Difference between revisions of "Surface mode"
Jump to navigation
Jump to search
(→Syntax) |
|||
| Line 25: | Line 25: | ||
</source> | </source> | ||
| − | == | + | == Usage == |
<source lang="python"> | <source lang="python"> | ||
set surface_mode, int | set surface_mode, int | ||
| Line 31: | Line 31: | ||
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 09:34, 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