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Difference between revisions of "Isosurface"

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===DESCRIPTION===
 
 
'''isosurface''' creates a new surface object from a map object.
 
'''isosurface''' creates a new surface object from a map object.
  
===USAGE===
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== Usage ==
 +
 
 
<source lang="python">
 
<source lang="python">
  isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]
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  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.
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* level = the contour level. (default=1.0)
* selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
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* 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=0 to append new surface as a new state)
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* 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.
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* 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 ==
 +
 
 +
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.
  
===NOTES===
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== See Also ==
If the surface object already exists, then the new surface will be appended onto the object as a new state (unless you indicate a state).
 
  
===SEE ALSO===
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* [[volume]]
[[isodot]], [[isomesh]], [[load]]  
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* [[isodot]]
 +
* [[isomesh]]
 +
* [[load]]
 +
* [[Dynamic_mesh]]
  
 
[[Category:Commands|Isosurface]]
 
[[Category:Commands|Isosurface]]
 
[[Category:States|Isosurface]]
 
[[Category:States|Isosurface]]
 +
[[Category:Electron_Density]]
 +
[[Category:Maps]]

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.

See Also