MD Movie

MD Movie is a tool for trajectory (or ensemble) viewing and analysis. For examples of use, see the Trajectory and Ensemble Analysis tutorial. See also: Morph Conformations

There are several ways to start MD Movie, a tool in the MD/Ensemble Analysis category.

Several formats are supported:

These input files can be gzipped.

The PDB options generally require coordinates for the same set of atoms to be supplied for each frame. However, if the coordinates supplied for a frame represent only a subset of the atoms in the preceding frame, it will be inferred that the remaining atoms are present but have the same coordinates as in the preceding frame. Changes are cumulated in the forward direction and based on all frames, even when frames are skipped during playback (step size > 1).

All or a contiguous subsegment of a trajectory can be loaded. If pipe is entered as the ending frame number, the input trajectory will be read until it runs out, as long as no other input specifies a smaller ending frame number. For example, for a GROMOS trajectory, the NSTLIM variable in the PROMD file should also be increased to at least the total number of frames expected. When a pipe has been specified, there will be an attempt to load the entire trajectory up front.

A further option is a metafile, simply a text file that specifies the input files/parameters. The first line designates trajectory type (such as amber or gromos, where case is unimportant) and optionally, starting and ending frame numbers of the range to be loaded. A pipe can be specified as described above. If no frame numbers are supplied, the entire trajectory will be loaded; however, if "?" is given for both the starting and ending frame numbers, a dialog for entering this information will appear. The remaining lines specify input files and parameters in the same order as in the dialog. For example:

amber 500 1000
dna.prmtop
dna.mdcrd

pdb
single
108d.pdb

After input files and parameters have been specified, the first set of coordinates will be displayed and the MD Movie controller will appear:

If a subsegment was specified, a message about the restricted frame range will be displayed temporarily. The total number of frames in the trajectory (whether loaded or not) will continue to be reported. For all input formats except PDB, the coordinates for a given frame are not read in until that frame is viewed or used for analysis.

From left to right, the buttons mean: play backward continuously; go back one step; stop; go forward one step; and play forward continuously. When the Loop 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; up to a 1-second delay can be added between frame advances. The Frame number is reported and can also be entered directly to view a specific frame. The Step size controls the level of sampling for viewing purposes. For example, a step size of 3 indicates that only every third frame will be viewed; however, when forward play loops from end to beginning, the movie will start at the first frame loaded, and when reverse play loops from beginning to end, the movie will start at the last frame loaded. Frame number and step size changes take effect when return (Enter) is pressed.

Protein secondary structure assignments are not recomputed automatically over the course of a trajectory. If displaying protein as a ribbon, see the note below.

The current frame or all frames that have been viewed can be saved as a PDB file with File... Save PDB. The view can be held steady on selected atoms. One can define scripts to be executed at each frame update. A complete menu listing with short descriptions is included below.

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

Images can be captured during trajectory playback and automatically assembled into a movie file. Manipulations in Chimera can be performed and per-frame scripts executed during the playback/image-saving process. See also: coordset, making movies

Important notes:
• Protein secondary structure assignments are not recomputed automatically over the course of a trajectory. If a protein or peptide is displayed as a ribbon and significant conformational changes are occurring, users may want to reassign secondary structure at each frame. This can be done with a per-frame script that includes the Chimera command ksdssp.
• For a one-to-one relationship between trajectory frames and recorded image frames, the Playback speed slider should be moved to the far right. Otherwise, identical image frames will be inserted between the unique data frames to slow playback. The frame number parameters described below refer only to the unique data frames.
• On certain platforms, other windows should not overlap the Chimera graphics window during recording (details...). This is not an issue when raytracing is used.

