PyMOL Commands Cheat Sheet: The Essential Reference for Structural Biologists
Every PyMOL command you’ll reach for regularly — organized by task, not alphabetically. Bookmark this page and keep it open alongside PyMOL while you work.
How to use this reference
All commands are entered in the PyMOL command line at the bottom of the External GUI window. Arguments in [ ] are optional. selection can be any named selection, object name, or selection expression like chain A or resi 100-150.
Loading & fetching
| Command | What it does |
|---|---|
| fetch 4XYZ | Download structure from RCSB PDB and load it |
| fetch 4XYZ, name | Fetch and assign a custom object name |
| load protein.pdb | Load a local PDB file |
| load traj.xtc, protein | Load an MD trajectory into an existing object |
| load_traj traj.dcd, protein | Alternative trajectory loading (DCD format) |
| delete all | Remove all loaded objects |
| delete object_name | Remove a specific object |
| reinitialize | Reset PyMOL to a completely clean state |
Navigation & view
| Command | What it does |
|---|---|
| zoom [selection] | Fit the view to the selection (or everything) |
| orient [selection] | Orient along principal axes of the selection |
| center [selection] | Center the view on a selection without zooming |
| reset | Reset camera to default position |
| get_view | Print the current view matrix — copy to reproduce later |
| set_view (matrix) | Restore a previously saved view matrix |
| turn x, 90 | Rotate 90° around the x-axis (also y, z) |
| rotate x, 45, object | Rotate a specific object by 45° around x |
| clip near, -5 | Adjust near clipping plane |
| clip far, 5 | Adjust far clipping plane |
Selections
The backbone of everything in PyMOL. Every command operates on a selection.
| Command / syntax | What it does |
|---|---|
| Creating selections | |
| select name, expression | Create a named selection from an expression |
| select site, chain A and resi 100-150 | Select residues 100–150 of chain A |
| select pocket, byres (LIG around 5) | Select all residues within 5 Å of LIG |
| select iface, chain A and (byres chain B around 4) | Interface residues of chain A near chain B |
| Selection keywords | |
| chain A | All atoms in chain A |
| resi 100-150 | Residue numbers 100 through 150 |
| resi 100+150+273 | Specific residue numbers (use + to list) |
| resn LYS | All lysine residues (3-letter code) |
| name CA | Alpha carbon atoms only |
| elem C | All carbon atoms |
| hetatm | Heteroatoms (ligands, waters, ions) |
| resn HOH | Water molecules only |
| b > 70 | Atoms with B-factor above 70 (pLDDT for AF) |
| Boolean operators | |
| chain A and resi 100 | Residue 100 in chain A specifically |
| chain A or chain B | Both chains A and B |
| not resn HOH | Everything except water |
| sel1 within 5 of sel2 | Atoms in sel1 within 5 Å of sel2 |
| byres (sel around 5) | Complete residues with any atom within 5 Å |
Display modes
| Command | What it does |
|---|---|
| show — add a representation | |
| show cartoon [, sel] | Ribbon cartoon for protein backbone |
| show sticks [, sel] | All bonds as sticks — for residues and ligands |
| show lines [, sel] | Thin line bonds — lightweight background display |
| show spheres [, sel] | Space-filling (van der Waals) representation |
| show surface [, sel] | Molecular surface |
| show dots [, sel] | Dot surface (accessible surface area) |
| show mesh [, sel] | Wireframe mesh surface |
| show nb_spheres [, sel] | Non-bonded atoms as small spheres (ions) |
| hide — remove a representation | |
| hide everything [, sel] | Remove all representations |
| hide cartoon [, sel] | Remove cartoon only |
| hide everything, resn HOH | Remove water molecules from view |
| as — show only this representation | |
| as cartoon | Cartoon only — hides everything else |
| as sticks, selection | Sticks only for the selection |
| as spheres, resn LIG | Space-filling for ligand only |
Coloring
| Command | What it does |
|---|---|
| color red [, sel] | Single color — named colors: red, blue, green, white, slate, marine, wheat… |
| util.cbc [sel] | Color by chain — each chain gets a distinct color |
| util.cbs [sel] | Color by secondary structure (helix/sheet/loop) |
| util.cbaw [sel] | Color by atom type — classic CPK scheme, white carbons |
| util.cbag [sel] | Color by atom type — green carbons (ligand standard) |
| spectrum b, blue_red | Spectrum by B-factor (pLDDT in AlphaFold structures) |
| spectrum b, blue_cyan_yellow_orange_red, min=50, max=100 | AlphaFold pLDDT color scale (blue=confident, red=disordered) |
| spectrum count, rainbow | N→C terminus rainbow coloring |
| spectrum resi, blue_red | Gradient from first to last residue |
| set_color myblue, [0.1, 0.4, 0.8] | Define a custom color with RGB values (0–1 scale) |
| color myblue, chain A | Apply custom color to a selection |
Surfaces
| Command | What it does |
|---|---|
| show surface | Display molecular surface for all objects |
| set transparency, 0.5 | Make surface 50% transparent (0=opaque, 1=invisible) |
| set surface_quality, 1 | Higher quality surface (default 0; use 2 for publication) |
| set surface_color, white | Force surface to a single color regardless of atom colors |
