Pymol

Generate Surface From Cube

Pre-Disclaimer

Most of my work with PyMol is actually stored in my PyMOL scripts on github, so this is ultimately unmaintained

Use cubegen or Psi4 to make a cubefile

isomesh <name of surface>, <name of cube>, <density level>

isomesh keppra-opt-gas-homo2, keppra-opt-gas-homo, -0.02

To get nice surfaces and colour them, iterate this script for each of the cubes you input:

isosurface pyrrole-BF4-32-surf, pyrrole-BF4-32, -0.02
color tv_green, pyrrole-BF4-32-surf
set surface_negative_color, tv_red
set surface_negative_visible

Generate ESP From Psi4 Cubes

After loading in Dt.cube, ESP.cube and your geom.xyz

preset.simple(selection='all')
color grey40
color atomic, (not elem C)
isosurface Dt2, Dt, 0.001
ramp_new espcol, ESP, [-.05,-.025,0,.025,.05], [red,orange, yellow,green, blue]
set surface_color, espcol, Dt2
set transparency, 0.3

Set to Simple and Colour by Element

preset.simple(selection='all')
color grey40
color atomic, (not elem C)

Set to Ball and Stick and Colour by Element

preset.ball_and_stick(selection='all', mode=1)
color grey40
color atomic, (not elem C)

A Full Copy/Paste Script

A full copy and paste block open everything, generate the ESP and ramps, render the image and delete everyhting might look like this:

cd /data/Computation/Scratch/psi4-esp/benzene
load Dt.cube
load ESP.cube
load geom.xyz
preset.simple(selection='all')
color grey40
color atomic, (not elem C)
isosurface Dt2, Dt, 0.001
ramp_new espcol, ESP, [-.04,-.02,0,.02,.04], [red,orange, yellow,green, blue]
set surface_color, espcol, Dt2
set transparency, 0.3
disable espcol
png benzene.png, width=1000px, dpi=300, ray=1
delete Dt
delete Dt2
delete ESP
delete geom
delete espcol