Hi Eric, Thank you for the feedback. Is it possible to do this workflow via a script: 1. Align structures using MatchMaker and define the reference and structures to match and select 'pairwise alignments'. 2. Extract the RMSD headers for backbone atoms of pairwise alignments to a text file 3. Save the pdb structures after alignment to a new pdb file with reference coordinates to the reference structure selected 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 ✉ maa32@illinois.edu<mailto:maa32@illinois.edu> [Outlook-uo3k2g0y.png] linkedin.com/in/asif1/<https://urldefense.com/v3/__http://linkedin.com/in/asif1/__;!!DZ3fjg!8v_Rkit...> [Outlook-signature_.png]<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.
