[chimerax-users] Scripting Resources

[Elaine Meng]

Hello Lauren,
This is a partial answer:  you could consider ChimeraX command scripts or python scripts.

For ChimeraX command scripts at least, there is complete documentation of syntax and options for nearly every command:

<http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>

Also, there are several tutorials with commands shown, and most of the “feature highlights” and “example images” on the ChimeraX website link to the respective .cxc files (ChimeraX command files) used to set up the images.

<http://www.rbvi.ucsf.edu/chimerax/tutorials.html>
<http://www.rbvi.ucsf.edu/chimerax/features.html>
<http://www.rbvi.ucsf.edu/chimerax/gallery.html>

Further, using many of the GUIs or icons to perform actions shows the corresponding command in the Log to facilitate learning the commands.  As time goes by we will have more examples, more highlights, and more tutorials. 

On the python side, I know we plan to have APIs available, but as resources are limited I can’t give much details or a timeline.

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

> On Jan 21, 2020, at 12:39 PM, llehmann at uoregon.edu wrote:
> 
> Hello,
> 
> I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time.
> 
> Best,
> 
> Lauren Lehmann
> 
> Biochemistry Graduate Student
> University of Oregon
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