[chimerax-users] Feature request: save cxc

[Zack Gainsforth]

Hi Elaine, Eric,

Thank you for your response on this.  I’ll look into the command history and log a little deeper — that seems like it could be very useful to me. 

I’ll keep an eye out for the improvement tickets.

Thanks,

Zack

> On Apr 2, 2019, at 1:24 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Zack,
> 	In addition to what Elaine says, we want to make the log contents save/restore with sessions (previous contents hidden under dated disclosure triangles, to make it easier to see what was done when).  Once that is implemented, then we would want to make it possible to save commands directly from the log — saving from the Command History works, but those commands are a mishmash of all the sessions you’ve worked on whereas the commands in the log are specific to the current session.
> 	I will open some feature-request tickets in our issue-tracking database and put you on them, so you will get notified when they get implemented (it will be awhile in all likelihood).
> 
> —Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Apr 2, 2019, at 8:52 AM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> 
>> 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>>
>> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/cli.html#history <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 <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 at berkeley.edu <mailto:zackg at 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
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>> 
>> 
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