Surface mode: Difference between revisions
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== | == Usage == | ||
<source lang="python"> | <source lang="python"> | ||
set surface_mode, int | set surface_mode, int | ||
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where int is in the range of 0 to 4. | where int is in the range of 0 to 4. | ||
0 | Options: | ||
1 | |||
''0'' | |||
::Default mode, surfacing with respect to [[flag]]s. | |||
''1'' | |||
:: Surface everything, including HET and hydrogens | |||
''2'' | |||
:: Surface only heavy atoms | |||
''3'' | |||
:: Surface only visible | |||
''4'' | |||
::Surface visible and heavy | |||
[[Category:Settings|Surface mode]] | [[Category:Settings|Surface mode]] | ||
Revision as of 08:34, 23 August 2011
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