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/
