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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Hughes, Jonathan <jon.hug...@bot3.bio.uni-giessen.de> Sent: Thursday, May 27, 2021 3:03:57 PM To: CCP4BB@JISCMAIL.AC.UK <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 <g...@globalphasing.com> Gesendet: Donnerstag, 27. Mai 2021 20:19 An: Hughes, Jonathan <jon.hug...@bot3.bio.uni-giessen.de> 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 +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 <g...@globalphasing.com> > Gesendet: Donnerstag, 27. Mai 2021 19:05 > An: Hughes, Jonathan <jon.hug...@bot3.bio.uni-giessen.de> > 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 +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 <ianj...@gmail.com<mailto:ianj...@gmail.com>> > > > Gesendet: Donnerstag, 27. Mai 2021 18:32 > > > An: Hughes, Jonathan > > <jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-g > > iessen.de>> > > > Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > > > Betreff: Re: [ccp4bb] (R)MS > > > > > > > > > Hi Jonathan > > > > > > It's historical, it's simply how it appears in the expression for the > > Debye-Waller factor, i.e. exp(-B sin^2(theta)/lambda^2). So it must have > > the same units as lambda^2. > > > > > > Cheers > > > > > > -- Ian > > > > > > > > > On Thu, 27 May 2021 at 13:25, Hughes, Jonathan > > <jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de<mailto:jon.hug...@bot3.bio.uni-giessen.de%3cmailto:jon.hug...@bot3.bio.uni-giessen.de>>> > > wrote: > > > o yes! but maybe the crystal people could explain to me why the B factor is > > the variance (with units of Ų) rather than the standard deviation (i.e. > > RMS, with units of Å) when, to my simple mind, the latter would seem be the > > more appropriate description of variability in space? > > > cheers > > > jon > > > > > > Von: CCP4 bulletin board > > > <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JI > > SCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>>> Im Auftrag von > > > Pearce, N.M. (Nick) > > > Gesendet: Donnerstag, 27. Mai 2021 12:38 > > > An: > > CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JIS > > CMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK>> > > > Betreff: Re: [ccp4bb] 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 > > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk%3cmailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk>>> > > 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 > > <000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk%3cmailto:000019a0c5f649e5-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 > > > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:0000193323b1e616-dmarc-requ...@jiscmail.ac.uk%3cmailto:0000193323b1e616-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://urldefense.com/v3/__https://theobald.brandeis.edu/theseus/__;!!P4SdNyxKAPE!R_V2YdKGBs4a6hGDnGMeYwpOlhIIVzqyqYkJEJEiq8cz8IFPyiS9OnFUS59Hbg$ > > ) > > > Bernhard: Molmol > > (https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/8744573/__;!!P4SdNyxKAPE!R_V2YdKGBs4a6hGDnGMeYwpOlhIIVzqyqYkJEJEiq8cz8IFPyiS9OnEF8EFoZg$ > > ) > > > Rasmus CYRANGE > > (https://urldefense.com/v3/__http://www.bpc.uni-frankfurt.de/cyrange.html__;!!P4SdNyxKAPE!R_V2YdKGBs4a6hGDnGMeYwpOlhIIVzqyqYkJEJEiq8cz8IFPyiS9OnFQ1mD0Lw$ > > ) > > and > > https://urldefense.com/v3/__https://www.ccpn.ac.uk/__;!!P4SdNyxKAPE!R_V2YdKGBs4a6hGDnGMeYwpOlhIIVzqyqYkJEJEiq8cz8IFPyiS9OnFd1FgKdw$ > > (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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