The “interModel false” option is a great suggestion. Thanks a lot! Perhaps that should be false by default?

Regards,

Daniel

From: Eric Pettersen <pett@cgl.ucsf.edu>
Reply to: <chimerax-users@cgl.ucsf.edu>
Date: Friday, 22 August 2025 at 18:24
To: Daniel Larsson <daniel.larsson@icm.uu.se>
Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] aborting slow hbonds command

Hi Daniel,

There isn't any way to stop an ongoing command that I know of (other than killing ChimeraX).  I also don't have any great advice for the situation where you've mistyped atom-spec2.  However, if you want to only look for H-bonds within atom-spec1's model and not to other models, then add the argument "interModel false" (which can be shortened to "interm f").  If you do this frequently, you might want to make an alias for that version of the command.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Aug 22, 2025, at 7:08 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Is it possible to prematurely stop a command issued on the command line that takes too long time?

I often have sessions with many (more than 20) large ribosome structures open at the same time. I sometimes mistype the restrict atom-spec2 argument for the hbonds command and ChimeraX goes through each of the structures one by one twice, which can take very long time.

I wish there were a flag to the hbonds command to only consider the models in atom-spec1, so that those typos does not spawn a search across all models.

In addition, it would be great if the code for the hbonds command could be optimized. Why iterate over all models if only atoms in one model are in atom-spec1?

Regards,

Daniel

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