Hi Zack, I agree that something along those lines would be very useful, and we’ve been working to make all ChimeraX actions (even with the menu or by clicking icons) show up in the Log as commands.
It’s not exactly what you suggest, but you can show the Command History with up to N (user-specified, default 500) commands and save all or part to a cxc file. It may list the “typed commands only” but it remembers the other ones too, e.g. from clicking icons, and you can switch between showing typed-only or all commands using the context menu in the Command History.
http://rbvi.ucsf.edu/chimerax/docs/user/tools/cli.html http://rbvi.ucsf.edu/chimerax/docs/user/tools/cli.html#history
You can also save the Log itself as HTML. If you first use its context menu to make the command links executable, then save HTML (also from context menu), then reopen the HTML file in ChimeraX, clicking the links will re-execute the commands. http://rbvi.ucsf.edu/chimerax/docs/user/tools/log.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 1, 2019, at 7:20 PM, Zack Gainsforth zackg@berkeley.edu wrote:
Hi,
I am finding that saving my visualization as a cxc (scripting command) file leads to good reproducibility. Often, when I save a session (cxs) file, it doesn’t open again later (I think because directory path names change), but if I produce the visualization by coding a cxc file instead, then it hasn’t failed (yet!).
In addition, I want to keep track of actions such as median filters, and filter parameters, pixel scaling, all that jazz. When I code this into a cxc file, all that info is in the code record. When I save a session file I often cannot find that information again later (was it a gaussian filter? median? What do I write in the paper!?)
I would suggest a feature to save a cxc file or output a journal of all changes for a cxs file so I can see what I did at least for documentation/reproducability later.
Cheers,
Zack _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users