VMD with coloured isosurface

VMD can colour an (iso)surface based on some other value. In this example the van der Waals surface is coloured by the potential, but many other combinations are possible.

The example data file is available as caffeine_pot.cube.gz, which must be decompressed before VMD can read it.

It can then be loaded with File | New Molecule, and a simple line representation will be shown.

Next choose Graphics | Representations and select a Drawing Method of VDW and a Coloring Method of Volume.

VMD Graphics Reps dialogue Caffeine as VDW

VMD defaults to using a colour scale of red through white to blue. Unfortunately its autoscaling takes account of the extrema of the whole 3D dataset, not just the values which lie on the surface of interest. The whole range is about -200V to +2V, whereas the range on the surface is about -7.5V to -2V. So everything shows as blue.

The colour scale can be changed, and the relevant entries lie on the "Trajectory" tab of the Graphical Representations dialogue box. Knowing that blue is the high end of the scale, one can increase the lower limit until red starts appearing, and then reduce the upper limit until blue re-appears, and one soon finds a reasonable range. (Values outside the range get displayed as the maximum or minimum colour as appropriate.) For the next figure -7.5 and -2 are used, and the "Sphere Resolution" on the initial "Draw style" tab is increased to 24.

Caffeine as VDW, coloured by pot

VMD does contain an extension for adding a scale bar. This is found under Extensions | Visualization | Color Scale Bar. In the image below it has been set to autoscale on and label format decimal. Then the axes have been moved (Display | Axes | UpperLeft). It does not seem possible to move the scale, but one can instead move the molecule with Mouse | Translate Mode. Then one might achieve the below.

Caffeine as VDW, coloured by pot, with scale