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.
This is mentioned at the bottom of the web page listed above, and will equate the Maestro isovalue with the PyMOL isovalue.
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
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.
Keywords: PyMOL, SiteMap, surface
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