Surface mode
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Overview
Sets how PyMOL draws the surface. The default, surface_mode=0 does not include the heteroatoms within the surface; setting it to 1, does include them. See the example images.
- Surface Mode Examples
surface_mode set to 0, the default. The galactose (blue) is not considered part of the surface.
surface_mode set to 1 -- now including heteroatoms. The galactose and all heteroatoms (blue) are now considered part of the surface and colored blue.
Examples
# make the above images, or something like them
fetch 2v72
color wheat
color marine, het
zoom het and not resn HOH
hide
as surface, 2v72
# ray 800,600
# default
set surface_mode, 0
# non default
set surface_mode, 1
Usage
set surface_mode, int
where int is in the range of 0 to 4.
Options:
0
- Default mode, surfacing with respect to flags.
1
- Surface everything, including HET and hydrogens
2
- Surface only heavy atoms
3
- Surface only visible
4
- Surface visible and heavy