PyMOL: Representations, Coloring, and Publication Figures

PyMOL builds a molecular figure by stacking independent representations onto an atom selection, then coloring and rendering them. Because every step is a command, an entire publication figure can be captured as a short script that regenerates the identical image on any machine. This lesson covers the representation, coloring, camera, and ray-tracing commands you need for reproducible, high-resolution figures.

Representations With show/hide

fetch 4hhb, async=0
hide everything
show cartoon, polymer
show sticks, hetatm and not resn HOH
show spheres, elem Fe
set sphere_scale, 0.4, elem Fe

Representations are additive: show adds a rep to a selection without touching the others, and hide removes only the named rep. Selections use PyMOL's algebra, so hetatm and not resn HOH drops crystallographic waters and keeps the bound heteroatoms — the four heme groups (plus any crystallization ions) — while elem Fe picks just the heme irons. Surfaces are the most expensive rep to compute and ray-trace, so restrict them to the chain you care about with show surface, chain A and drop surface_quality to -1 (its default is 0) while iterating.

Coloring Strategies

bg_color white
# color the protein by chain, ligands by element (CPK)
util.cbc()
util.cnc("hetatm and not resn HOH")
# alternative scheme: color the backbone by crystallographic B-factor
spectrum b, blue_white_red, polymer and name CA

 Spectrum: range = 15.30 to 84.72

Views, Scenes, and Export

orient polymer
set ray_opaque_background, 0
set ray_shadows, 0
set antialias, 2
# print the current camera; paste the set_view(...) block back to restore it
get_view
# store the styled camera and reps as a named scene (recall with: scene F1)
scene F1, store
# ray-trace at explicit pixel dimensions, then write a PNG tagged 300 DPI
ray 2400, 1800
png /data/figures/4hhb_bfactor.png, dpi=300

### cut below here and paste into script ###
set_view (\
     0.638072908,   -0.176906988,    0.749390602,\
    -0.187744021,    0.905735910,    0.379648834,\
    -0.746740460,   -0.384833544,    0.543828726,\
     0.000000000,    0.000000000, -287.514801025,\
    16.428998947,   17.789674759,   10.379617691,\
   226.719360352,  348.310241699,  -20.000000000 )
### cut above here and paste into script ###
 Ray: render time: 4.21 sec. = 855.1 frames/hour (4.21 sec. accum.).
 ScenePNG: wrote 2400x1800 pixel image to file "/data/figures/4hhb_bfactor.png".