[Chimera-users] Putting MD trajectory in Animation

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 14 10:58:59 PDT 2022

Hi Ali,
First you need to already have the MD trajectory (previously calculated) open in Chimera.  If you use some other program like AMBER, GROMOS, etc. to calculate the trajectory, these can produce output files.  You can open the output MD trajectory files using the MD Movie tool (Chimera menu: Tools... MD/Ensemble Analysis... MD Movie).

See MD Movie help including what kinds of files it can read:

Or, you might have used the Morph Conformation in Chimera to calculate the trajectory, and in that case it will automatically be shown using the MD Movie tool.

After you have the trajectory shown in MD Movie, you  can choose from the MD Movie tool's menu:  File... Record Movie:

Or maybe you want to make a long animation where the MD is only a part -- other things may happen before and after -- in that case, if you are using the Animation tool, just use the MD Movie tool to go to the frame where you want to start showing the MD, create a scene (plus sign "+" in Scenes area of Animation), then use the MD Movie tool to go to the frame where you want to end showing the MD, create another scene.  Then you can drag these two scenes to the timeline in the bottom section of the Animation tool.  When you play back the animation using the play button over the timeline, it will play all the MD frames between those starting and ending ones.  See Animation help:

Finally all of the above describes using GUIs.  Alternatively you could make your movie using command scripts only, where the "movie" command does the recording, and the "coordset" command plays the MD trajectory, and you could have lots of other commands for coloring, showing/hiding, rotation etc.    See "making movies" help and links therein:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 14, 2022, at 2:41 AM, Ali Raza Azeemi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi,
> hope you are doing well? dear, we have a question about making an animation/movie in chimera.  I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you
> --
> Ali Raza Siddiqui
> Jr. Research Fellow
> Computer-Aided Drug Design (CAAD) unit. P-133, PCMD
> H.E.J. Research Institute of Chemistry 
> International Center for Chemical & Biological Sciences
> University of Karachi, 75270 Karachi- Pakistan.

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