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.
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, such as from molecular dynamics or Morph Conformations.
Morph Map (or command vop morph) creates an interpolated progression between two sets of volume data and allows recording the progression as a movie.
Additional tools step through different volume data displays over time and can be used together with Movie Recorder or the movie command:
- Volume Series displays an ordered sequence of data sets
- the planes feature in Volume Viewer displays sequential planes or slabs of data
- the volume command with the planes keyword displays sequential planes or slabs of data

The image frames can be rendered directly by Chimera or created by raytracing with POV-Ray. See below for information on developing movie content and troubleshooting problems in PowerPoint. See also: Movie preferences

Movie Content

The Chimera window should be adjusted to the desired dimensions before recording, for example with the command windowsize. Using a small and standard frame size (320 x 240, 640 x 480, or 800 x 600 pixels) may solve some playback problems. On certain platforms, other windows should not overlap the Chimera graphics window during recording (details...). This is not an issue when raytracing is used.

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

During recording, structures can be manipulated interactively and commands typed. However, for reproducibility and smoother results, often a command file will be used instead (see examples).

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
background - set background color(s) or image
clip - move global clipping planes
cofr - change the center of rotation
coordset - play through frames of a trajectory
fly - smoothly traverse a series of positions previously saved with savepos
freeze - stop all motion
mclip - control per-model clipping
move - translate models
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 - rotate models back and forth (oscillate)
roll - rotate models
savepos - save and name a "position" (model transformations, scale, etc.)
scale - scale the view
scene - save and restore scenes (positions plus styles, colors, labels, etc.)
section - move the clipping planes in parallel
select - activate/deactivate models for motion
set - set visual effects, make models rotate about individual centers
surftransparency - adjust surface transparency
thickness - move the clipping planes in opposite directions
turn - rotate models
wait - suspend command processing for a specified number of frames or until motion has stopped
windowsize - set the dimensions of the graphics window

In addition, the commands sleep and pause are useful for introducing pauses during live script execution, but not in movies, as no new frames are drawn during such pauses.

Command script execution can be aborted by pressing the Esc (escape) key, or paused/resumed (again, with no new frames being drawn during the pause) by pressing Shift-Esc.

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.

Movie Command File Examples

Simply opening a command file in Chimera will execute its contents. Opening any of the following example files in Chimera will show the content but not create a movie, as the movie-recording commands have been commented out with ##.

1gfl.com - fairly simple; fetches green fluorescent protein 1gfl from the Protein Data Bank, rotates it, changes display styles
trmovie.com - morphs between structures 1tde and 1f6m (movie Ball-and-socket motion in the Chimera Animation Gallery)
3hhr-scan.com - shows scanning mutagenesis results on structure 3hhr (movie Combinatorial scanning of human growth hormone in the Chimera Animation Gallery). Associated data:
- 3hhr-scan.txt (an attribute assignment file, to be placed in the same directory as the command file)

The online movie-making tutorial and the Chimera Animation Gallery contain additional examples.

Problems in PowerPoint

On Windows, some Chimera-generated movies cannot be inserted into PowerPoint presentations, or can be inserted but will not play.

Using a small and standard frame size (320 x 240, 640 x 480, or 800 x 600 pixels) may solve some playback problems. Before recording, the Chimera window can be set to specific dimensions using the command windowsize.

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 / January 2012