miscellaneous

name	miscellaneous
description	Collection of useful PyMOL patterns and commands that don't fit into specific workflow skills. Use as reference for edge cases and less common operations.
version	0.1.0

Miscellaneous PyMOL Patterns

Useful commands and patterns that don't fit neatly into other skills.

Send all cmd.* code via: ~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "..." (or heredoc for multi-line). See @pymol-fundamentals for details.

Object and State Information

List Objects

cmd.get_names()                    # All objects
cmd.get_names("objects")           # Only objects
cmd.get_names("selections")        # Only selections

Count Atoms

cmd.count_atoms("all")
cmd.count_atoms("polymer.protein")
cmd.count_atoms("organic")

Count States (for NMR/MD)

n = cmd.count_states("object_name")

Get Object Properties

# Get all residue names
resnames = []
cmd.iterate("all", "resnames.append(resn)", space={"resnames": resnames})
unique_resnames = list(set(resnames))

Session Management

Save Session

cmd.save("session.pse")

Load Session

cmd.load("session.pse")

Clear Everything

cmd.delete("all")
cmd.reset()

Object Manipulation

Copy Object

cmd.copy("new_name", "source_object")

Translate Object

cmd.translate([10, 0, 0], "object_name")  # Move 10 A along X

Rotate Object

cmd.rotate("y", 45, "object_name")  # Rotate 45 degrees around Y

Get Object List

objects = cmd.get_object_list()
print("Objects: " + str(objects))

Enable/Disable Objects

cmd.disable("object_name")  # Hide without changing representations
cmd.enable("object_name")   # Show again
cmd.toggle("object_name")   # Toggle visibility

Group Objects

cmd.group("group_name", "obj1 obj2 obj3")
cmd.disable("group_name")  # Disable entire group
cmd.enable("group_name")   # Enable entire group
cmd.ungroup("group_name")  # Remove group (keeps objects)

Show As (Hide Others)

cmd.show_as("sticks", "selection")  # Show sticks, hide other reps

Working with Chains

Get Chain IDs

chains = []
cmd.iterate("all", "chains.append(chain)", space={"chains": chains})
unique_chains = list(set(chains))

Split by Chain

cmd.split_chains("object_name")

Rename Chain

cmd.alter("chain A", "chain='X'")

Modifying Structures

Remove Water

cmd.remove("solvent")

Remove Hydrogens

cmd.remove("hydro")

Add Hydrogens

cmd.h_add("all")

Keep Only Protein

cmd.remove("not polymer.protein")

Selection Tricks

Expand Selection

# Atoms within distance
cmd.select("expanded", "all within 5 of ligand")

# Complete residues
cmd.select("expanded", "byres (all within 5 of ligand)")

# Complete chains
cmd.select("expanded", "bychain (all within 5 of ligand)")

Invert Selection

cmd.select("inverse", "not current_selection")

Backbone and Sidechain

cmd.select("backbone", "name N+CA+C+O")
cmd.select("sidechain", "not (name N+CA+C+O+H)")

Non-Water Heteroatoms

cmd.select("hetero", "hetatm and not solvent")

Get Residue Range

residues = []
cmd.iterate("protein and name CA", "residues.append(int(resi))",
            space={"residues": residues})
print("Range: " + str(min(residues)) + "-" + str(max(residues)))

Select by Sequence Motif

# pepseq uses single-letter amino acid codes
cmd.select("motif", "pepseq KTL")  # Find KTL tripeptide
cmd.select("leucines", "pepseq L")  # Find all leucines

Select Bonded Neighbors

cmd.select("neighbors", "neighbor resi 30 and name CA")
cmd.select("bonded", "bound_to resi 30 and name CA")

Around vs Within

# "within" includes the reference
cmd.select("s1", "all within 5 of ligand")  # Includes ligand atoms

# "around" excludes the reference
cmd.select("s2", "all around 5 of ligand")  # Excludes ligand atoms

Special Representations

Ball and Stick

cmd.show("sticks", "selection")
cmd.set("stick_ball", 1)
cmd.set("stick_ball_ratio", 1.5)

Putty (B-factor Tube)

cmd.show("cartoon", "selection")
cmd.cartoon("putty", "selection")

Dots for Surface Points

cmd.show("dots", "selection")
cmd.set("dot_density", 3)

Label Formatting

Custom Labels

cmd.label("name CA", "resn")           # Just residue name
cmd.label("name CA", "resi")           # Just residue number
cmd.label("name CA", "resn+resi")      # Combined: ALA45
cmd.label("name CA", "'%s%s'%(resn,resi)")  # Same result

Label Styling

cmd.set("label_size", 14)
cmd.set("label_font_id", 7)            # Bold font
cmd.set("label_color", "black", "all")
cmd.set("label_position", (0, 0, 2))   # Offset from atom

Clear Labels

cmd.label("all", "")

Symmetry Operations

Show Unit Cell

cmd.show("cell")

