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 ✉ maa32@illinois.edu <mailto:maa32@illinois.edu>  linkedin.com/in/asif1/ <http://linkedin.com/in/asif1/>
<http://illinois.edu/> Under the Illinois Freedom of Information Act any written communication to or from university employees regarding university business is a public record and may be subject to public disclosure.
