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Use when creating movies, animations, rotations, or morphing sequences in PyMOL.
Installer avec Codex ou Claude Copiez ce prompt, collez-le dans Codex, Claude ou un autre assistant, puis laissez-le vérifier la page du skill et l'installer pour vous.
Basé sur la classification professionnelle SOC
Use when working with PyMOL for molecular visualization tasks including loading structures, creating representations, coloring, selections, and basic analysis.
Use when connecting Claude to PyMOL, troubleshooting socket errors, or setting up the PyMOL integration for the first time
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.
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.
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.
Use when comparing multiple protein designs, ranking design candidates, tracking design iterations, overlaying before/after structures, or performing batch visual QC through PyMOL.
| name | movie-creation |
| description | Use when creating movies, animations, rotations, or morphing sequences in PyMOL. |
| version | 0.1.0 |
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.
cmd.mset("1 x360") # 360 frames (one state repeated)
cmd.mset("1 x90") # 90 frames
cmd.mset("") # Clear movie
cmd.frame(1) # Go to frame 1
cmd.frame(45) # Go to frame 45
cmd.forward() # Next frame
cmd.backward() # Previous frame
cmd.mplay() # Start playback
cmd.mstop() # Stop playback
cmd.rewind() # Go to first frame
# Full 360-degree rotation around Y axis
cmd.mset("1 x360")
cmd.util.mroll(1, 360, 1) # start_frame, end_frame, axis (1=Y)
1 = Y axis (horizontal rotation)2 = X axis (vertical rotation)3 = Z axis (in-plane rotation)cmd.orient()
cmd.scene("overview", "store")
cmd.zoom("ligand", 5)
cmd.scene("closeup", "store")
cmd.zoom("resi 100-120")
cmd.scene("domain", "store")
# 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")
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")
cmd.mview("interpolate") # Linear interpolation
cmd.mview("interpolate", power=1) # Linear
cmd.mview("interpolate", power=2) # Smooth (ease in/out)
# If structure has multiple states
cmd.mset("1 -%d" % cmd.count_states()) # All states
cmd.mplay()
n_states = cmd.count_states()
cmd.mset("1 x" + str(n_states))
# Each frame shows corresponding state
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.
cmd.set("ray_trace_frames", 1)
cmd.mpng(output_dir + "/frame")
cmd.set("ray_trace_frames", 0)
After exporting PNG sequence, use ffmpeg:
ffmpeg -framerate 30 -i frame%04d.png -c:v libx264 -pix_fmt yuv420p movie.mp4
# 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")
# 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)
# 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)
mview("interpolate", power=2) for smooth camera motionmset("") clears the movie completely