Generate Symmetry Mates

cmd.symexp("sym", "object", "object", 10)  # Within 10 Angstroms

File Formats

Export Formats

cmd.save("output.pdb", "selection")     # PDB
cmd.save("output.cif", "selection")     # mmCIF
cmd.save("output.mol2", "selection")    # MOL2
cmd.save("output.sdf", "selection")     # SDF

Image Formats

cmd.ray(width, height)
cmd.png("image.png")
cmd.save("image.pse")  # PyMOL session

Performance Tips

Disable Updates During Batch Operations

cmd.set("defer_updates", 1)
# ... batch operations ...
cmd.set("defer_updates", 0)
cmd.rebuild()

Reduce Quality for Large Systems

cmd.set("cartoon_sampling", 5)      # Lower = faster
cmd.set("surface_quality", 0)       # Lower = faster
cmd.set("hash_max", 200)            # For large structures

Debugging

Print Command Output

# Capture output
output = cmd.get("ray_trace_mode")
print("Current setting: " + str(output))

Check Selection Syntax

count = cmd.count_atoms("your_selection_here")
print("Matched atoms: " + str(count))

Metal and Cofactor Visualization

Select Metals

cmd.select("metals", "elem Cu+Fe+Zn+Mg+Mn+Ca")
cmd.show("spheres", "metals")
cmd.color("orange", "metals")

Select Heme Groups

cmd.select("heme", "resn HEM+HEC+HEA")
cmd.show("sticks", "heme")

Coordination Sphere

cmd.select("coord_sphere", "byres (polymer.protein within 3 of metals)")
cmd.show("sticks", "coord_sphere")
cmd.color("yellow", "coord_sphere and elem C")

Residue Property Selection

By Charge

cmd.select("basic", "resn ARG+LYS+HIS")
cmd.select("acidic", "resn ASP+GLU")
cmd.select("charged", "resn ARG+LYS+HIS+ASP+GLU")

By Hydrophobicity

cmd.select("hydrophobic", "resn ALA+VAL+ILE+LEU+MET+PHE+TRP+PRO")
cmd.select("polar", "resn SER+THR+CYS+TYR+ASN+GLN")

Color by Property

cmd.color("blue", "resn ARG+LYS+HIS")      # Basic (positive)
cmd.color("red", "resn ASP+GLU")            # Acidic (negative)
cmd.color("yellow", "hydrophobic")          # Hydrophobic
cmd.color("cyan", "polar")                   # Polar uncharged

---

NMR Ensemble Handling

Check Number of States

states = cmd.count_states("object_name")
print("States: " + str(states))

Show All States Overlaid

cmd.set("all_states", 1)  # Overlay all states
cmd.set("all_states", 0)  # Show one state at a time

Create Movie Through States

n_states = cmd.count_states("object_name")
cmd.mset("1 -" + str(n_states))  # Each frame = one state
cmd.mplay()  # Start playback

Style for Ensemble Visualization

cmd.set("all_states", 1)
cmd.show("lines", "all")
cmd.set("line_width", 1)
cmd.color("gray70", "all")
# Highlight specific state
cmd.set("state", 1)
cmd.color("red", "all")

Programmatic Measurements

Get Distance (Returns Value)

d = cmd.get_distance("sel1", "sel2")
print("Distance: " + str(round(d, 2)) + " A")

Get Angle

a = cmd.get_angle("atom1", "atom2", "atom3")
print("Angle: " + str(round(a, 1)) + " degrees")

Get Dihedral

# Backbone psi angle example
d = cmd.get_dihedral(
    "resi 10 and name N",
    "resi 10 and name CA",
    "resi 10 and name C",
    "resi 11 and name N"
)
print("Psi: " + str(round(d, 1)) + " degrees")

Pair Fit (Align Specific Atoms)

# Align first 30 CA atoms and return RMSD
rmsd = cmd.pair_fit(
    "mobile and resi 1-30 and name CA",
    "target and resi 1-30 and name CA"
)
print("Pair fit RMSD: " + str(round(rmsd, 2)) + " A")

Finding Contacts

Select Contacting Residues

# Select residues from A that contact B
cmd.select("contact_A", "byres (chain A within 4 of chain B)")
cmd.select("contact_B", "byres (chain B within 4 of chain A)")

Iterate to Get Contact List

contacts = []
cmd.iterate(
    "chain A within 4 of chain B",
    "contacts.append((resi, resn))",
    space={"contacts": contacts}
)
unique = list(set(contacts))
print("Contact residues: " + str(len(unique)))

Visualize Contacts

cmd.select("interface", "byres (chain A within 4 of chain B) or byres (chain B within 4 of chain A)")
cmd.show("sticks", "interface")
cmd.color("orange", "interface and chain A")
cmd.color("purple", "interface and chain B")

---

Known Limitations

• cmd.morph() may not work reliably through socket connection
• Electrostatic surfaces require APBS or similar external tools
• Some wizard operations may need interactive PyMOL

---

Solvent Accessible Surface Area

Calculate Total SASA

total_area = cmd.get_area("selection")
print("SASA: " + str(round(total_area, 1)) + " sq A")

