Visualization

Electric Fields

To be added.

Electrostatic Potentials

To be added.

Using write_transformed_pdb for Chimera/ChimeraX Electric Field Schemes

Chimera/ChimeraX unfortunately can only make boxes that are oriented in the softwares global frame, which is where write_transformed_pdb comes in handy. By using write_transformed_pdb: True and strip_filter: False in the options file along with writing a .bild file as follows:

.transparency 0.5
.color blue
.box x1 y1 z1 x2 y2 z2

, replacing x1 y1 z1 and x2 y2 z2 with the negative of the dimensions option and the dimensions option itself, you can get great schemes like this to show your volume calculation:

To be added.

API Examples for other Data Visualizations

It may be of interest, for example, to visualize field topologies, or observe the distribution of point fields across a trajectory. The API provided through pycpet makes this pretty straightforward.

Examples here to be added.