Movie

Movie replays molecular dynamics trajectories saved from AMBER. There are several ways to start Movie, a tool in the Molecular Dynamics category.

Two files from AMBER are required:

• a prmtop (parameter/topology) file; both an older format and the newer Amber format can be read (see Appendix E of the Amber 7 Manual)
• a trajectory (mdcrd) file

All or a contiguous subsegment of the trajectory can be loaded. Once the data has been read, the first set of coordinates will be displayed and a movie controller will appear:

A message indicating what part of the trajectory has been loaded is shown temporarily; the total number of frames in the trajectory continues to be reported (whether loaded or not).

From left to right, the buttons mean: play backward continuously; go back one frame; stop; go forward one frame; and play forward continuously. The Loop button toggles between on and off states; when the option is on, forward play can wrap from the end to the beginning of the loaded trajectory and reverse play can wrap from the beginning to the end. The rate of continuous play can be adjusted with the Playback speed slider.

The Movie Actions menu allows the view to be steadied based on selected atoms; the Movie Per-Frame menu allows the definition of scripts to be executed at each trajectory frame update.

Hide closes the interface without exiting from Movie; the interface can be reopened using the Tools menu entry for the instance of Movie. Quit exits from Movie and removes the structure from the Chimera window. Help opens this manual page in a browser window.

• Hold selection steady - transform subsequent trajectory frames to keep the selected atoms in the same place and orientation, as much as possible (since the atoms may move relative to one another). For best results, the selection should include at least three atoms, not linearly arranged, to define a frame of reference. If the selection is changed, Hold selection steady must be chosen again to start using the new selection.
  
  
• Stop holding steady - return to the default behavior of only transforming the coordinates according to user manipulations and commands

• Run script... open a dialog for entering a script to be executed after each trajectory frame update. Scripts can consist of Chimera commands or Python code, and the frame number can be incorporated. Script contents can be entered directly or inserted from a text file. OK and Apply execute the script with and without closing the dialog, respectively. If the movie is playing, the script will continue to be executed for each trajectory frame until Stop running script is chosen; if the movie is halted on a single frame, the script will be executed for that frame and will not be executed again until a different frame is shown. Python scripts do not need to import the chimera module since it is automatically imported. A script can be saved to a file for later use. Clear deletes the contents of the script area.
  
  
• Stop running script - do not run the script after subsequent trajectory frame updates