Category:Uncategorized: Difference between revisions

Alter key bindings

It's not GUI, but you could simply bind a function key such as F1 to a command:

cmd.set_key('F1',lambda :cmd.show('sticks'))

Coloring Surface with Electrostatic Potential

You have to load the potential data by Delphi or some other program like AMBER version 9:

load sample.pdb, molecule
load sample.delphi, potential
show surface, molecule
ramp_new level, potential, [-7,0,7]
set surface_color, level, molecule

Van der Waals radii

van der Waals Radii are hard coded in Pymol. They may be obtained for given atoms from:

iterate (name C), print vdw

Default values are:

• C : 1.70
• O : 1.52
• N : 1.55
• H : 1.20
• P : 1.80

and may be changed with the command alter

Tutorial for Beginners

I'm in the process of writing a PyMol tutorial for first time users. Intended for undergraduate biology/biochemistry students with no previous visualization experience, it will focus on common operations and practical uses. For now, I'm calling it Practical Pymol for Beginners. I'm not sure where to categorize it.