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
© 2017 Schrödinger, Inc.