Best Regards,

M. Asif Ali (He/Him/His)

PhD Bioinformatics: Crop Sciences

University of Illinois Urbana-Champaign

Researcher @ GCA Lab | NSRC

Teaching Assistant | HORT 105

✉ maa32@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.

Hi Asif,

Sorry, still not possible. The sequence viewer is another tool where the functionality is completely intertwined with the GUI code. There is a reason we started over from scratch with ChimeraX! With great difficulty you could possibly eventually get this to work with a script that ran while the GUI was showing. This really would be a lot simpler in ChimeraX. In ChimeraX the pseudocode for you script would be:

foreach pair of PDB files:

open first PDB

open second PDB

matchmaker #1 to #2 showAlignment true (in nogui mode "showAlignment" is somewhat of a misnomer -- it creates the alignment but does not attempt to show it)

sequence header rmsd save filename

close

If you still want to try to get this to work in Chimera rather than ChimeraX, the Chimera Programmer's Guide is here.

--Eric

On Dec 19, 2025, at 12:29 PM, Ali, Asif via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Eric,

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

Align structures using MatchMaker and define the reference and structures to match and select 'pairwise alignments'.

Extract the RMSD headers for backbone atoms of pairwise alignments to a text file

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

<Outlook-uo3k2g0y.png> linkedin.com/in/asif1/

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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.

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