Making Movies

Chimera includes the following approaches for capturing image frames and assembling them into a movie file:

Movie Recorder is a graphical interface with buttons to start recording, stop recording, and encode the saved images as a movie file. Several parameters can be adjusted.
The command movie provides access to the same features, but with keywords and arguments. This allows integration of movie recording and content within a single command file.
MD Movie provides an interface for recording trajectories, with the same adjustable parameters as the other approaches.

The image frames can be captured directly from Chimera or created by raytracing with POV-Ray. Available output movie formats are MPEG-1, MPEG-2 MPEG-4, AVI MSMPEG-4v2, and Quicktime. See below for information on developing movie content (often in the form of command files) and troubleshooting problems in PowerPoint.

Movie Content

The window size should be adjusted as desired before recording is started, for example, with the command windowsize. During recording, operations in Chimera can be performed interactively and commands can be entered at the Command Line. Frequently, however, a command file will be used (see examples). Unless raytracing is used, other windows should not overlap the Chimera window during recording.

The frame rate in Chimera is nominally 30/s, but is performance-limited (may be slower depending on what is displayed and what hardware is being used). Saving frames will slow the process further, but this slowing will not affect the playback rate of the resulting movie (default 25 fps). Thus, movie playback may be faster or slower than the original process in Chimera.

Certain commands are especially useful for scripting continuous motion and/or specifying movie content:

2dlabels - display 2D labels, which can be faded in or out over a specified number of frames
clip - move global clipping planes
cofr - change the center of rotation
freeze - stop all motion
mclip - control per-model clipping
move - translate along the X, Y, or Z axis
movie - capture image frames and assemble them into a movie file
perframe - specify an alias to be executed at each display frame
reset - interpolate from the current position to one previously saved with savepos
rock - rock back and forth about the X, Y, or Z axis
roll - rotate about the X, Y, or Z axis
savepos - save and name a "position" (a set of model transformations, etc.)
scale - scale the view
section - move the clipping planes in parallel
select - activate/deactivate models for motion (to move one model relative to another)
set independent - make models rotate about their own centers instead of a collective center
thickness - move the clipping planes in opposite directions
turn - rotate about the X, Y, or Z axis
wait - suspend command processing for a specified number of frames or until motion has stopped
windowsize - set the dimensions of the graphics window

Since a movie is fundamentally a series of images, many of the tips on preparing images also pertain to movies.

Movie Command File Examples

Simply opening a command file in Chimera executes its contents. Note: Executing either of the following examples "as is" will show the content but not create a movie; the movie-recording commands have been commented out.

1gfl.com - fairly simple; rotates green fluorescent protein, changes display styles. Inputs:
- 1gfl (fetched from the Protein Data Bank)
3hhr-scan.com - more elaborate; shows combinatorial scanning results for human growth hormone. Inputs:
- 3hhr (fetched from the Protein Data Bank)
- 3hhr-scan.txt (an attribute assignment file, to be placed in the same directory as the command file)
The movie made with this script (after removing ## from movie-recording commands) is included in the Chimera Animation Gallery.

See rules and tips for constructing command files.

Problems in PowerPoint

On Windows, some Chimera-generated movies cannot be inserted into PowerPoint presentations, or can be inserted but will not play. In PowerPoint 2000, only the Chimera MPEG-1 format works, but the quality is very low. Using PowerPoint 2003 or newer is recommended. With PowerPoint 2003 on Windows, the Chimera AVI MSMPEG-4v2 format is recommended. Although a movie in this format can be inserted into a presentation, it may play as a black rectangle. To remedy this, try reducing the video acceleration in Windows Media Player (instructions are for Media Player 10.0, but should be similar for other versions):

start Windows Media Player (for example, by right-clicking a movie icon and choosing Play with Media Player)
right-click the top bar of the Windows Media Player window and choose menu entry Tools / Options...
click the Performance tab in the Options dialog
click the Advanced... button in the Video Acceleration panel
turn off Use video mixing renderer

After PowerPoint 2003 has been restarted, the movie should play correctly within the presentation. We have not tested movie playing in PowerPoint 2007. A more drastic alternative to the last two steps above is to move the slider in the Video Acceleration panel in the Performance tab to None.

Video acceleration in Media Player is not the only potential source of trouble. If the problem persists, see the following information from Microsoft:

UCSF Computer Graphics Laboratory / February 2008