OK, time to brush up on my vector math. Thanks Angel and Rolf! Victor
2014-07-11 15:17 GMT-05:00 <jmol-users-requ...@lists.sourceforge.net>: > 7. bond-plane angle (Victor Rosas Garcia) > 8. Re: bond-plane angle (Angel Herr?ez) > 12. Re: bond-plane angle (Rolf Huehne) > > > ------------------------------ > > Message: 7 > Date: Mon, 7 Jul 2014 11:42:47 -0500 > From: Victor Rosas Garcia <rosas.vic...@gmail.com> > Subject: [Jmol-users] bond-plane angle > To: jmol-users@lists.sourceforge.net > Message-ID: > <CAJota7Ar6n= > qdy3ixg0ummccvro4mxne-wau4ffoobtajjh...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello everybody, > > I have defined a solvated system, and I have defined a plane using three > hydrogen atoms on separate water molecules. Now I have my solute and one of > its bonds is almost perpendicular to the defined plane. How can I find out > the bond-plane angle? Is such a measurement possible in Jmol? > > Thanks for your attention > > Victor > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 8 > Date: Mon, 7 Jul 2014 20:26:10 +0200 > From: Angel Herr?ez <angel.herr...@uah.es> > Subject: Re: [Jmol-users] bond-plane angle > To: <jmol-users@lists.sourceforge.net> > Message-ID: <53bae642.21188.577a...@angel.herraez.uah.es> > Content-Type: text/plain; charset="US-ASCII" > > Hi Victor, > > Maybe; try some combination of JmolMath functions, e.g. > angle() > intersection() > measure() > plane() > > http://chemapps.stolaf.edu/jmol/docs/#functions > > > ------------------------------ > > Message: 12 > Date: Tue, 08 Jul 2014 19:08:22 +0200 > From: Rolf Huehne <rhue...@fli-leibniz.de> > Subject: Re: [Jmol-users] bond-plane angle > To: jmol-users@lists.sourceforge.net > Message-ID: <53bc2586.9060...@fli-leibniz.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 07/07/2014 06:42 PM, Victor Rosas Garcia wrote: > > Hello everybody, > > > > I have defined a solvated system, and I have defined a plane using three > > hydrogen atoms on separate water molecules. Now I have my solute and one > of > > its bonds is almost perpendicular to the defined plane. How can I find > out > > the bond-plane angle? Is such a measurement possible in Jmol? > > > There doesn't seem to be a special function available to do this. But > you should be able to write one yourself if you dig a little bit into > vector mathematics. > > I think this page (http://www.netcomuk.co.uk/~jenolive/vect14.html) > illustrates what you are looking for in the section "The angle between a > line and a plane". > So you would need to define the "normal vector" of your plane (this page > might be helpful: > > http://math.stackexchange.com/questions/137538/calculate-the-vector-normal-to-the-plane-by-given-points > ) > and determine the angles. > Jmol math includes vector operations (see > http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm?ver=14.0#jmolmath > ). > So it shouldn't be to hard to do this. > Maybe quaternions (implemented in Jmol) can be helpful here but I don't > know enough about them to be sure. > > Regards, > Rolf > > -- > > Rolf Huehne > Postdoc > > Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) > Beutenbergstrasse 11 > 07745 Jena, Germany > > Phone: +49 3641 65 6205 > Fax: +49 3641 65 6210 > E-Mail: rhue...@fli-leibniz.de > Website: http://www.fli-leibniz.de > > Scientific Director: Prof. Dr. K. Lenhard Rudolph > Head of Administration: Dr. Daniele Barthel > Chairman of Board of Trustees: Dennys Klein > > VAT No: DE 153 925 464 > Register of Associations: No. 230296, Amtsgericht Jena > Tax Number: 162/141/08228 > > > > > ------------------------------ > > Message: 13 > Date: Wed, 9 Jul 2014 23:58:18 -0400 > From: Otis Rothenberger <osrot...@chemagic.com> > Subject: [Jmol-users] State Question > To: jmol-users@lists.sourceforge.net > Message-ID: > < > cajopumcqgjh0ubyqvbpwruxjuhczclafesb86q9atoe8srd...