www.pymol.org

How to Use Volumes

PyMOL Volumes is available as an update (PyMOL v1.4 to be released in the coming months)  for current subscribers. If you do not already have a subscription, purchase incentive PyMOL to access this feature.

Load Files and Render Volumes

Volume data is easily loaded into the workspace alongside structural data, allowing for immediate comparison of volumetric and structural data. To bring your structural and volumetric (e.g., density) data into the workspace, select File > Open, and select your files. Then, for the newly loaded volumetric data, select select A >  Volume > Default. Your data will then be shown as a volume. To control the colors and opacity, just click on the new Volume button in the Upper Control Window.

 Customize Colors and Transparency

Volume data is represented by color and transparency that is graded according to the value of the volume. By default, volumes with higher scalar values (e.g., high electron density) will appear more opaque red and volumes with lower scalar values (e.g. low  more transparent with lower electron density will appear in a less opaque blue. However, coloring and transparency are fully customizable using a new built-in interface. To control the color ramp for your data, select the Volume button from the Upper Control Panel.

To set transparency levels for any number of isosurfaces, CTRL-click on the desired iso-level (eg. +1 sigma) in the upper control panel and an isomesh will be created.  To remove a color point, just middle click on it.  To update density or opacity values for a color, just drag the color point with your mouse.  PyMOL updates the colors on the fly.

Performance

Rendering settings can be modulated to improve performance or quality. If your video card is somewhat older, try turning down the quality of the volume representation to improve performance.There are two main settings that can be controlled to modulate the quality-speed tradeoff - volume_layers (default = 256) and volume_bit_depth (default = 16). Change the volume_layers variable by typing set volume_layers, X, where X is some number like 256 or 512--or even 4096 if your machine is fast enough. Try setting X to 32 if your machine isn't that powerful. Change the volume_bit_depth variable to 4, 8, 16, or 32 by typing set volume_bit_depth, X, where X is 4, 8, 16 or 32, at the command line. The default values for these variables should enable reasonable quality and performance on a fairly new computer.
 

Hardware Requirements

Volume visualization in PyMOL requires a computer video card with some fortitude. For 120Hz stereoscopic viewing, we suggest the NVidia Quadro 580 and higher (Quadro 4000, Quadro 6000, etc) cards with the NVidia NVision 3D setup. GeForce cards only support Zalman-based 3D stereoscopic viewing.  For large data sets (e.g., electron microscopy data), we suggest a video card with more memory, at least 512 MB.