Volume

Volume visualization of electron density for PDB 1oky

Volume panel for the 1oky volume example. It has the iso-levels on the x-axis and the opacity (1.0 - transparency) on the y-axis.

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

Ray Tracing

There is no actual ray tracing support. The volume rendering is implemented exclusively with OpenGL shaders. The recommended way to render a high resolution image is to use the draw command. Example:

# render high resolution image on screen
draw 4000, 3000, antialias=2
png highres.png

Ray trace specific features like shadows or outlines (ray_trace_mode) are not available with this approach. If such features are needed, the ray_volume setting activates a hybrid solution, which blends the OpenGL rendered volume with the ray traced non-volume objects. Image sizes other than the current window size are not possible.

# compose on-screen volume with ray traced image
set ray_volume
ray
png composed.png

Neither of these two solutions work with headless (batch) mode.

Known Limitations

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

See Also

• http://pymol.org/volume
• http://pymol.org/d/media:volumevisualization
• volume_color
• volume_ramp_new
• map_new
• isomesh
• isosurface