BV_VolumeVisualization

Volume Visualization

Step by Step

Please note, that this example relates to the non-raytracing variant of BALLView.

A great example to experience BALLView's volume visualization functionality is the Acetylcholinesterase in complex with its inhibition fasciculin, the toxin of Mambas.

The data is given in the pdb file 1MAH, which you can easily downloaded into BALLView.

To be able to visualize the volume of the protein, the ligand in chain F must be deleted.

Then, highlight the system and calculate a 3D grid via Tools -> FDPB Electrostatics -> add Hydrogens, use default parameters and click the ok button.

After some calculation time the 3D grid appears in a new window. Right click on the grid and choose the option create normalized grid.

Then highlight the normalized grid and choose via right click Resize for rendering.

The highlighted resized grid is rendered via right click and

Render grid -> interpolation range, click the auto button and choose volume : 40 for numerous planes and press the ok button.

A suitable background color for this representation is white.

Change the background color via Edit -> Preferences -> Display -> Main -> Edit of Background Color.

Data format

Currently we support only regular spaced data inside BALL and BALLView.

The binary format we currently use is as follows:

(in the following, I separate the fields by "|". In the binary file, they are just next to each other. Also, a field name beginning with f indicates a float value, s indicates BALL's size type, i indicates BALL's Index type)

s_size_in_bytes|f_origin_x|f_origin_y|f_origin_z|f_dimension_x|f_dimension_y|f_dimension_z|f_spacing_x|f_spacing_y|f_spacing_z|f_num_points_x|f_num_points_y|f_num_points_z|f_value_1|....|f_value_n

The code to peek for reading and writing those files can be found in include/BALL/DATATYPE/regularData3D.h binaryRead() and binaryWrite().

To interact, e.g. move the grid representation, switch to the move mode via Display -> Move Mode in the main menu.