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Difference between revisions of "Isosurface"
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<source lang="python"> | <source lang="python"> | ||
| − | isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]] | + | isosurface name, map, [,level [,(selection) [,buffer [,state [,carve [,source_state [,side [,mode ]]]]]]]] |
</source> | </source> | ||
* name = the name for the new mesh isosurface object. | * name = the name for the new mesh isosurface object. | ||
* map = the name of the map object to use for computing the mesh. | * map = the name of the map object to use for computing the mesh. | ||
| − | * level = the contour level. | + | * level = the contour level. (default=1.0) |
| − | * selection = an atom selection about which to display the mesh with an additional "buffer" (if provided). | + | * selection = an atom selection about which to display the mesh with an additional "buffer" (if provided). (default="") |
* state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state) | * state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state) | ||
| − | * carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed. | + | * carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed. (default=None) |
| + | * source_state = the state of the map from which the object should be loaded. (default=0) | ||
| + | * Front or back face. Triangle-winding/normal direction. (default=1) | ||
| + | * mode = surface geometry (0: dots; 1: lines; 2: triangle triangle-normals; 3: triangle gradient-normals) (default=3) | ||
| + | |||
| + | == Algorithm == | ||
| + | |||
| + | PyMOL offers three different algorithms for isosurface generation. Each of these can be activated by the <code>isosurface_algorithm</code> setting | ||
| + | |||
| + | * 0: Marching Cubes via VTKm (default) (requires VTKm) | ||
| + | * 1: Marching Cubes basic (fallback if VTKm not installed) | ||
| + | * 2: Marching tetrahedra (legacy) | ||
== Examples == | == Examples == | ||
Latest revision as of 03:21, 22 June 2021
isosurface creates a new surface object from a map object.
Usage
isosurface name, map, [,level [,(selection) [,buffer [,state [,carve [,source_state [,side [,mode ]]]]]]]]
- name = the name for the new mesh isosurface object.
- map = the name of the map object to use for computing the mesh.
- level = the contour level. (default=1.0)
- selection = an atom selection about which to display the mesh with an additional "buffer" (if provided). (default="")
- state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state)
- carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed. (default=None)
- source_state = the state of the map from which the object should be loaded. (default=0)
- Front or back face. Triangle-winding/normal direction. (default=1)
- mode = surface geometry (0: dots; 1: lines; 2: triangle triangle-normals; 3: triangle gradient-normals) (default=3)
Algorithm
PyMOL offers three different algorithms for isosurface generation. Each of these can be activated by the isosurface_algorithm setting
- 0: Marching Cubes via VTKm (default) (requires VTKm)
- 1: Marching Cubes basic (fallback if VTKm not installed)
- 2: Marching tetrahedra (legacy)
Examples
fetch 1oky, type=2fofc, async=0 isosurface 1okySurf, 1oky_2fofc
With carving at 2 Angstrom around the molecular model:
fetch 1oky, async=0 fetch 1oky, type=2fofc, async=0 isosurface 1okySurf, 1oky_2fofc, 1.0, (1oky), carve=2.0
Notes
If there exists a non-map object with the same name, then the new surface will overwrite that object. Surface objects can be appended onto existing surface objects using the aforementioned state argument.