PyMOL transforms the output geometry in order to deliver a default view matching what's seen in the viewer window.  To prevent that, you'll need to effectively eliminate PyMOL's camera transformation by restoring to a transformation-less identity matrix:
At this point, there may not be anything visible in the viewer window, but the output WRL file will have the same coordinate system as the input PDB, DX map, etc.

From: Raluca Mihaela ANDREI [mailto:r.andrei@sns.it]
Sent: Fri 5/22/2009 10:51 AM
To: pymol-users
Subject: [PyMOL] wrl and dx files problem

I save the surface of a protein as a .wrl, then I calculate
the electrostatic potential and I save again the surface of
the protein. I import the two surfaces in Blender (a 3D
software) and I see that they are shifted. Why does this
happen? Then I open the .wrl files and the .dx file in another
home made program and I see that the surfaces and the grid
have not the same origin. Can somebody tell me why the surface
and the grid don't have the same origin and what do I have to
do in order to fix this?

Thank you,

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