I am interested in plotting RMSD values vs time from molecular dynamics. Is there a way to extract the RMSD values from a the RMSD map in the analysis tool of MD movie. Or maybe exists another way to do this with Chimera.
Hi Luis,
Chimera cannot do a linear plot of RMSD values, though it's certainly something I'd like to add to MD Movie's plotting capabilities when I have time.
You can very easily extract the RMSD values from the RMSD map. Just use the "Save RMSDs" button at the bottom of the map dialog to save the values to a file.