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:
To export SiteMap surfaces, follow the sequence below.
- Run SiteMap.
- From the Manage Surfaces panel in Maestro, export the SiteMap surface using "Export to Map". Choose CCP4 as the file format.
- 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.
Optionally, at the PyMOL command line, enter the command
This is mentioned at the bottom of the web page listed above, and will equate the Maestro isovalue with the PyMOL isovalue.
- 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
To display the map, use the "isomesh" command. The
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_doublecommand mentioned in the web page above to increase the mesh density. In addition, there are other suggestions to increase the quality of the image.
Keywords: PyMOL, SiteMap, surface
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