Simon,
although you seem to have the solution, I'd like to give my view
As I understand it, "zoom 100" will fit the model in spacefill into the window,
at any rotation angle; maybe yor perception is due to your having a single
"best" orientation, for which there may be empty margin left.
I do not think the bounding box has any influence.
As Eric pointed out, the state of "zoomlarge" is relevant if the Jmol is not
square.
That said, I am not familiar with your "zoom 0" as it is --although it may well
be correct. This is what I would do:
zoomto 0.01 {visible} 0;
zoomto 0.01 {visible} 0 *1.1; //for a slightly larger model
zoomto 0.01 {visible} 0 *0.9; //for a slightly smaller model
Those should fit the model to the Jmol window in all cases, for any rotation.
0.01 is a time in seconds, which may be reduced to zero
Please see http://chemapps.stolaf.edu/jmol/docs/#zoomto
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