This is a read-only mirror of pymolwiki.org

Difference between revisions of "Isosurface"

From PyMOL Wiki
Jump to navigation Jump to search
m (1 revision)
m (2 revisions)
(2 intermediate revisions by the same user not shown)
Line 11: Line 11:
 
* level = the contour level.
 
* level = the contour level.
 
* 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).
* state = the state into which the object should be loaded (default=1) (set state=0 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.
  
Line 27: Line 27:
 
== Notes ==
 
== Notes ==
  
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).
+
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 ==
 
== See Also ==

Revision as of 03:40, 3 February 2020

isosurface creates a new surface object from a map object.

Usage

 isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]
  • 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.
  • selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
  • 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.

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