[Chimera-users] Putting MD trajectory in Animation

[Ali Raza Azeemi]

Hi Elaine,
issue resolved. Thanks a lot dear. I have no words to thank you.

On Thu, Apr 14, 2022 at 10:59 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
>
> 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:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#recording
> >
>
> 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:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.html
> >
>
> 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:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 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.
>
>

-- 
*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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