Hi Eric
I think you can get what you want using "set scale3d"
I've used it before to compare the size of different proteins
( http://biomodel.uah.es/model1j/prot/tamano.htm it's in Spanish, but you
can get the feel; just choose proteins from the drop-down list on the right)
I have done some tests and the value of scale3d needed is equal to
72 x (dimension in angstroms) / (dimension in pixels)
e.g., with "set scale3d 3.6", 300 pixels correspond to 3.6 x 300 / 72 = 15 Å.
or for a molecule measuring 40 Å to ocuppy 200 pixels, you must use "set
scale3d 14.4" (= 72 x 40 / 200).
Good luck
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