Difference between revisions of "Isosurface"
Jump to navigation
Jump to search
m |
m (corrected appending state) |
||
| (8 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
| − | |||
'''isosurface''' creates a new surface object from a map object. | '''isosurface''' creates a new surface object from a map object. | ||
| − | == | + | == Usage == |
| + | |||
<source lang="python"> | <source lang="python"> | ||
isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]] | isosurface name, map, level [,(selection) [,buffer [,state [,carve ]]]] | ||
| 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= | + | * 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. | ||
| − | === | + | == Examples == |
| − | If the | + | |
| + | 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| | + | [[Category:Commands|Isosurface]] |
| + | [[Category:States|Isosurface]] | ||
| + | [[Category:Electron_Density]] | ||
| + | [[Category:Maps]] | ||
Revision as of 16:51, 16 January 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.