Hi Eric,

Thank you for the feedback. Is it possible to do this workflow via a script:


I am trying to automate a workflow as much as possible and I have only ever used the GUI but it has gotten difficult to do with numerous structures open in one session. Additionally, could you point me to resources where I can find example scripts and run examples (helper code).

Thanks again!

Best,
Asif
From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Friday, December 19, 2025 1:28 PM
To: Ali, Asif <maa32@illinois.edu>
Cc: Chimera BB <chimera-users@cgl.ucsf.edu>
Subject: Re: Chimera Scripting Query
 
Hi Ali,
You might be able to make a non-GUI script using MatchMaker's match() function.  However, the Match→Align functionality is completely intertwined with its GUI and there is no way to access it in a non-GUI fashion.
ChimeraX does a much better job of separating functionality so that it is available both to scripting and the GUI, but Match→Align hasn't been implemented in ChimeraX (yet).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Dec 19, 2025, at 9:52 AM, Ali, Asif <maa32@illinois.edu> wrote:

Hi Eric,

I wanted to script running MatchMaker and MatchAlign on pdb structures in a directory and extract RMSD headers without having to use the GUI application?

Thank you for your time.


Best Regards,

Mr. Asif Ali (He/Him/His)
PhD Student, Bioinformatics: Crop Sciences
University of Illinois Urbana-Champaign
Researcher @ GCA Lab | NSRC
Teaching Assistant | HORT 105

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