The main coordset command displays the frames (coordinate sets) of a trajectory, whereas coordset slider shows a graphical interface for interactive playback. The number of coordinate sets in a trajectory can be reported with the command info. See also: morph, mseries, making movies
Playback via Command
Coordset Slider and Plotting
Recomputing Secondary Structure
Meaning of “Frames”
Usage: coordset model-spec frame [ computeSs true | false ] [ holdSteady atom-spec ]
Usage: coordset model-spec [start,][end][,step] [ computeSs true | false ] [ holdSteady atom-spec ] [ pauseFrames M ] [ loop N [ bounce true | false ]]
Usage: coordset stop model-spec
The coordset command displays the frames (coordinate sets) of a trajectory, whereas playback in progress can be halted with coordset stop. 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.
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 slider context menu includes:
In general, each measurement is defined by
selecting the desired atoms
(two for Distances, three for Angles, four for Torsions)
and clicking Plot. Several different measurements of the same type
(for example, several distances) can be shown on the same plot.
Each measurement is listed in a table on the right along with a
show/hide checkbox and
a color well that can be clicked to change the line color interactively.
Choosing one or more rows in the table and clicking Delete
removes the associated measurement(s).
Each plot is effectively a timeline with a “scrubber,” in that clicking a specific frame shows the corresponding coordinate set in the graphics window, and dragging the vertical line left or right plays through the corresponding part of the trajectory. It is important to avoid closing the plot window, as the measurement definitions will be lost if that occurs. If the plot window is left open but gets lost behind other windows, it can be resurrected using the slider context menu.
See also: movie, vseries slider
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
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.