[chimerax-users] [Chimera-users] Utilizing Chimera in Web-Based Workflows

[Tom Goddard]

Hi Rafi,

  You could have a Google Colab notebook install ChimeraX and then you could run ChimeraX command in nogui mode or python code through the ChimeraX REST facility, and possibly save images of the graphics to show in the notebook.  But I don’t grasp the value of it since ChimeraX is all about interactive visualization where you can rotate and inspect structures.  One issue you will face is that ChimeraX cannot be installed without agreeing to a license when dowloading - not sure how you might handle that in a notebook.  But I suggest figuring out the valuable use case first.

   Tom

> On Apr 21, 2023, at 5:28 AM, Zach Pearson via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Rafi, 
> 
> We are working hard to fully deprecate Chimera, and haven’t made its source code accessible for use or extension outside of the desktop application. I would caution against looking for it; the compilation process is complex and depends on resources that may not even be available anymore. Chimera was also written in Python 2.7, a language the computing community is working hard to put to rest — Colab doesn’t support it anymore! 
> 
> We do have plans to release a substantial part of ChimeraX on PyPi this year as a public beta, and I’ll make a note to send you an email when that release happens. Then you should be able to use it in Colab like any other PyPi package. Let me know if I can answer any other questions you may have.
> 
> -------------------
> Zach Pearson
> Programmer, ChimeraX Team
> UCSF RBVI
> zjp at cgl.ucsf.edu
> 
> 
> 
>> On Apr 20, 2023, at 13:44, Rafi Brent via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> To whom it may concern,
>>     I'm wondering if there's any way to access Chimera without having the GUI downloaded on a local computer. Specifically, I'd like to run chimera as part of a public Google Colab (.ipynb) notebook, which would allow users to access the chimera functionality through either installing a PyPi package or calls to a web-accessible API. Do you know of any tool like this, or have any other ideas for how Chimera could be used in Colab notebook? Thanks so much for any advice you may have.
>> 
>> Sincerely,
>> Rafi Brent
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