Chimera Commands Index

coordset  model-spec  frame [ holdSteady  atom-spec ] [ load true | false ]

coordset  model-spec [start],[end][,step] [ holdSteady  atom-spec ] [ loop  N ] [ load true | false ]

Coordset displays the frames of a trajectory. See the video mini-example. See also: morph, play, MD Movie, movie-related commands

To be shown with coordset, the coordinates for each frame must have been loaded into Chimera. This is automatically true for morphing results and the PDB and XYZ trajectory formats. Otherwise, load true (default) can be used to specify reading in the coordinates for all frames in the trajectory. The load false option may be useful when the entire trajectory is very large and just the part of interest has already been read in by playback in MD Movie.

** Protein secondary structure assignments are not recomputed automatically over the course of a trajectory. If a protein is displayed as ribbon, users may want to reassign secondary structure at each frame, as described below. **

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. Atoms to hold as steady as possible upon frame updates can be specified using the holdSteady keyword.

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.

The coordset command and MD Movie graphical interface are integrated, in that frame updates with the command will be reflected in the graphical interface, and hold-steady and per-frame operations specified in the graphical interface will be applied during playback with the command. Examples:

coordset #0 10
   - go to frame 10 of trajectory model #0
coordset #0 -10
   - go to the 10th-to-last frame
Supplying comma-separated frame numbers or even commas without preceding numbers indicates playing from start (default is the current frame) to end (default is the last frame) in increments of step. 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. The loop option indicates repeating playback N times, wrapping directly from end to start. Examples:
coordset #0 1,21 holdSteady @ca
   - play from frame 1 to 21 of trajectory model #0, holding CA atoms steady
coordset #0 1,
   - play from frame 1 to the end
coordset #0 ,15
   - play from the current frame to 15
coordset #0 ,,5
   - play from the current frame to the end, every 5th frame
coordset #0 21,1
   - play from frame 21 to 1, backwards
coordset #0 -1,1,-10
   - play from the last frame to the first, every 10th frame, backwards

Recomputing Secondary Structure

If a protein or peptide is displayed as a ribbon with secondary-structure-specific scaling (width and height) and significant conformational changes are occurring, users may want to reassign secondary structure at each frame. This can be done with the command perframe in combination with ksdssp, for example:

perframe ksdssp; coordset #2 1,21; wait 21; ~perframe