Knowledge Base

Article ID: 812 - Last Modified: April 19, 2011

Is there a way to export SiteMap surfaces to PyMOL?

Yes, using maps. There is an article on the PyMOLWiki that discusses working with maps:

http://www.pymolwiki.org/index.php/Display_CCP4_Maps

To export SiteMap surfaces, follow the sequence below.

  1. Run SiteMap.
  2. From the Manage Surfaces panel in Maestro, export the SiteMap surface using "Export to Map". Choose CCP4 as the file format.
  3. Transfer the structural information to Pymol. One way is to put the receptor and ligand into the Maestro Workspace, choose Maestro → PyMOL, then click Send: Workspace in the Pymol for Maestro panel. You can also start Pymol, and Import the structure with File → Open.
  4. Optionally, at the PyMOL command line, enter the command

    unset normalize_ccp4_maps

    This is mentioned at the bottom of the web page listed above, and will equate the Maestro isovalue with the PyMOL isovalue.
  5. Use File → Open to import the surface into PyMOL. You will need to select the file type. The surface will be listed as a separate object in the structure table
  6. To display the map, use the "isomesh" command. The usage is:

    isomesh object-name, map-name, iso-value, structure-object, carve=n

    For instance, if the SiteMap surface was named test1_map.ccp4, and the structure is called "maestro01" in the Pymol table, then a command with isovalue "-8" would look like

    isomesh my_map, test1_map, -8, maestro01, carve=3.0

    Experiment with the isovalue and carve value to adjust the surface for your preferences. Also consider the map_double command mentioned in the web page above to increase the mesh density. In addition, there are other suggestions to increase the quality of the image.

  7. Keywords: PyMOL, SiteMap, surface

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