• File name - name for the resulting movie file
• File type (movie format) choices:
  • MPEG-1 [.mpg]
  • MPEG-2 [.mpg]
  • MPEG-4 [.mp4]
  • AVI MSMPEG-4v2 [.avi]
  • Quicktime [.mov]
• Starting frame (first frame loaded, by default) - number of the first frame at which to save an image
• Step size [n] - level of sampling within the indicated range (every n^th frame will be used)
• Ending frame (last frame loaded, by default) - number of the last frame to possibly include (if not skipped by sampling); must be within the range originally loaded
• Encode forward then backward ("roundtrip") (true/false) - whether to include the frames in reverse order as the second half of the movie
• Frame quality (screen/supersampled) - whether to increase the image quality over what is displayed on the screen. The supersampled option (even with 1x1 sampling) allows the subdivision quality to be adjusted automatically.
• Samples (1x1/2x2/3x3/4x4/5x5/6x6) - When supersampling, how many pixels to sample in the X and Y dimensions for each pixel in the final saved image. Supersampling at levels greater than 1x1 entails generating initial images larger than the window and sampling them down to the final size. Higher values increase smoothness but also calculation time.
• Raytrace with POV-Ray (true/false) - whether to raytrace with POV-Ray rather than saving the contents of the Chimera graphics window. Raytraced images include fancier effects like shadows, but take longer to compute. The POV-Ray Options button opens the POV-Ray Options preferences (see balancing time requirements and results).
• Additional recording options - options are the same as for the command movie record; if this field is left blank, image frames will be saved in the PPM format with default names in a default location (but normally deleted upon movie creation, depending on the encoding options)
• Additional encoding options - options are the same as for the command movie encode; if this field is left blank, the movie will be encoded to play at 25 frames per second with a default constant bit rate and buffer size, and image frames will be deleted after the movie has been encoded

Close closes the dialog without initiating recording. Help opens this manual page in a browser window.

Per-Frame... Define script allows specification of a script to be executed at each trajectory frame. Scripts can be written in Chimera commands or Python code, and can incorporate trajectory frame numbers. Python scripts can also access the molecule model instance.

Examples:

• the following Chimera command script (eachFrame.com) identifies hydrogen bonds at each frame and shows only the residues involved:

  chain @ca
  ~disp solvent
  hb line 2 color yellow reveal true
  

  Commands to be executed only at a specific frame can be indicated with a leading #frame_num: (for example, #50:) that will be stripped before the command is executed.
  
  
• the following Python script (specificFrames.py) initiates events at specific frames:

  from chimera import runCommand
  frame = mdInfo['frame']
  if frame == mdInfo['startFrame']:
          runCommand("roll y 3 40")
  elif frame == 10:
          runCommand("color green")
  elif frame == 50:
          runCommand("color orange")
          runCommand("rl :ala; color dodger blue :ala; rep stick :ala")
  elif frame == 90:
          runCommand("~rl; rep wire :ala")
  else:
          runCommand("color byhet")
  

Note: Frame arguments in commands such as roll refer to image frames rather than to unique data (trajectory) frames. For a one-to-one correspondence between image and trajectory frames, the Playback speed slider must be positioned all the way to the right and the viewing step size set to 1. Whereas an MD Movie per-frame script executes at each trajectory frame, commands to be executed at each image frame (independent of any trajectory) can be specified with the perframe command.

Insert text file allows browsing to a text file and placing its contents in the script area. Save to file saves the current contents of the script area to 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. Clear deletes the contents of the script area. Close closes the dialog without executing the script, and Help opens this manual page in a browser window.

It may be interesting to see which regions of space are highly populated by certain atoms relative to others in the trajectory or ensemble. For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group. Occupancies can be represented as a three-dimensional grid of values, or volume data. Analysis... Calculate occupancy can be used to generate such data and display it with Volume Viewer. The occupancy map can be saved to a file and later reopened in Chimera.

Usually, one should first define a reference set of atoms to hold steady (the trajectory frames will be transformed to keep these atoms in the same place and orientation, as much as possible). This is accomplished by selecting the desired reference atoms and then choosing Actions... Hold selection steady. When the selection is later changed, the "hold steady" atoms will not change unless Actions... Hold selection steady is used again.

