Hi Brenton 

> > I generally like CPK colours but I would like to change the colour for
> > carbon to black. 

color carbon black;
color _H [xE0FFFF];
color carbon none; //reset to default

http://chemapps.stolaf.edu/jmol/docs/#colorelement


> > I think I may have asked this before, so if so I
> > apologize, but is it possible to set the background in Jmol to
> > transparent? 

In brief, no. There was one attempt some time, but it was not realiable.
Why do you want that? Is that for the application or the applet?
Remember you can set an image for background, using "set echo image"


> > Also, is it possible to move a molecule down directly, by
> > clicking on it and pulling it down by hand? 

Ctrl+Right drag
translate Y 10;




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