Hi Tom,

 

Thanks! While I struggle to understand the use for reading the output of cofr, I appreciate that you are keeping the needs of the majority of users in mind. I also understand that resources are probably limiting, but if it would be possible in the future, maybe there could be a toggle somewhere in the settings for “script-friendly output from reporting commands in the log”? Just to throw that idea out there.

 

I want to balance the message by saying that I really appreciate ChimeraX, it’s my main workhorse and I don’t know what I’d do without it. Thanks for keeping it running!

 

Cheers,

EP

 

From: Tom Goddard <goddard@sonic.net>
Date: Monday, 13. May 2024 at 23.11
To: Kumpula, Esa-Pekka <esa-pekka.kumpula@helsinki.fi>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Cofr command output in log

Hi EP,

 

  Putting cofr output in the log with comma's and no spaces so it could be pasted into a command script without editing would help you, but for people who want the log to be legible, probably the majority of users, it seems to make it worse.

 

  With commas

 

> cofr

Center of rotation: -9.8798,1.6928,0.0084028 front center

 

  With spaces

 

> cofr

Center of rotation: -9.8798 1.6928 0.0084028 front center

 

I'm inclined not to change it for the copy-and-paste to a script use.  Unfortunately we have to compromise to do what is best for the majority of people using ChimeraX.  The only way to customize the ChimeraX logged output is to edit the Python code.  Not sure how you envision requesting different output formats -- that does seem like a fantasy world.

 

Tom

 



On May 10, 2024, at 3:26 AM, Kumpula, Esa-Pekka via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

 

Dear ChimeraX crew,

 

A minor quality-of-life improvement request: would it be possible to have the command cofr output the values as a comma-separated list instead of a whitespace separated one? I am including cofr information reatively often in my figure preparation scripts and having NOT to always replace these when copy&pasting would be a nice improvement!

 

Also, in general, can I customize the output of commands to the log (such as view matrix, cofr, zoom, clip list) within an alias for example? In a fluffy dream world, I would have an output from these that I can directly copy&paste to my scripts and get the camera positioned Just Right.

 

Cheers,

EP

 

 

--

Esa-Pekka Kumpula, PhD

Senior Postdoctoral Researcher

Laboratory of Structural Biology

Institute of Biotechnology

Helsinki Institute of Life Science HiLIFE

University of Helsinki

 

 

 

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