[chimerax-users] Making a movie from a group in PDB file

[Elaine Meng]

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.html>

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 at 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