coordset

Usage:
coordset model-spec frame [ holdSteady atom-spec ]

Usage:
coordset model-spec [start],[end][,step] [ holdSteady atom-spec ]

Coordset plays through frames of a trajectory previously loaded into Chimera. Please note:

Depending on the format, fully loading a trajectory may require using the MD Movie graphical interface to play every frame beforehand (not just to read the input and show the first frame). This initial playthrough is not required, however, for trajectories read from PDB files or created by morphing.
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.

Model-spec is the model number of the trajectory, preceded by #. 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.

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.

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)

Important Note

Protein secondary structure assignments are not recomputed automatically over the course of a trajectory. 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 alias and ksdssp, for example:

alias ^redefine ksdssp #2
perframe redefine
coordset #2 1,21; wait 21; ~perframe

See also: morph, MD Movie, movie-related commands

Usage: coordset model-spec frame [ holdSteady atom-spec ]

Usage: coordset model-spec [start],[end][,step] [ holdSteady atom-spec ]

** Important Note **

Usage:
coordset model-spec frame [ holdSteady atom-spec ]

Usage:
coordset model-spec [start],[end][,step] [ holdSteady atom-spec ]

Important Note