Hi All --
I've just stumbled into an odd behavior that is either a bug, or more likely my mis-understanding some aspect of how PyMOL works.  I've created "low resolution" surfaces on a hetero-meric protein complex to illustrate the packing together of various protein chains.  I've made these surfaces somewhat transparent so that the underlying protein chain can still be seen.
Here's how the gaussian maps are made (a la Warren DeLano's recent suggestions):
pymol> alter /proteinA, b=120
pymol> alter /proteinB, b=120
pymol> (etc)
pymol> alter /proteinA, q=1
pymol> alter /proteinB, q=1
pymol> (etc)
pymol> set gaussian_resolution, 4
pymol> map_new mapA, gaussian, 1, /proteinA
pymol> map_new mapB, gaussian, 1, /proteinB
pymol> (etc)
Now, for the odd behavior.  After I've created figure one as above, I want to rotate the complex by 90 degrees and create a figure viewing down the orthogonal axis.  If I click and drag with the mouse, all objects rotate as expected.  However, issuing:
pymol> rotate x, 90
results in the proteins rotating appropriately, but the gaussian maps remain in place.  Is there some setting required to allow transformations to be applied to maps from the command line?

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