| set solvent_radius, 1.4 | Probe radius for surface (default 1.4 Å) |
| show surface, pocket | Surface for a named selection only |
| hide surface, resn HOH | Remove surface for water molecules |
Analysis & measurements
| Command | What it does |
|---|---|
| distance d1, atom1, atom2 | Draw and display distance between two atoms |
| distance hbonds, sel1, sel2, mode=2 | Show H-bonds between two selections |
| distance contacts, sel1, sel2, 4 | All contacts within 4 Å between selections |
| angle a1, atom1, atom2, atom3 | Measure bond angle |
| dihedral d1, a1, a2, a3, a4 | Measure dihedral angle between four atoms |
| hide labels | Hide all distance/angle labels (keep the lines) |
| get_area selection | Calculate solvent-accessible surface area |
| iterate selection, print(resi, resn, b) | Print per-residue data (B-factor, residue info) |
| centerofmass selection | Calculate and print center of mass coordinates |
Alignment & RMSD
| Command | What it does |
|---|---|
| align mobile, reference | Sequence-aware alignment — best when sequences are similar |
| super mobile, reference | Structure-based alignment — ignores sequence, good for distant homologs |
| cealign mobile, reference | CE algorithm — best for different fold topologies |
| align mobile and chain A, reference and chain A | Align on specific chains only |
| rms_cur mobile and backbone, reference and backbone | Calculate backbone RMSD without moving structures |
| pair_fit atom1, atom2, atom3, atom4 | Align based on specific atom pairs |
Labels & annotations
| Command | What it does |
|---|---|
| label selection, “text” | Add a static text label to a selection |
| label selection, resn+resi | Label each residue with its name and number |
| label name CA, “%s%s” % (resn, resi) | Label alpha carbons with residue identity |
| set label_size, 14 | Change label font size |
| set label_color, black | Change label color |
| hide labels [, sel] | Hide all labels for a selection |
| set label_position, [0, 0, 2] | Offset label position (x, y, z in Å) |
Saving & export
| Command | What it does |
|---|---|
| Saving images | |
| ray [width, height] | Ray trace the current view (high quality render) |
| ray 1200, 900 | Ray trace at 1200×900 pixels |
| png filename.png, dpi=300 | Export the ray-traced image at 300 DPI |
| png filename.png, width=1200, height=900, dpi=300, ray=1 | Ray trace and export in one command |
| set ray_opaque_background, 1 | White background (set before ray) |
| bg_color white | Set background color to white |
| Saving sessions and structures | |
| save session.pse | Save full PyMOL session (all objects, views, settings) |
| load session.pse | Restore a saved session |
| save output.pdb [, selection] | Export coordinates as PDB (optionally, just a selection) |
| save output.cif [, selection] | Export as mmCIF format |
| log_open commands.pml | Start recording all commands to a script file |
| log_close | Stop recording commands |
| @script.pml | Run a saved .pml script file |
Useful settings
| Setting command | Effect |
|---|---|
| set cartoon_fancy_helices, 1 | Rounded ribbon helices — standard for publications |
| set cartoon_smooth_loops, 1 | Smooth loop interpolation |
| set cartoon_tube_radius, 0.4 | Thinner loop tubes (default 0.5) |
| set stick_radius, 0.15 | Thinner sticks (default 0.25) — useful for ligands |
| set sphere_scale, 0.25 | Smaller spheres (useful for ball-and-stick) |
| set ambient, 0.4 | Ambient light level — higher = softer shadows |
| set specular, 0.3 | Shininess — lower = more matte |
| set light_count, 4 | Number of lights — more = smoother shading |
| set depth_cue, 0 | Disable distance fog / depth cueing |
| set ray_shadow, 1 | Enable shadows during ray trace |
| set antialias, 2 | Anti-aliasing level for ray trace (1–4) |
Quick workflows
New structure — starting sequence
fetch 4XYZ
as cartoon
hide everything, resn HOH
util.cbc
zoomAlphaFold pLDDT coloring
load AF-P04637-F1-model_v4.pdb
as cartoon
spectrum b, blue_cyan_yellow_orange_red, minimum=50, maximum=100
bg_color whiteBinding site figure
fetch 4XYZ
as cartoon
hide everything, resn HOH
color slate, protein
util.cbag LIG # green carbons for ligand
select site, byres (LIG around 5)
show sticks, site
show surface, site
set transparency, 0.4
zoom sitePublication figure export
bg_color white
set ray_opaque_background, 1
set cartoon_fancy_helices, 1
set ambient, 0.4
set specular, 0.3
ray 1200, 900
png figure1a.png, dpi=300Align two structures and calculate RMSD
fetch 4XYZ
fetch 5ABC
align 5ABC, 4XYZ # aligns and reports RMSD
zoomSave every session before closing
PyMOL doesn’t auto-save. Before closing, run save session.pse — the PSE file captures everything: loaded structures, selections, colors, measurements, and the current view. Loading the PSE later restores the exact state. Get in the habit of saving PSE files the way you save documents.
The 10 commands you’ll use every day
fetch · as cartoon · hide everything, resn HOH · util.cbc · select · color · show sticks · zoom · get_view · ray + png. Learn these ten cold and every other PyMOL task becomes a variation on a pattern you already know.
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