I wonder if you could use actual MOs. On Mon, Aug 20, 2012 at 4:42 AM, Greeves, Nick <[email protected]> wrote: > We are attempting to use lcao cartoons in a model of a Diels-Alder reaction, > but the orientation of the cartoons is not perpendicular to the plane of the > diene/dienophile, probably due to the molecular axis being defined across > both molecules. We have attempted to rectify this using the code described > below, but so far I have only managed to rotate the LCAOcartoon about one > axis. > > > If anyone has a suggestion of how I can fix this it would be appreciated. > > We were also wondering if it was possible to alter the orientation of the > cartoons using set picking - as works so well for arrows and lines etc. > > [Jmol-users] lcaocartoon orbitals -- new feature "rotate" > > Bob Hanson > Sun, 19 Aug 2007 16:34:56 -0700 > > Just checked in: > > 11.3.11 will include: > > lcaoCartoon rotate [x|y|z] [number_of_degrees] create "px" > > This allows a more precise positioning of LCAO cartoons. The axes are > defined automatically by Jmol based on the local molecular structure > around the specified center(s) and will be different for each center. > > Bob > > My code: > > jmolButton('load model/kate/DA8model.xyz;set axesMolecular;set axesScale > 5;axes on;moveto 0.0 20 453 891 145.8;wireframe on;spacefill off;anim mode > once;anim off;connect (atomno=15 and model >=1.1 AND model <= 1.126) > (atomno=16) triple; > > connect (atomno=8 and model >=1.1 AND model <= 1.100) (atomno=10) > double;connect (atomno=4 and model >=1.1 AND model <= 1.100) (atomno=7) > double; connect (atomno=1 and model >=1.1 AND model <= 1.100) (atomno=13) > double;select (atomno=1);lcaoCartoon scale 1.25 color translucent 4 blue red > rotate y 30 create "pz" MOLECULAR;select (atomno=7);lcaoCartoon scale 1.0 > color translucent 4 blue red rotate y 30 create "pz" MOLECULAR;select > (atomno=13);lcaoCartoon scale 1.25 color translucent 4 red blue rotate y 30 > create "pz" MOLECULAR;select (atomno=4);lcaoCartoon scale 1.75 color > translucent 4 blue red rotate y 30 create "pz" MOLECULAR;select > (atomno=10);lcaoCartoon scale 1.25 color translucent 4 red blue rotate y 30 > create "pz" MOLECULAR;select (atomno=8);lcaoCartoon scale 1.0 color > translucent 4 red blue rotate y 30 create "pz" MOLECULAR;',"lcao cartoons") > > > 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: [email protected] > WWW Pages: http://www.chemtube3d.com > Tel: +44 (0)151-794-3506 (3500 secretary) > Dept Fax: +44 (0)151-794-3588 > > > > > > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users >
-- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
