Use when working with PyMOL for molecular visualization tasks including loading structures, creating representations, coloring, selections, and basic analysis.

2026-03-313

pymol-setup

ANaka/claudemol

Use when connecting Claude to PyMOL, troubleshooting socket errors, or setting up the PyMOL integration for the first time

2026-03-313

la-proteina-viz

ANaka/claudemol

Use when setting up, configuring, running, or inspecting La-Proteina protein generation tasks including unconditional design and motif scaffolding. Helps build configs and visualize outputs through PyMOL.

2026-03-313

proteina-complexa-viz

ANaka/claudemol

Use when setting up, configuring, running, or inspecting Proteina-Complexa protein binder design, ligand binder design, AME motif scaffolding, or monomer motif scaffolding. Helps build configs, select targets, and visualize outputs through PyMOL.

2026-03-313

alphafold-validation

ANaka/claudemol

Use when validating protein designs with AlphaFold2/AlphaFold3/ESMFold predictions, coloring by pLDDT or pAE, computing self-consistency RMSD, or screening design candidates through PyMOL.

2026-03-313

design-comparison

ANaka/claudemol

Use when comparing multiple protein designs, ranking design candidates, tracking design iterations, overlaying before/after structures, or performing batch visual QC through PyMOL.

2026-03-313

name	movie-creation
description	Use when creating movies, animations, rotations, or morphing sequences in PyMOL.
version	0.1.0

Movie Creation

Workflows for creating animations and movies in PyMOL.

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

Movie Basics

Set Frame Count

cmd.mset("1 x360")  # 360 frames (one state repeated)
cmd.mset("1 x90")   # 90 frames
cmd.mset("")        # Clear movie

Frame Navigation

cmd.frame(1)        # Go to frame 1
cmd.frame(45)       # Go to frame 45
cmd.forward()       # Next frame
cmd.backward()      # Previous frame

Playback Control

cmd.mplay()         # Start playback
cmd.mstop()         # Stop playback
cmd.rewind()        # Go to first frame

Simple Rotation Movie

Using mroll

# Full 360-degree rotation around Y axis
cmd.mset("1 x360")
cmd.util.mroll(1, 360, 1)  # start_frame, end_frame, axis (1=Y)

Axis Options for mroll

1 = Y axis (horizontal rotation)
2 = X axis (vertical rotation)
3 = Z axis (in-plane rotation)

Scene-Based Movies

Store Scenes

cmd.orient()
cmd.scene("overview", "store")

cmd.zoom("ligand", 5)
cmd.scene("closeup", "store")

cmd.zoom("resi 100-120")
cmd.scene("domain", "store")

Create Movie from Scenes

# Set total frames
cmd.mset("1 x90")

# Store keyframes
cmd.frame(1)
cmd.scene("overview", "recall")
cmd.mview("store")

cmd.frame(30)
cmd.scene("closeup", "recall")
cmd.mview("store")

cmd.frame(60)
cmd.scene("domain", "recall")
cmd.mview("store")

cmd.frame(90)
cmd.scene("overview", "recall")
cmd.mview("store")

# Interpolate between keyframes
cmd.mview("interpolate")

Camera Movement

Store View Keyframes

cmd.mset("1 x60")

# Starting view
cmd.frame(1)
cmd.orient()
cmd.mview("store")

# Rotated view
cmd.frame(30)
cmd.turn("y", 90)
cmd.mview("store")

# Zoomed view
cmd.frame(60)
cmd.zoom("resi 50", 5)
cmd.mview("store")

# Smooth interpolation
cmd.mview("interpolate")

Interpolation Modes

cmd.mview("interpolate")           # Linear interpolation
cmd.mview("interpolate", power=1)  # Linear
cmd.mview("interpolate", power=2)  # Smooth (ease in/out)

Multi-State Movies

For NMR Ensembles or MD Trajectories

# If structure has multiple states
cmd.mset("1 -%d" % cmd.count_states())  # All states
cmd.mplay()

Loop Through States

n_states = cmd.count_states()
cmd.mset("1 x" + str(n_states))
# Each frame shows corresponding state

Exporting Movies

PNG Sequence

import os
output_dir = os.path.expanduser("~/Desktop/movie_frames")
os.makedirs(output_dir, exist_ok=True)

cmd.mpng(output_dir + "/frame")
# Creates frame0001.png, frame0002.png, etc.

With Ray Tracing (Slow but High Quality)

cmd.set("ray_trace_frames", 1)
cmd.mpng(output_dir + "/frame")
cmd.set("ray_trace_frames", 0)

Convert to Video (External)

After exporting PNG sequence, use ffmpeg:

ffmpeg -framerate 30 -i frame%04d.png -c:v libx264 -pix_fmt yuv420p movie.mp4

Complete Workflows

360-Degree Rotation

# Setup
cmd.delete("all")
cmd.fetch("1ubq")
cmd.show("cartoon")
cmd.hide("lines")
cmd.color("green")
cmd.bg_color("white")

# Create rotation movie
cmd.mset("1 x360")
cmd.util.mroll(1, 360, 1)

# Export (optional)
# cmd.mpng("~/Desktop/rotation/frame")

Zoom In/Out Animation

# Setup structure
cmd.orient()
cmd.mset("1 x60")

# Full view
cmd.frame(1)
cmd.zoom("all", 5)
cmd.mview("store")

# Close-up
cmd.frame(30)
cmd.zoom("resi 45-50", 3)
cmd.mview("store")

# Back to full
cmd.frame(60)
cmd.zoom("all", 5)
cmd.mview("store")

# Smooth transition
cmd.mview("interpolate", power=2)

Tour of Binding Site

# Assume structure with ligand loaded
cmd.select("lig", "organic")
cmd.select("pocket", "byres (polymer.protein within 5 of lig)")

# Store views
cmd.zoom("all")
cmd.scene("full", "store")

cmd.zoom("lig", 8)
cmd.scene("ligand", "store")

cmd.zoom("pocket", 5)
cmd.turn("y", 45)
cmd.scene("pocket_side", "store")

# Create movie
cmd.mset("1 x120")

cmd.frame(1)
cmd.scene("full", "recall")
cmd.mview("store")

cmd.frame(40)
cmd.scene("ligand", "recall")
cmd.mview("store")

cmd.frame(80)
cmd.scene("pocket_side", "recall")
cmd.mview("store")

cmd.frame(120)
cmd.scene("full", "recall")
cmd.mview("store")

cmd.mview("interpolate", power=2)

Tips

Use mview("interpolate", power=2) for smooth camera motion
30 frames = 1 second at typical playback
Store scenes before creating movies for easier editing
Ray tracing movies takes significant time
Export as PNG sequence, then convert to video externally
mset("") clears the movie completely