Chimera Extension written by Steve Ludke.
Usage notes by Tom Goddard.
February 19, 2004
Animator (also known as EMANimator) is a Chimera extension to make animations. It was written by Steve Ludke at the National Center for Macromolecular Imaging and is distributed with the source code of Steve's EMAN package. The EMAN package is for computing 3-dimensional density maps using "single particle reconstruction". This technique takes thousands of 2 dimensional electron microscope images of a large molecular complex like a virus, and produces a 3-dimensional density map.
The extension is under development, has quite a few rough edges, and Steve has not written documentation. Steve uses it on Linux. It is all Python code so will run on other platforms. This page describes what I learned about Animator from using the version from the EMAN nightly snapshot downloaded February 19, 2004 together with Chimera 1.1899. The extension is in the EMAN source code *.tar.gz file under EMAN/chimeraext/Animator.
The Animator extension lets you script motions and color changes of models and outputs a sequence of jpeg images that can be used to create a movie. It tries to run a program called mencoder to create an mpeg4 format movie from these jpeg images. The mencoder program is part of the mplayer package available for Linux and Mac machines.
An animation is created as a sequence of
Each step of the animation is created using the Animotor dialog and positioned in a time-line displayed by the dialog.
The above actions are the only ones possible. Many changes to molecules cannot be animated. For example, animations cannot change molecule display from wire mode to ribbon, or hide selected atoms, or rotate bonds. The Animator code is written to allow adding new kinds of actions. Steve has been primarily interested in animations displaying volumetric data. Adding code for a new type of action looks like it would take a few hundred of lines of Python code, and a great deal of Chimera programming knownledge.
The Animator extension (menu entry Tools/EMAN/Animator) shows two dialogs. One is titled Model Parameter Memories and the other is Animator.
The Memories dialog records the positions, colors, show/hide state for all models, the threshold level volume surfaces, and the camera parameters. It records this whenever the "New" button is pressed. Each memory is numbered (starting from 0), and has a corresponding column of small buttons. Pressing the top-most button that shows the memory number restores that configuration in the Chimera graphics window. The buttons below in that column restore individual settings, like model color, or orientation, or camera zoom.
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The Animator dialog has a row of 4 buttons at the top, 3 panels in the middle, and some buttons and entry fields at the bottom. The buttons along the top, "Mem A->B", Spin, Color/Fade, and Sequence are used to create specific types of animation segments. Pressing one of these buttons shows entry fields for the parameters associated with that type of segment in the upper right panel, the segment parameters panel. Pressing the Apply button in the segment parameters panel creates an animation segment which is shown in the lower timeline panel. The models and attributes (color, orientation, ...) that are changed during a segment are shown selected in the upper left panel, the model attributes panel. The buttons and frame rate and size entries at the bottom of the Animator dialog are for playing the animation or recording it to files.
The most basic kind of segment of an animation starts at one configuration memory and smoothly transitions to another one. First record two configurations using the New button of the Memories dialog. Then press the "Mem A->B" button at the top of the Animator dialog and enter the start and stop memory numbers. In the model attributes panel (upper left) of the Animator dialog select the attributes (color, threshold, show/hide state, orientation, and camera zoom) that you want to have smoothly interpolated. You can select one or more attributes. Then press the Apply button in the parameters panel (upper right). This will add one or more blue colored bars to the timeline (lower panel) in the Animator dialog. There is one bar for each attribute that you chose to change. Pressing the Play button at the bottom of the Animator dialog will now play through this animation consisting of one segment. The duration (in seconds) of the transition can be set using the Duration entry field in the parameters panel.
There are 3 other types of segments. A Spin segment allows you to rotate the models about a specified axis by a specified angle. There are cases where you cannot do this with the "Mem A->B" type segment. For example, when you want to rotate 360 degrees. The start and end positions are then identical and a "Mem A->B" segment will not produce any motion. There is a Color/Fade segment that lets you transition smoothly from one model color to another. The last segment type is Sequence which shows a sequence of different models, each for an equal time. I think you can get the same effect as the Color/Fade and Sequence segment types using Mem A->B segments, but Color/Fade and Sequence are easier to setup.
Each segment is created and placed on the timeline by pressing the Apply button. Segments can be dragged with the mouse along the timeline. Clicking on a segment bar on the timeline displays the parameters for that segment in the segment parameters panel (upper right). The parameters can then be edited after which you must press Apply for the changes to take effect.
The bars on the timeline can have one of 4 colors (blue, green, pink, yellow) corresponding to the 4 types of segments (Mem A->B, Spin, Color/Fade, Sequence). The Mem A->B, Spin, Color/Fade, and Sequence buttons at the top of the Animator dialog have matching colors.
To delete a segment, click on its bar in the timeline, the press the Delete button in the segment parameter panel (upper right).
Each model attribute gets its own row in the timeline panel. The model numbers are shown in the row labels ending in :0, :1, .... The model attributes panel (upper left) also indicates the different model numbers by rows starting with 0:, 1:, .... These are the same model numbers that can be seen in the Chimera Model Panel.
The vertical black line accross the timeline moves from left to right when you press Play indicating the time. You can drag the vertical line with the mouse and the segments play as the line is moved.
The Snapshot button on the Memories dialog writes jpeg images of each of the memory configurations to files in the current directory (where Chimera was started). The file names end in the memory number.
Using Chimera save session saves all the animation segments and parameter memories.
The Record button plays the animation outputing a series of jpeg images emanframeXXXXX.jpg to the current directory (the one Chimera was started in) and tries to run mencoder on these images to make a MPEG4 format movie. The frames per second and size of the image are set in entry fields next to the Record button. The image saving uses Chimera's standard tiled supersampled rendering.
If you don't select anything in the model attributes panel and press Apply in the segment parameters panel it will not create a segment, and the segment parameters panel changes to just show start time and duration losing your other settings for the segment.
If you type in a new duration in the Duration entry field of the segment parameters panel, you have to press the enter key. Otherwise, pressing Apply will not pick up the changed value.
After creating model memories and then opening new models and creating more memories, Animator started raising exceptions about index out of range. It may be necessary to open all the needed models before starting to make an animation.
A spin segment has to have a starting memory. If you overlap in time the spin segment with another segment that reorients the model the starting position for the spin segment will cause a jump in model position. Would be nice to permit having no starting memory.
Molecule coloring only controls molecule level color. Ribbon and Atom colors cannot be changed as part of the movie.
The model parameters memory window provides no way to delete the remembered states. Each new state is added as another column making the window wider.