Next, one should select the atoms for which occupancy data will be collected. The atoms in the selection can be combined into a single set of occupancy data, or segregated by atom type.

• Starting frame (first frame loaded, by default) - number of the first frame to include in occupancy calculations; must be within the range originally loaded
• Step size [n] - level of sampling within the indicated range (every n^th frame will be used)
• Ending frame (last frame loaded, by default) - number of the last frame to possibly include (if not skipped by sampling); must be within the range originally loaded
• Limit data collection to within cutoff distance of any "held steady" atoms (true/false) - whether data should be collected only within the cutoff distance of any atom in the prior hold steady specification. This option is ignored if there was no hold steady specification.
• Cutoff distance (10.0 by default) - angstrom distance used to limit the volume data region to a zone around atoms in a prior hold steady specification
• Volume grid spacing (1.0 by default) - angstrom resolution of the resulting volume data grid
• Volume data name - name to use for the resulting volume data set(s); the name(s) will be listed in the Volume Viewer interface. For separate data sets collected for different atom types, the atom type symbol is enclosed in brackets and appended to the name.
• Collect data separately for each atom type in selection (true/false) - whether to make a separate set of volume data for each atom type in the selection

Close closes the dialog without initiating the calculation. Help opens this manual page in a browser window.

• Starting frame (first frame loaded, by default) - number of the first frame to include in RMSD calculations; must be within the range originally loaded
• Step size [n] - level of sampling within the indicated range (every n^th frame will be used)
• Ending frame (last frame loaded, by default) - number of the last frame to possibly include (if not skipped by sampling); must be within the range originally loaded
• Lower RMSD threshold (white) (0.5 by default) - initial lower RMSD threshold for coloring, in angstroms; white will be used for this value and lower. If auto-recoloring is turned on, the threshold may change after all of the values have been computed.
• Upper RMSD threshold (black) (3.0 by default) - initial upper RMSD threshold for coloring, in angstroms; black will be used for this value and higher. RMSD values between the thresholds will be mapped to grayscale. If auto-recoloring is turned on, the threshold may change after all of the values have been computed.
• Restrict map to current selection, if any (true/false) - whether to use only the selected atoms, when a selection exists
• Ignore solvent/ions (true/false) - whether to omit atoms classified as solvent and ions from the calculations
• Ignore hydrogens (true/false) - whether to omit hydrogen atoms from the calculations
• Auto-recolor for contrast (true/false) - whether the RMSD map should be recolored automatically after all values have been computed, using thresholds that enclose the middle third of values (i.e., the lowest third of values will be white, the middle third in grayscale, the highest third black)

For each frame-to-frame comparison, the least-squares-fit RMSD between the indicated sets of atoms will be calculated, without applying any transformation.

OK and Apply initiate the RMSD calculations with and without closing the dialog, respectively. Close closes the dialog without initiating the calculation. Help opens this manual page in a browser window.

The calculations may require additional frames to be read (frames within the loaded range are not actually read until viewed or otherwise used) and may take several minutes, depending on the size of the system and the number of frames. The Abort button on the RMSD map dialog allows termination of a calculation in progress.

The following approaches are recommended for examining long trajectories or long trajectory segments:

• using sparser sampling
• limiting the calculation to fewer atoms, such as the backbone only; the calculation can be limited by including only selected atoms, omitting solvent/ions, and/or omitting hydrogens

Multiple RMSD maps can be open at the same time. However, a given map can be recolored (without recalculation of RMSD values) using the map's menu option RMSD... Change thresholds... to adjust the white/black threshold settings. When the cursor is placed over a map, the corresponding frame numbers and RMSD value are given near the bottom of the dialog. Clicking on a map places the corresponding frame numbers in the Frame fields. Clicking Go changes the graphics display to the corresponding frame.

