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
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