[chimerax-users] closest to playing animation chimer to chimerax

[Krishnan Raman]

Hi Elaine,
Thank you so much.
krish

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, September 14, 2022 2:15 PM
To: Krishnan Raman <RKrishnan at BIOCRYST.com>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] closest to playing animation chimer to chimerax

[EXTERNAL]

Hi Krishnan,
The best way (or really, only way) is to have a ChimeraX script that you execute to "play" this content.  This is also how any movie content would be developed, except you would skip the last phase which is to bracket the content with movie-recording and movie-encoding commands.  The commands are in a text file myscript.cxc and simply opening the file executes the commands.
<https://link.edgepilot.com/s/03d64d8f/i923HhY3b0ecUhimcqsDsA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html%23cxc-files>

You would probably use this script in conjunction with a saved session file that contains all the data and possibly various 2D labels to be hidden/shown at appropriate times and saved (named) views.

Although Chimera has "scenes" which include both the positions and what is displayed at the time along with colors and styles, this is not (yet) available in ChimeraX.  So although you can use "view" to restore saved positions, all the showing and hiding and changing of styles would have to be done through the respective commands (show, hide, color, transparency, style, cartoon style, etc.).

See summaries of which commands may be especially pertinent to creating images and scripting movie content:
<https://link.edgepilot.com/s/28b77f17/FTq6Qc_gHkeAZqXGmkIvBQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
<https://link.edgepilot.com/s/47a9dbe3/V88SC8f51ECrPePduEZ6ag?u=https://rbvi.ucsf.edu/chimerax/docs/user/images.html>

If you prefer to have multiple stages where you actuate each stage, a related possibility is to create an outline with text and images in HTML and add "click-to-execute" links which will work when the HTML is viewed in the ChimeraX built-in web browser.  Again all the content needs to be scripted via ChimeraX commands, so you would probably develop it as a single .cxc file first (as above) but then divide it into smaller pieces.  Then in the HTML with special execution links, you could execute command "open blah.cxc" or even individual commands (or semicolon-conjoined small sets of commands).  This mechanism is explained here:
<https://link.edgepilot.com/s/3425154f/82kvyhFJYUuON7a3DRvMzA?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html>

....and the Quick Start Guide and some of the other tutorials exemplify this approach for individual/few commands per link:
<https://link.edgepilot.com/s/3cb96199/JWCWKbQ-3UyTTUsqDEN4ag?u=https://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>
<https://link.edgepilot.com/s/db6d9351/ujNzS7UG00GiU4T9xxNZZQ?u=https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>
...etc...

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

> On Sep 14, 2022, at 11:43 AM, Krishnan Raman via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> What is best way to play a series of frames(images)with changing representation/colors, zooming in on regions of interest etc. in chimerax?
> In chimera I used to create them as individual frames and play them using the animation tool/player.
> I do not want to encode a movie as I want them to be in stereo3d to
> play them within  the chimerax . All suggestions welcome…
>
>
> Krishnan Raman
> Executive Director, Structural Biology BioCryst Pharmaceuticals
>
>
>
>
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