Alternatively, the Ensemble Match tool can be used to calculate all-by-all pairwise RMSD values for an ensemble read from a single PDB file. The file would need to be opened in a standard way rather than with MD Movie. Unlike MD Movie, Ensemble Match can perform the corresponding pairwise superpositions (i.e. match one structure to another), but its use is impractical for ensembles with very many members.

• Save PDB... open a dialog to save the current frame or all frames that have been viewed as a PDB file
• Record movie... set parameters for saving image frames and encoding them as a movie file
• Load Additional Frames... (only available for Amber format) read an additional trajectory file and append its frames to the end of the current trajectory

• 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

• Define script... open a dialog for entering a script (written in Chimera commands or Python code) to be executed after each trajectory frame update. 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.
• Stop running script - do not run the script after subsequent trajectory frame updates

• Calculate occupancy... collect and display (with Volume Viewer) occupancy data for the selected atoms over a specified set of frames
• RMSD map... calculate a two-dimensional RMSD map containing all-by-all comparisons among specified frames

MD Movie uses the Trajectory module to read the various formats (chimera/share/Trajectory, where chimera is the Chimera installation location). Trajectory contains a subdirectory, formats, which in turn contains subdirectories that each correspond to the Python module for a supported format. By convention, the module (and directory) name for each format is the name of the format with the first letter of each word capitalized and all other letters lowercase. For example, the MMTK module's name is Mmtk.

A format's module is typically structured so that the code that interfaces with Trajectory's generic format handling is in __init__.py, and the code specific to reading a particular format is in another python file, usually named after the format itself (for example, Gromos.py).

__init__.py must support the following:

• If the format name displayed to the user should be different from the module name (usually it should, due to capitalization), then there must be a global variable named formatName that is initialized to the display name of the format.
• A class named ParamGUI must be defined to handle presenting the file-loading interface to the user. It must have two methods:
  • __init__, which receives a Tkinter.Frame instance argument. The __init__ method should populate the frame with widgets for gathering the input information for the format from the user.
  • loadEnsemble, which takes as arguments a starting frame number, ending frame number, and callback function. loadEnsemble needs to compose a list of the arguments that were provided by the user to the widgets defined in __init__, and then call this module's global loadEnsemble function (see below) with that list as the first argument and the start/end frame number and callback as the remaining three arguments.
• A global loadEnsemble function that generates an ensemble instance (discussed later). This function is not only called by the ParamGUI.loadEnsemble method, but also when a metafile is used to specify the input parameters. This function takes four arguments: a format-specific list of input parameters, a starting frame number, an ending frame number, and a callback function to start the MD Movie interface. The global loadEnsemble function should call the interface with the generated ensemble as an argument, and should remember the provided format-specific values as preferred defaults for future uses of the format.

The format-specific .py file defines an ensemble class that gets instantiated from __init__.py's loadEnsemble function. The ensemble class must support the following methods:

• An __init__ method that takes the format's input parameters and start/end frames as arguments. The __init__ method may read input files or do whatever is necessary to support the other instance methods (such as call into a C/C++ module to read the files, as is done for Amber format).
• A GetDict method that takes a string argument. The string specifies what data should be returned. The possible string values are:
  • atomnames - return a list of the atom names; a residue's atoms must be consecutive
  • elements - return a list of the atom elements. These should be instances of chimera.Element (which can be initialized with a string such as "Fe" or a number). Trajectory's determineElementFromMass function may be useful if the format does not specify the atomic number directly or it cannot be determined easily from the atom name.
  • resnames - return a list of the residue names
  • bonds - return a list of bonds (2-tuples of indices into the atomnames list)
  • ipres - a list of the first atom of each residue (indices into atomnames, but unlike previous indices these are 1-based, so the first element of ipres will always be 1)
• A __getitem__ method taking a frame-number argument (starting with 1): return a list of 3-tuples corresponding to the xyz coordinates of the atoms in that frame (in the same order as atomnames). The coordinates should be in angstroms.
• A __len__ method that returns the total number of frames in the trajectory (not just the number of frames between the user-specified start/end frames).