vmd_cube
A Python script for rendering cube files generated by Psi4
Adaptive isocontour values
If the cube files are generated with Psi4, vmd_cube will automatically use the adaptive isocontour values reported in the comment section:
Psi4 Gaussian Cube File.
Property: Psi_a_1_1-Ag. Isocontour range for 85% of the density: (0.0535039,0)
These isocountour values capture 85% of the probability density using the least amount of grid points.
Alternatively, the isocontour range can be set with the --iso option. For example, --iso 0.03 -0.03.
If vmd_cube is not provided isocountour values, it will use the default ([0.05,-0.05]).
Color schemes
The vmd_cube color scheme is customizable using the --color1/--color2 options.
Alternatively the user can request one of the following color schemes (Emory is the default one).
Specifying arbitrary isosurface values/colors
vmd_cube can plot an arbitrary number of isosrufaces. This can be specified with the options --isovalue and --isocolor.
For example, to draw three surfaces with values [0.03,0.04,0.05] call vmd_cube with the following argument --isovalue 0.03 0.04 0.05 --isocolor 3 23 12.
Note that the number of arguments passed to --isovalue and --isocolor must be the same.
The following is an example of a plot containing three isosurfaces
vmd_cube.py --isovalue -0.03 -0.06 -0.12 --isocolor 3 3 3 --opacity=0.3 --rx=0 --ry=90 --rz=0
vmd_cube options
>>> ./vmd_cube.py --help
usage: vmd_cube.py [-h] [--isovalue [<isovalue> [<isovalue> ...]]]
[--isocolor [<integer> [<integer> ...]]] [--rx [<angle>]]
[--ry [<angle>]] [--rz [<angle>]] [--tx [<length>]]
[--ty [<length>]] [--tz [<length>]] [--opacity [<opacity>]]
[--scale [<factor>]] [--no-montage] [--no-labels]
[--imagew [<integer>]] [--imageh [<integer>]]
[--fontsize [<integer>]] [--interactive] [--gzip]
[--national_scheme] [--silver_scheme] [--bright_scheme]
[--electron_scheme]
[<cubefile dir>]
vmd_cube is a script to render cube files with vmd. To generate cube files
with Psi4 add the command cubeprop() at the end of your input file.
positional arguments:
<cubefile dir> The directory containing the cube files.
optional arguments:
-h, --help show this help message and exit
--isovalue [<isovalue> [<isovalue> ...]]
a list of isosurface values (a list of floats, default
= [0.05,-0.05])
--isocolor [<integer> [<integer> ...]]
a list of isosurface color IDs (a list of integers,
default = [3,23])
--rx [<angle>] the x-axis rotation angle (float, default = 30.0)
--ry [<angle>] the y-axis rotation angle (float, default = 40.0)
--rz [<angle>] the z-axis rotation angle (float, default = 15.0)
--tx [<length>] the x-axis translation (float, default = 0.0)
--ty [<length>] the y-axis translation (float, default = 0.0)
--tz [<length>] the z-axis translation (float, default = 0.0)
--opacity [<opacity>]
opacity of the isosurface (float, default = 1.0)
--scale [<factor>] the scaling factor (float, default = 1.0)
--no-montage call montage to combine images. (string, default =
false)
--no-labels do not add labels to images. (string, default = false)
--imagew [<integer>] the width of images (integer, default = 250)
--imageh [<integer>] the height of images (integer, default = 250)
--fontsize [<integer>]
the font size (integer, default = 20)
--interactive run in interactive mode (default = false)
--gzip gzip cube files (default = false)
--national_scheme use a red/blue color scheme. (string, default = false)
--silver_scheme use a gray/white color scheme. (string, default =
false)
--bright_scheme use a soft yellow/blue color scheme. (string, default
= false)
--electron_scheme use a purple/green color scheme. (string, default =
false)