[Chimera-users] Visualizing trajectory

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 7 15:06:13 PST 2014

On Mar 7, 2014, at 2:46 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> (2) You can load the trajectory partly by specifying starting and ending frame, but I don't know of any way to load only every Nth frame.  You can play back only every Nth frame, but that's after every one in the specified start-end range is loaded.  As far as I know, if somebody wants to only load every Nth frame, they would have to use some other processing program or script to create a new trajectory that only contains those frames.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html>

For some formats, such as Amber, specifying a "step size" greater than 1 will skip reading intervening frames.  This isn't the case for Gromacs since Chimera uses the Gromacs "XTC Library" (XTC Library - Gromacs) to read the trajectory coordinates and that library has no facility for skipping any frames.  In fact, it will read the entire trajectory regardless of your setting for start/end frames, though only the frames in the start/end range will get translated from the raw floating-point numbers that the XTC Library returns into the atomic coordinate data used by Chimera.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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