[Chimera-users] MD simulation movie in chimeraX

[Elaine Meng]

Hello!
For ChimeraX questions you may want to use the other address,  chimerax-users at cgl.ucsf.edu CC'd here.

You can see what formats ChimeraX reads by using command "open formats," or view this User Guide page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>

ChimeraX can read .trr trajectory coordinates, but it cannot read .tpr trajectory topology.  If your MD program can output a single PDB snapshot you can use that for the topology.  First you would open the PDB file.  Then to open the .trr file you would need to use the "open" command and also specify the already-open PDB file with the "structureModel" option.  For example, if you open the PDB file as model #1, then something like:

open myfile.trr structureModel #1

See details and more examples:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>
 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#structureModel>

When you open the trajectory in ChimeraX, I believe that a playback slider will automatically appear.  However, if it does not you can use "coordset slider" to show it.  The "coordset" command can also be used to play the trajectory frames directly (not using the interactive slider):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 Nov 8, 2022, at 6:17 PM, Shivam Gupta via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello Support Team,
> 
> I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much.
> 
> Please help me out by guiding me to generate MD movies.
> Please reply to this email inline.
> 
> I am Looking forward to hearing from you.
> Thanks
> 
> -- 
> With Regards
> Gupta　Shivam グプタ　シヴァム
> E-mail: shivam-gupta at pharmafoods.co.jp
> Biomedical Department
> Pharma Foods International, Kyoto Japan
> 株式会社ファーマフーズ
> 〒615-8245　京都市西京区御陵大原1-49
> TEL:075-748-9811
> FAX:075-948-9818
> URL: http://www.pharmafoods.co.jp/