Step 0:  If  you wish to load this page to your own computer, save these files (right-click/save link as):

moveutil.htm:  This web page
help.htm: The help page
0.mol: A blank molecule image to initialize the Chime plug-in's
initial.spt:  A chime script file to generate the default blank image.
myo.pdb:  A sample pdb file (optional - you can also enter your own file name).

Step 1: Enter the name of an image file (pdb, mol, etc). or the URL of an image file and press the Load button.

This button loads the same image file into the two Chime windows (inital and final view). You can enter just the file name if you are running this page from your own computer and the image file is in the same folder as the web page file (moveutil.htm). If you are running this page from the original server, you can can enter the URL for an image file such as:

http:/faculty.gvsu.edu/carlsont/grant/moveutil/myo.pdb

or you can enter myo.pdb to load a sample myoglobin pdb file for practice.

The rotation parameters needed in the move command to get from the initial to final view depends on the total number of frames over which the animation will be iterated (Total frames = Total Time x FPS). The total time is up to you. The FPS will determine the smoothness of the animation. Chime's default FPS is 30 FPS. However, if the FPS is set at a rate faster than your computer redraw the image, Chime will automatically accelerate the animation by dividing the FPS by an integer (Acceleration), up to the Maximum Acceleration set by the user. The amount of acceleration necessary depends on the size of the molecule, the complexity of the image, and the speed of the user's computer. This means that a portion of an animation set for 30 FPS and Max Accel=5 could accually take place at 6 FPS (i.e. 30/5). Since the final image generated by the animation is a function of the total number of frames, this acceleration feature can produce some unpredictable results. The user has a few options to get around this problem.

• Don't worry about it: The error caused by the acceleration feature may not be big enough to cause a problem, depending on your application.
• Use a lower FPS: If you can find the FPS that prevents the need for Chime to use the acceleration feature, then the final image will be correct, however the aniamation will not be as smooth.
• Use a lower Maximum Acceleration: Setting the Max Accel to 1 will disable the acceleration feature, however the total time for the amination may be unacceptably long, depending on the application.
• Use a longer Total Time: Longer animations will use more total frames which makes the cacluations less sensitve to the acceleration error.

You have two options for obtaining the initial view parameters.

• You can use the mouse to set the desired initial view in the left Chime window and then press the Get View button. In the box below you will see six numbers. These correspond to the first six parameters of the View Set View output from Chime (x-rot y-rot z-rot zoom x-trans y-trans). Note these are not move parameters, but rather the series of rotation, zoom, and translation commands that would be needed to generate the image on the screen starting with the default orientation that appears after a Reset command (Chime assumes that rotations are done in the order z, y, x). The output for the default image would be 0 0 0 100 0 0.
• If you already know the rotations, zoom, and translation parameters for the view you want to start with, you may type them in the box manually (six numbers separated by a single blank space) and press the Set View button. The desired image should appear in the Chime window above. The last 5 parameters of the View Set command are not supported by this utility. They should not be entered and will be automatically set to zero.

Get or set the desired final view in the right Chime window. Use the same procedure as above.

When you press the Get Move Command button, the algorithm in the javascript uses the set view parameters obtained in steps 3 and 4, as well as the move parameters set in step 2 to calculate the Chime move command needed to go directly from the initial to final view. The acceleration parameter has no effect on the calculation, but may influence the actual final view generated as explained in step 2. However, the move command you calculate is only valid for the set number of total frames. So if you cacluate a move command at 30 FPS in 2 seconds (60 frames), you could use this same command to move at 20 FPS in 3 seconds, or at 15 FPS in 4 seconds. But if you need to do the move at 20 FPS for 2 seconds, you will need to calculate a new move command.

When you press the Try It button, the left Chime window will execute the calculated move command. When complete, the image in the left window should match the image in the right window. If it doesn't, consult step 2 for adjusting the move parameters to get better results. After the move, you can press the Set View button below the left window to take you back to the initial view.

The features of this web page have been automated in the MoveTo Chime function. When this function is present, the javascript will automatically obtain the current view parameters (whatever they are) and execute the move command needed to get to the view called in the MoveTo function.  This page explains the MoveTo function in detail.  This is a simple MoveTo page, with all features in a single file for easy downloading.