Shot 2021-05-27 at 10.13.59.png> > > > > > > Harry > > > > > > On 27 May 2021, at 10:01, Stuart McNicholas > > <[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>> > > 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 > > > <[email protected]<mailto:[email protected]<mailto:[email protected]%3cmailto:[email protected]>>> > > 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&A=1 > > > > > > This message was issued to members of > > > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB<http://ww > > w.jiscmail.ac.uk/CCP4BB%3chttp:/www.jiscmail.ac.uk/CCP4BB>>, a > > mailing > > > list hosted by > > www.jiscmail.ac.uk<http://www.jiscmail.ac.uk<http://www.jiscmail.ac. > > uk%3chttp:/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&A=1 > > > > > > This message was issued to members of > > > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB<http://ww > > w.jiscmail.ac.uk/CCP4BB%3chttp:/www.jiscmail.ac.uk/CCP4BB>>, a > > mailing > > > list hosted by > > www.jiscmail.ac.uk<http://www.jiscmail.ac.uk<http://www.jiscmail.ac. > > uk%3chttp:/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&A=1 > > > > > > > > > ________________________________ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > ________________________________ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > #################################################################### > > ## > > > ## > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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/
