Chimera Movie Making

Tom Goddard
October 3, 2012

This tutorial shows how to make animations using Chimera for use on web sites, in journal articles, and talks. We will use maltotriose binding protein, PDB 2gha, and Chimera 1.7 snapshot version from September 2012 for our examples.

Topics

Spinning a molecule
Special effects: silhouette edges, shadows, background color
Movies with several motions: command scripts
What to show in an animation: morphing example
Saving your work: use a session file to set up the initial scene
Optional: How to put an animation in a web page

Spinning a molecule

Open 2GHA.pdb.
Delete chain B. Select / Chain / B and Actions / Atoms / Delete
Color ribbon. Presets / Interactive 1 (ribbons)
Highlight ligand. Select / Structure / Ligand and Actions / Atoms / Sphere
Clear selection. Select / Clear Selection

Rotate 360 degrees. Favorites / Command Line
- turn y 1 360
Record “spin” movie.
- movie record ; turn y 1 360 ; wait ; movie encode
Semicolons separate commands on one line.
movie record starts capturing images.
wait prevents going to the next command until motion finishes.
movie encode writes the images to a movie file.

Special effects: silhouette edges, shadows, background color

Background white. Command set bg white *
*as of Chimera 1.9, set bgcolor white
Silhouette edges. Tools / Viewing Controls / Effects
Enable shadows.
Background gradient. Favorites / Preferences,
category Background, background method gradient
Gray gradient. Click background gradient color well.
Set window size. Command windowsize 640 480.
Record movie, 2 degree steps, supersample to smooth edges.

movie record supersample 3 ; turn y 2 180 ; wait ; movie encode

Movies with several motions: command scripts

To make more complex movies put commands in a plain text file and run it.
Try this using Text Edit on Mac, or Note Pad on Windows, or any text editor.

movie record
turn y 2 180
wait
movie encode

Zoom in on ligand and do second spin.
Interactively try this command: scale 1.02 80
Make rotation about center of ligand. Select central ligand atom. Actions / Set Pivot

movie record
turn y 2 180
wait
scale 1.02 80
wait
turn y 2 180
wait
movie encode ~/Desktop/spin3.mp4

Fade out ribbon so it does not block view of ligand.
Interactively try this command: transp 80,r
Turn off silhouettes to deemphasize ribbon.
To make duller transparency try: set flat
Make ribbons opaque again with: transp 0,r
To smoothly fade to transparent ribbon, use movie crossfade 25 before the transparency command in the script:

movie record
turn y 2 180
wait
scale 1.02 80
wait
movie crossfade 25
transp 80,r ; set flat
turn y 2 180
wait
movie encode ~/Desktop/spin5.mp4

What to show in an animation: morphing example

Many of the commands useful in making movies are demonstrated on the Movie Command Examples page on the Chimera web site under Documentation.

Morphing is one of the most useful kinds of animation, making it easier to see differences between two conformations of a molecule.

Open 2ghb.pdb, no maltotriose ligand bound.
Delete chains B and C.
Go back to black background and opaque ribbons. Presets / Interactive 1 (ribbons)
Show ligand as spheres again. Command repr sphere ligand
Use MatchMaker to align 2ghb to 2gha. Tools / Structure Comparison / MatchMaker
Color 2gha ribbon pink. Command color pink,r #0
Morph 2gha → 2ghb → 2gha again using Tools / Structure Comparison / Morph Conformations
Hide original structure of 2ghb by unchecking its “S” box in Favorites / Model Panel
Keep 2gha shown, but undisplay everything in it except ligand: ~ribbon #0 ; ~display #0 ; display ligand
Show morph residues near ligand: disp #2 & ligand zr<5
Use MD Movie dialog File / Record Movie...
To use morph in a command script: coordset #2 1,41


Structure superposition.	Morph movie.

Saving your work: use a session file to set up the initial scene

To save your movie making work, save a Chimera session that sets up the scene, and use a command script that records the movie.

Save session with calculated morph. File / Save Session As...

Save command script that records the movie.

movie record
coordset #2 1,41
wait
movie encode

For each movie you make keep 3 files: the Chimera session, the command script, and the movie (morph.py, morph.cmd, morph.mp4).
This allows you to later improve the movie, change its size, etc. with little effort.

A fancier movie example

Includes titling (2dlabel), ligand fly in (savepos / reset), hydrogen bond display (hbond), surface display (surf).

Other example animations are on the Chimera Animation Gallery web page.

How to put an animation in a web page

Use HTML5 video tag to embed a movie in a web page.

<html>
<body>

<video width="640" height="480" controls="controls">
  <source src="movie.mp4" type="video/mp4" />
  Your browser does not support the video tag.
</video> 

</body>
</html>

Chimera records movies in H.264 format by default.