Mod:jmol
Installing Jmol and JSmol
Useful Jmol commands which might be difficult to find in the manual
Connecting bonds to atoms by type
connect {_XX} {*} none will remove all bonds to dummy atoms.
Orientating a molecule into a desired viewpoint
- Load molecule (Jmol or JSmol)
- Right click to open console
- Into dialog box enter show orientation
- Using (on a Mac) cmd-c to copy, grab the string moveto /* time, axisAngle */ 1.0 { -296 824 -483 148.14} (which is the first in the rather voluminous output and 1.0 is the time taken to move to that orientation).
- Add moveto /* time, axisAngle */ 0.0 { -296 824 -483 148.14}; to your script, where 1.0 is replaced by 0.0 to instantly orientate.