Difference between revisions of "Surface mode"

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(Syntax)
(move usage to top)
 
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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.
 
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.
  
<gallery caption="Surface Mode Examples" heights="175px" widths="175px">
+
== 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>
  
== Examples ==
 
 
<source lang="python">
 
<source lang="python">
 
# make the above images, or something like them
 
# make the above images, or something like them
fetch 2v72
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fetch 2v72, async=0
 
color wheat
 
color wheat
 
color marine, het
 
color marine, het
zoom het and not resn HOH
+
show surface
hide
 
as surface, 2v72
 
# ray 800,600
 
  
 
# default
 
# default
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set surface_mode, 1
 
set surface_mode, 1
 
</source>
 
</source>
 
== Usage ==
 
<source lang="python">
 
set surface_mode, int
 
</source>
 
where int is in the range of 0 to 4.
 
 
Options:
 
 
''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]]

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

# 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