I would like to export the results of a SiteMap analysis into another format so I can use special visualization software like PyMOL to create pictures for publication. Since the results are principally just surfaces, they don't have any coordinates. Is there another way to save the SiteMap grid points as pseudo atoms?

First, note that Maestro can save high-quality images in tiff format. From Suite 2010 on, choose Workspace → Save Image. For Suite 2009 or earlier, select Maestro → Save Image.

If you want to export the surfaces to be read into another application like PyMOL, you can save the surfaces in CCP4 or CNS format. Click Export to Map in the Manage Surfaces panel, and select a format. If you export in CNS format and want to import this to PyMOL, type load map.cns, format=xplor in PyMOL. You should also export the site entries and the protein entry from the Project Table in PDB format, and import them into PyMOL. Make sure that you set Action → Mesh → @ level 1.0 in PyMOL, and that you match the isolevel with the isovalues used in Maestro for the surfaces.

If you want the grids that are used for the SiteMap surfaces in text format, you can use the following utility to convert the output files:

$SCHRODINGER/utilities/visdump volume.vis > volume.txt

The resulting file will have the grid point values that can be modified to be the coordinates for dummy atoms or just points in space for any ray-tracing software to be used to render the images.

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