Difference between revisions of "Volume"

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[[Volume]] creates a new volume object from a map object.  The data (3D scalar fields) are shown as a true 3D object using coloring and transparencies defined by the user to illustrate the data values.
 
[[Volume]] creates a new volume object from a map object.  The data (3D scalar fields) are shown as a true 3D object using coloring and transparencies defined by the user to illustrate the data values.
 +
This technique supports single and multiple isosurfaces.
  
This technique supports single and multiple isosurfaces.
+
== Usage ==
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 +
volume name, map [, ramp [, selection [, buffer [, state [, carve ]]]]]
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 +
== Arguments ==
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 +
* name = the name for the new volume object.
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* map = the name of the map object to use for computing the volume.
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* ramp = str: named color ramp {default: }
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* selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
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* carve = a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.
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 +
== Example ==
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fetch 1oky, type=2fofc, async=0
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volume 1okyVol, 1oky_2fofc
  
= Usage =
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== Screencasts ==
  
= Examples =
 
 
* [http://www.youtube.com/watch?v=tuAo_8-_HIc Silent demo movie] showing the basics of loading and using a volume in PyMOL.  There are more capabilities, but this is the basic functionality.
 
* [http://www.youtube.com/watch?v=tuAo_8-_HIc Silent demo movie] showing the basics of loading and using a volume in PyMOL.  There are more capabilities, but this is the basic functionality.
  
= See Also =
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== Changes with PyMOL Version ==
[[Map_new]] [[Isomesh]] [[Isosurface]]
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 +
* 1.4.0: first version with volume support
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* 1.7.2:
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** pre-integrated volume rendering (volume_mode=1) as Incentive-PyMOL-only feature.
 +
** scripting support with custom color ramp ([[volume_color]], [[volume_ramp_new]])
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** improved volume panel, panel can be opened from the object menu ("C > panel")
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** lots of bugs fixed
 +
 
 +
== Known Limitations ==
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 +
* No real ray-tracing support yet
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* Multiple volume objects don't blend properly
 +
 
 +
== See Also ==
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* http://pymol.org/volume
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* http://pymol.org/d/media:volumevisualization
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* [[volume_color]]
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* [[volume_ramp_new]]
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* [[map_new]]
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* [[isomesh]]
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* [[isosurface]]
  
 
[[Category:Commands]] [[Category:Volume]] [[Category:Representations]]
 
[[Category:Commands]] [[Category:Volume]] [[Category:Representations]]

Revision as of 14:57, 30 June 2014

Volume creates a new volume object from a map object. The data (3D scalar fields) are shown as a true 3D object using coloring and transparencies defined by the user to illustrate the data values. This technique supports single and multiple isosurfaces.

Usage

volume name, map [, ramp [, selection [, buffer [, state [, carve ]]]]]

Arguments

  • name = the name for the new volume object.
  • map = the name of the map object to use for computing the volume.
  • ramp = str: named color ramp {default: }
  • selection = an atom selection about which to display the mesh with an additional "buffer" (if provided).
  • carve = a radius about each atom in the selection for which to include density. If "carve" is not provided, then the whole brick is displayed.

Example

fetch 1oky, type=2fofc, async=0
volume 1okyVol, 1oky_2fofc

Screencasts

  • Silent demo movie showing the basics of loading and using a volume in PyMOL. There are more capabilities, but this is the basic functionality.

Changes with PyMOL Version

  • 1.4.0: first version with volume support
  • 1.7.2:
    • pre-integrated volume rendering (volume_mode=1) as Incentive-PyMOL-only feature.
    • scripting support with custom color ramp (volume_color, volume_ramp_new)
    • improved volume panel, panel can be opened from the object menu ("C > panel")
    • lots of bugs fixed

Known Limitations

  • No real ray-tracing support yet
  • Multiple volume objects don't blend properly

See Also