Hi Aleks, You can specify that a multi-model PDB file is a trajectory (time series) when you open it. In ChimeraX you can use the command "open" with the option "coordset true", e.g. open ~/Desktop/1plx.pdb coordset true Then there will be playback slider GUI, and/or you can use the separate command "coordset" to play it back (e.g. within a movie command script). See ChimeraX trajectories help, and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> In Chimera, instead of just using the command open or menu File...Open, you would open the file using the MD Movie tool. menu: Tools... MD/Ensemble Analysis... MD Movie, specify format PDB, frames in single file, the file name/location, etc. See Chimera MD Movie help: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 19, 2023, at 3:19 PM, Aleksandar Donev via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I am trying to create a simple animation of a demo molecular dynamics program
https://github.com/stochasticHydroTools/DemoMD
using either chimerax or chimera. The code creates a .pdb file that has multiple time frames in it, which show up in chimerax as a "group". How do I make chimera show the frames one by one and then make a movie out of that or save each frame as an image? I used to be able to do that in chimera but either the interface has changed or I have forgotten. I found lots of instructions about how to make movies by manipulating one data set (say rotating a molecule) but could not find anything about animation in time. Thanks, Aleks