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Bob, > > I use the following script to duplicate a model in the Jmol window: > > scpt = 'center;var mod2 = "' + Jmol.getPropertyAsString(jmolApplet0, > "extractModel") + '";'; > scpt += 'set echo top left;echo;set appendNew false;var z=' + bbMax() + > ';'; > scpt += 'select *;translateSelected {@z @z 0};load APPEND "@mod2";'; > scpt += 'hover "";select *;wireframe 0.15;spacefill 23%;boundbox > {*};centerat boundbox;minimize CLEAR;'; > scpt += 'for (var i = 1; i < {*}.length +1; i++){ {*}[i].atomno = i }'; > Jmol.script(jmolApplet0, scpt); > > bbMax() simply calculates the longest dimension of the bound box. This all > works, BUT the resulting model pair has a Jmol state problem. I can write a > state, but it will not restore. Is my atomno renumbering screwing this up? > > The renumbering may seem strange, but I'm working with edited models, and > the renumbering prevents atomno overlap produced by duplicating edited > models. > > This is not a huge problem. I'm just curious if the renumbering is the > guilty party. > > Otis > > -- > Otis Rothenberger > o...@chemagic.com > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 14 > Date: Fri, 11 Jul 2014 08:45:00 +0000 > From: mark <m...@haunted-river.net> > Subject: [Jmol-users] JMol PHP Recentl error with Firefox 30 > To: jmol-us...@lists.sf.net > Message-ID: <53bfa40c.6000...@haunted-river.net> > Content-Type: text/plain; charset="iso-8859-1" > > Approximately 1 week ago, after a Firefox update my website no longer > shows my Jmol structures in Firefox. It still works in IE. > > Firefox fails to load the models on mutiple machines running both Linux > and Windows. > > > Here is the error: > > Error connecting to server: > > http://your.server.here/jsmol.php?call=getRawDataFromDatabase&database=_&query=http%3A%2F%2Fchemapps.stolaf.edu%2Fjmol%2Fjsmol%2Fj2s%2Fcore%2Fcorescript.z.js > > > Here is the web console output: > > SyntaxError: syntax error Jmol.js:1 > "JSmol load jmolApplet0 loadClazz..." jmol.php:272 > "JSmol load jmolApplet0 start applet..." jmol.php:272 > "JSmol exec jmolApplet0 loadClazz null -- OK" jmol.php:273 > "JSmol exec jmolApplet0 start applet null -- OK" jmol.php:273 > Synchronous XMLHttpRequest on the main thread is deprecated because of > its detrimental effects to the end user's experience. For more help > http://xhr.spec.whatwg.org/ jmol.php:181 > > > > Here is the relevant code on the site: > > <script type="text/javascript" > src="http://chemapps.stolaf.edu/jmol/jmol.php? > source=http://mark-bishop.net/mdl/elemicen.txt > &inline > &width=200px > &depth=200px" > ?JMOLJAR=SIGNED> > </script> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 15 > Date: Fri, 11 Jul 2014 20:17:17 +0000 > From: "Greeves, Nick" <ngree...@liverpool.ac.uk> > Subject: [Jmol-users] JMol PHP Recentl error with Firefox 30 > To: "<jmol-users@lists.sourceforge.net>" > <jmol-users@lists.sourceforge.net> > Message-ID: <295abf1e-7d8f-4991-8489-5e520af23...@liverpool.ac.uk> > Content-Type: text/plain; charset="windows-1252" > > Hi Mark et al, > > I?ve just noticed this error too. > > "Synchronous XMLHttpRequest on the main thread is deprecated because of > its detrimental effects to the end user's experience. For more help > http://xhr.spec.whatwg.org/? > > Pages with .xyz structures seem to load OK. > > This error > > Error connecting to server: > > http://your.server.here/jsmol.php?call=getRawDataFromDatabase&database=_&query=http%3A%2F%2Fchemapps.stolaf.edu%2Fjmol%2Fjsmol%2Fj2s%2Fcore%2Fcorescript.z.js > > > > is where you can add your own server name to supply the jsmol.php file > that facilitates loading of binary files into JSmol. Previously Firefox did > not rely on this php route (unlike Safari and Chrome ) but maybe the update > now sends it down this route? > > If you add the jsmol.php file to your server and correct the URL in var > Info for your page, it may solve the problem. > > I use serverURL: "http://www.chemtube3d.com/php/jsmol.php?, and it works > for me BUT I am seeing the deprecated message in the Firefox Console. > > > Best regards > Nick > -- > Nick Greeves via OS X Mail > Director of Teaching and Learning > Department of Chemistry > University of Liverpool > Donnan and Robert Robinson Laboratories > Crown Street, LIVERPOOL L69 7ZD U.K. > Email address: ngree...@liverpool.ac.uk<mailto:ngree...@liverpool.ac.uk > > > WWW Pages: http://www.chemtube3d.com > Tel: +44 (0)151-794-3506 (3500 secretary) > Dept Fax: +44 (0)151-794-3588 > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > ------------------------------------------------------------------------------ > > > ------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > End of Jmol-users Digest, Vol 98, Issue 2 > ***************************************** >
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