Isosurface - Revision history

Cchem: 2 revisions

2021-06-22T03:21:02Z

2 revisions

New page

'''isosurface''' creates a new surface object from a map object.

== Usage ==

<source lang="python">
isosurface name, map, [,level [,(selection) [,buffer [,state [,carve [,source_state [,side [,mode ]]]]]]]]
</source>

* 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 <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.

== See Also ==

* [[volume]]
* [[isodot]]
* [[isomesh]]
* [[load]]
* [[Dynamic_mesh]]

[[Category:Commands|Isosurface]]
[[Category:States|Isosurface]]
[[Category:Electron_Density]]
[[Category:Maps]]

Cchem: 2 revisions

2020-02-03T03:40:42Z

2 revisions

New page

'''isosurface''' creates a new surface object from a map object.

== Usage ==

<source lang="python">
isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]
</source>

* 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 ==

* [[volume]]
* [[isodot]]
* [[isomesh]]
* [[load]]
* [[Dynamic_mesh]]

[[Category:Commands|Isosurface]]
[[Category:States|Isosurface]]
[[Category:Electron_Density]]
[[Category:Maps]]

Cchem: 1 revision

2019-10-14T18:49:22Z

1 revision

Speleo3: examples

2019-10-14T13:30:23Z

examples

Bell: 7 revisions

2014-03-28T03:06:31Z

7 revisions

Pyadmin: 1 revision

2014-03-28T02:16:16Z

1 revision

Tlinnet: /* SEE ALSO */

2012-09-28T09:34:56Z

Vinnyrose at 14:08, 20 June 2009

2009-06-20T14:08:26Z

New page

===DESCRIPTION===
'''isosurface''' creates a new surface object from a map object.

===USAGE===
<source lang="python">
isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]
</source>

* 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=0 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.

===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).

===SEE ALSO===
[[isodot]], [[isomesh]], [[load]]

[[Category:Commands|Isosurface]]
[[Category:States|Isosurface]]

Tree at 05:57, 23 February 2005

2005-02-23T05:57:47Z

New page

===DESCRIPTION===

"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=0 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.

===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).

===SEE ALSO===

[[Cmd isodot]], [[Cmd isomesh]], [[Cmd load]]

[[Category:Commands|isosurface]]

← Older revision	Revision as of 18:49, 14 October 2019
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@@ Line 1: / Line 1: @@
 '''isosurface''' creates a new surface object from a map object.
-===USAGE===
+== Usage ==
 <source lang="python">
   isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]]
@@ Line 13: / Line 14: @@
 * carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed.
-===NOTES===
+== Examples ==
 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===
+== See Also ==
-[[isodot]], [[isomesh]], [[load]] , [[Dynamic_mesh]]
 [[Category:Commands|Isosurface]]

← Older revision	Revision as of 03:06, 28 March 2014
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← Older revision	Revision as of 02:16, 28 March 2014
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