This is a read-only mirror of pymolwiki.org

Volume

From PyMOL Wiki
Jump to navigation Jump to search
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