Advanced Scripting Workshop

Part 1: Interactive Command Line

To get familiar with the PyMOL command line, enter the following commands one by one.

Make use of auto-completion (Tab key) for command-, color- and representation names!

# download PDB file (most important command! :-))
fetch 1a00

# show only cartoon representation
as cartoon

We have loaded hemoglobin, which is a hetero-tetramer of two alpha and two beta chains. Let's color alpha different from beta.

# hemoglobin alpha
color orange, chain A+C

# hemoglobin beta
color marine, chain B+D

Right now we only see polymer chains, because other molecules don't have a cartoon representation (we did "as cartoon"). Let's show "sticks" (bonds) for non-polymer atoms.

show sticks, not polymer

# automatically set the camera on the heme cofactor of the first chain
orient resn HEM and chain A

Small molecules are better visualized with color-by-element and bond orders.

# color non-carbon atoms by element
color atomic, not elem C

# show bond orders
set valence