Difference between revisions of "Surface mode"
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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. | 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. | ||
| − | + | == Usage == | |
| + | |||
| + | set surface_mode, int | ||
| + | |||
| + | where ''int'' is one of the following values: | ||
| + | |||
| + | * 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 | ||
| + | |||
| + | == Examples == | ||
| + | |||
| + | <gallery heights="175px" widths="175px"> | ||
Image:sm0.png|[[surface_mode]] set to 0, the default. The galactose (blue) is not considered part of the surface. | Image:sm0.png|[[surface_mode]] set to 0, the default. The galactose (blue) is not considered part of the surface. | ||
Image:sm1.png|[[surface_mode]] set to 1 -- now including heteroatoms. The galactose and all heteroatoms (blue) are now considered part of the surface and colored blue. | Image:sm1.png|[[surface_mode]] set to 1 -- now including heteroatoms. The galactose and all heteroatoms (blue) are now considered part of the surface and colored blue. | ||
</gallery> | </gallery> | ||
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<source lang="python"> | <source lang="python"> | ||
# make the above images, or something like them | # make the above images, or something like them | ||
| − | fetch 2v72 | + | fetch 2v72, async=0 |
color wheat | color wheat | ||
color marine, het | color marine, het | ||
| − | + | show surface | |
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# default | # default | ||
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set surface_mode, 1 | set surface_mode, 1 | ||
</source> | </source> | ||
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[[Category:Settings|Surface mode]] | [[Category:Settings|Surface mode]] | ||
Latest revision as of 13:41, 15 February 2014
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.
Usage
set surface_mode, int
where int is one of the following values:
- 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
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.
# make the above images, or something like them
fetch 2v72, async=0
color wheat
color marine, het
show surface
# default
set surface_mode, 0
# non default
set surface_mode, 1