> 1) Is it possible to draw a sphere, filled or sketched like the one > on: http://accelrys.com/products/discovery-studio/pharmacophores/ > pharmacophore.jpg or http://www.biomedcentral.com/content/figures/ > 1471-2210-6-11-7.jpg?
Yes, you can draw spheres using "isosurface" and make them opaque/translucent; not sure about mesh-wire, but maybe A bit outdated doc, but simpler and still useful: http://biomodel.uah.es/Jmol/surfaces/inicio.htm#nonMol and the full doc: http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#isosurface Example (sphere around atom): isoSurface mySphere center (atomno=6) sphere 1.5 mesh nofill or around the center of an atom set: isoSurface mySphere center (C2, C3, C4) sphere 1.5 mesh nofill or in a 3D coordinate: soSurface mySphere center {1.5 0 -0.5} sphere 1.5 mesh nofill (play with mesh/nomesh, fill/nofill, dots/nodots, opaque/translucent) > 2) Can I add atoms/bonds via the scripting language? If not, I guess > I can create a simple input file and append it? Probably both ways. Bonds are created using "connect": connect (C1) (O3) connect (C1) (O3) double Atoms... maybe with the "data" command, but I'm not used to that. You can also fake them as big dots using "draw", depending on your needs ยท Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
