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Command: coordset

coordset  model-spec  framecomputeSs  true | false ] [ holdSteady  atom-spec ]

coordset  model-spec  [start,][end][,step] [ computeSs  true | false ] [ holdSteady  atom-spec ] [ pauseFrames  M ] [ loop  N ] [ bounce  true | false ]

coordset stop  model-spec

The coordset command displays the frames (coordinate sets) of a trajectory, and the coordset slider subcommand shows a graphical interface for interactive playback. Trajectory playback in progress can be halted with coordset stop. The number of coordinate sets in a trajectory can be reported with the command info. See also: morph, mseries, making movies

The model-spec is the model number of the trajectory, preceded by #. A comma-separated list or range of model numbers can be used to specify multiple trajectories at once.

Protein cartoon (ribbon) display depends on which residues are in helices and strands, but these secondary structure assignments are not recomputed automatically as the coordinates change. The computeSs option (default false) can be used to update secondary structure assignments as each frame is shown. It runs dssp with default parameters; to use different dssp parameters or to run it less frequently than every frame shown, see below. Running the calculation may slow playback.

Atoms to hold as steady as possible upon frame updates can be specified using the holdSteady keyword. The pauseFrames option can be used to slow playback by showing each trajectory frame for M image update frames (default 1; see frames terminology).

Supplying only one frame number without commas indicates simply going to that frame. A positive number is taken literally, whereas a negative number N is interpreted as the Nth-to-last frame. Examples:

coordset #1 10
   - go to frame 10 of trajectory model #1
coordset #1 -10
   - go to the 10th-to-last frame

Supplying comma-separated frame numbers indicates playing from start to end in increments of step. As shown in the examples below, using “.” for the start number indicates the current frame. The end number can be omitted to indicate the last frame, and omitting all three numbers (start, end, step) indicates playing from the first frame to the last. The default step is 1 if start < end, –1 if start > end, determined after any negative frame numbers are converted to the corresponding actual frame numbers. Examples:

coordset #1 1,21 holdSteady @ca
   - play from frame 1 to 21 of trajectory model #1, holding CA atoms steady
coordset #1 .,15
   - play from the current frame to frame 15
coordset #1 5,
   - play from frame 5 to the end
coordset #1
   - play from frame 1 to the end
coordset #1 21,1
   - play from frame 21 to 1, backwards
coordset #1 -1,1,-10
   - play from the last frame to the first, every 10th frame, backwards

The loop option indicates repeating playback N times, jumping directly from end to start if bounce is false (default). If bounce is true, each loop plays forward from start to end and backward from end to start instead of abruptly wrapping.

Coordset Slider

Usage: coordset slider  model-spec  [ computeSs  true | false ] [ holdSteady  atom-spec ] [ pauseFrames  M ] [ movieFramerate  fps ]

The coordset slider subcommand shows a graphical interface for trajectory playback. The computeSs, holdSteady, and pauseFrames options are as described above for the main coordset command. The slider can be dragged or a frame number entered directly. The interface also includes a play/pause button, a    value to increase for slower playback (pauseFrames as described above), and a button for recording a movie (). Sequential integers are added to the movie filename (movie1.mp4, movie2.mp4, ...) so that repeated recordings will not overwrite the previous ones, and the save location can be set with the snapshot command. The movie will start at the current slider position, so to include the whole trajectory, place the slider at the far left before clicking the record button. The movieFramerate option specifies the playback rate of movies recorded from the slider interface (default 25 frames per second).

A separate slider is shown for each specified trajectory model. By default, opening a trajectory automatically shows a slider. The slider is saved in sessions. The Loop Playback setting in the slider context menu controls whether interactive playback should automatically wrap around from the end to the beginning (initially on). See also: movie, vseries slider

Frames Terminology

Note that “frames” is commonly used for two disparate concepts:

Because of such broad usage, the documentation also uses “frames” in both senses, but context and wording should indicate which meaning applies in a particular situation.

Recomputing Secondary Structure

If a protein is displayed as a cartoon (ribbon) and conformational changes are occurring over the trajectory, users may want to re-evaluate secondary structure assignments periodically. The computeSs option of coordset already provides a convenient way to reassign secondary structure at every frame shown. However, an alternative approach with perframe can be used to run dssp less frequently or with nondefault settings. For example, to reassign secondary structure at every fifth frame:

perframe dssp interval 5; coord #1 1,200; wait 200; ~perframe

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2024