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> > Gesendet: Donnerstag, 27. Mai 2021 18:32 > An: Hughes, Jonathan <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 > <jon.hug...@bot3.bio.uni-giessen.de<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 > <CCP4BB@JISCMAIL.AC.UK<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 > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto: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>> > 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>> > 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>, 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<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 > > > ________________________________ > > 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, 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&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/
