Ball and Stick
Ball and Stick
The ball and stick representation is very often used to display macromolecules. PyMOL allows the user the ability to turn on this representation for certain selections, or roll their own hand-made versions of the command (see below).
Using the mouse, for the desired object or selection click A > Preset > ball and stick.
# turn on the representation for everything in PyMOL preset.ball_and_stick(selection='all', mode=1)
or... (keeping in mind that the single-word selectors page includes more possible selections to substitute
r. STI with)
# turn on representation for one ligand (in this example STI or imatinib) in PyMOL preset.ball_and_stick(selection='r. STI', mode=1)
Parameter mode can be 1 or 2. With mode=1 you'll have...
set_bond stick_color, white, selection, selection set_bond stick_radius, 0.14, selection, selection set sphere_scale, 0.25, selection show sticks, selection show spheres, selection
If mode=2 than you'll get...
set_bond stick_color, white, selection, selection set_bond stick_radius, -0.14, selection, selection set stick_ball, 1 set stick_ball_ratio, -1.0 set stick_ball_color, atomic show sticks, selection
hide lines show sticks show spheres set stick_radius, 0.1, (all) set sphere_scale, 0.25, (all)
show sticks set valence, on set stick_ball, on set stick_ball_ratio, 3 set stick_radius, 0.12
You can adjust the two numbers above to your taste.
Ed. As of 0.98bXX there is a GUI-enable Ball & Stick representation available to users. Tree