On Jul 16, 2019, at 9:55 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

2) the second issue that it seems that the smooth-md script does not
work properly with chimera-X (in the script, I tried to increase
number of frames to be smoothed up to 8, but eventually on the video
it looked without smoothed effect like it was in the case of Chimera,
shown on my previous video :-)

The issue really is that the MD player from the toolshed is using its own cached (original, unsmoothed) set of coordinates, so the smoothing is lost. You need to stop using the MD player and just play through the coordinates using the ‘coordset’ command.