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]<mailto:[email protected]>
WWW Pages: http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)
Dept Fax: +44 (0)151-794-3588
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