Color by SASA

# Load SASA into B-factor column
cmd.get_area("selection", load_b=1)
# Color by SASA value
cmd.spectrum("b", "blue_white_red", "selection")

Find Buried Residues

cmd.get_area("protein", load_b=1)
buried = []
cmd.iterate(
    "protein and name CA",
    "buried.append((resi, resn)) if b < 10 else None",
    space={"buried": buried}
)
print("Buried residues: " + str(len(buried)))

Select by Exposure

cmd.get_area("protein", load_b=1)
cmd.select("exposed", "protein and name CA and b > 50")
cmd.select("buried", "protein and name CA and b < 10")

---

Salt Bridges

Select Salt Bridge Atoms

# Basic nitrogen atoms
cmd.select("basic_atoms",
    "(resn ARG and name NH1+NH2+NE) or "
    "(resn LYS and name NZ) or "
    "(resn HIS and name ND1+NE2)")

# Acidic oxygen atoms
cmd.select("acidic_atoms",
    "(resn ASP and name OD1+OD2) or "
    "(resn GLU and name OE1+OE2)")

Find and Display Salt Bridges

cmd.distance("salt_bridges", "basic_atoms", "acidic_atoms",
             cutoff=4.0, mode=0)
cmd.set("dash_color", "yellow", "salt_bridges")

Aromatic Interactions

Select Aromatic Residues

cmd.select("aromatic", "resn PHE+TYR+TRP")
cmd.select("aromatic_HIS", "resn HIS")  # Sometimes aromatic

Visualize Aromatic Rings

cmd.show("sticks", "resn PHE+TYR+TRP")
cmd.color("purple", "resn PHE+TYR+TRP and elem C")

---

Data Extraction

Get FASTA Sequence

seq = cmd.get_fastastr("object_name")
print(seq)  # Full FASTA with header

Get Residue List

residues = []
cmd.iterate(
    "object and name CA",
    "residues.append((resi, resn))",
    space={"residues": residues}
)
print("Residues: " + str(len(residues)))

Get Coordinates

# Returns numpy array of shape (N, 3)
coords = cmd.get_coords("selection")
print("First atom: " + str(coords[0]))

Center of Mass

com = cmd.centerofmass("selection")
print("Center: " + str([round(c, 2) for c in com]))

Get Model Object (Full Atom Data)

model = cmd.get_model("selection")
for atom in model.atom:
    print(f"{atom.resn} {atom.resi} {atom.name}")

Iterate with Atom Properties

Available properties: name, resn, resi, chain, b (B-factor), q (occupancy), ss (secondary structure), elem, x, y, z

# Get secondary structure assignments
helices = []
cmd.iterate("name CA", "helices.append(resi) if ss=='H' else None",
            space={"helices": helices})

# Get B-factors
bfactors = []
cmd.iterate("name CA", "bfactors.append(b)", space={"bfactors": bfactors})
avg_b = sum(bfactors) / len(bfactors)

# Find low occupancy atoms
low_occ = []
cmd.iterate("all", "low_occ.append((resi, name)) if q < 1.0 else None",
            space={"low_occ": low_occ})

---

Pseudoatoms and Markers

Create Marker at Center of Mass

com = cmd.centerofmass("selection")
cmd.pseudoatom("marker", pos=com)
cmd.show("spheres", "marker")
cmd.color("red", "marker")
cmd.set("sphere_scale", 1.0, "marker")

Create Origin Marker

cmd.pseudoatom("origin", pos=[0, 0, 0])
cmd.show("spheres", "origin")
cmd.color("blue", "origin")

Bounding Box

Get Extent (Bounding Box)

extent = cmd.get_extent("selection")
# extent = [[min_x, min_y, min_z], [max_x, max_y, max_z]]
print("Min: " + str(extent[0]))
print("Max: " + str(extent[1]))

Calculate Box Size

extent = cmd.get_extent("selection")
size = [extent[1][i] - extent[0][i] for i in range(3)]
print("Box dimensions: " + str([round(s, 1) for s in size]))

Calculate Box Center

extent = cmd.get_extent("selection")
center = [(extent[0][i] + extent[1][i]) / 2 for i in range(3)]
print("Box center: " + str([round(c, 1) for c in center]))

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Custom Colors

Define Custom Color

cmd.set_color("my_color", [0.5, 0.8, 0.3])  # RGB 0-1
cmd.color("my_color", "selection")

Common Custom Colors

# Define useful colors
cmd.set_color("light_gray", [0.8, 0.8, 0.8])
cmd.set_color("dark_gray", [0.4, 0.4, 0.4])
cmd.set_color("light_blue", [0.6, 0.8, 1.0])
cmd.set_color("coral", [1.0, 0.5, 0.31])

Representation-Specific Colors

cmd.set("stick_color", "gray", "selection")
cmd.set("cartoon_color", "green", "selection")
cmd.set("sphere_color", "red", "selection")

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