chemtools.utils.output.print_vmd_script_isosurface

chemtools.utils.output.print_vmd_script_isosurface(scriptfile, isofile, colorfile=None, isosurf=0.5, material='Opaque', scalemin=-0.05, scalemax=0.05, colorscheme=None, negative=False)[source]

Generate VMD (Visual Molecular Dynamics) script for visualizing the isosurface.

Visualize isosurface based on one cube file when coloring by the value of another cube file on the isosurface.

Parameters:
  • scriptfile (str) – Name of VMD script file to generate.
  • isofile (str) – Name of cube file used in VMD script for visualizing the isosurface.
  • colorfile (str, default=None) – Name of cube file used in VMD script for coloring the isosurface. If None, the isofile is used for coloring.
  • isosurf (float, default=0.5) – The value of the isosurface to visualize used in VMD script.
  • material (str, default='Opaque') –

    The material setting of the isosurface used in VMD script.

    Options: ‘Opaque’, ‘Transparent’, ‘BrushedMetal’, ‘Diffuse’, ‘Ghost’, ‘Glass1’, ‘Glass2’, ‘Glass3’, ‘Glossy’, ‘HardPlastic’, ‘MetallicPastel’, ‘Steel’, ‘Translucent’, ‘Edgy’, ‘EdgyShiny’, ‘EdgyGlass’, ‘Goodsell’, ‘AOShiny’, ‘AOChalky’, ‘AOEdgy’, ‘BlownGlass’, ‘GlassBubble’, ‘RTChrome’.
  • scalemin (float, default=-0.05) – Smallest value to color on the isosurface used in VMD script.
  • scalemax (float, default=0.05) – Largest value to color on the isosurface used in VMD script.
  • colorscheme (str or int, default='RGB') –

    Color scheme used in VMD script for coloring the isosurface.

    For color-scale, a sting is needed specifying the color scheme. The default is ‘RGB’, ans more options are available in table below. Alternatively, the isosurface can be colored with just one color. For this option, an integer is needed specifying the color. 1057 colors are available in VMD, check the program or website for more details. If you want to plot the negative isosurface as well, a list of two colors can be given to specify the color of positive and negative iso-surfaces. e.g. [0, 1]
    Options Description
    ‘RGB’ small=red, middle=green, large=blue
    ‘BGR’ small=blue, middle=green, large=red
    ‘RWB’ small=red, middle=white, large=blue
    ‘BWR’ small=blue, middle=white, large=red
    ‘RWG’ small=red, middle=white, large=green
    ‘GWR’ small=green, middle=white, large=red
    ‘GWB’ small=green, middle=white, large=blue
    ‘BWG’ small=blue, middle=white, large=green
    ‘BlkW’ small=black, large=white
    ‘WBlk’ small=white, large=black
  • negative (bool, default=False) – Determines if you want to plot the negative of the isosurface as well. The default is false.