Hi Rajarshi 1. The standard element-id for "unknown" atoms in Jmol is Xx. You may use that and select them successfully using e.g. "select _Xx" (I've had some trouble with this syntax before, but don't remember the final solution; I may search and dig it up if you need so)
2. I'd bet (but haven't tested it) that you can use any id for your dummy atoms --as long as it is not an existent element symbol, Jmol will treat them as unknowns, give them the default pink color and default small radius, but you should be able to select them by "element" name, such as e.g. "select _R". However, my experience with this is mostly in PDB format; I am not sure if it will behave the same with SD (or MOL) format. 3. If you manage to use custom symbols, then you may be able to assign them different default colors using "color _R green" and even radii in a less direct way which I cannot say right away. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
