HI Vincent, Other than technical questions about how to do something in ChimeraX, many details are individual research project decisions that you have to make for yourself in consultation with your adviser, and also based on the knowledge of your specific proteins and what you plan to do with the results. There's no single ultimate correct best way to do something (i.e. no ideal recipe I can give you) because it will always depend on the specifics of the project. We try to make the default values reasonable for most situations. Yes, you can superimpose protein chains with Matchmaker. Since I have no idea what "minor issues" means you will first have to figure out what that means, and then see if there are ways to resolve them. I.e., you could try changing parameter values in Matchmaker, or instead using "align" to specify exactly which atoms to superimpose. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 12, 2026, at 9:40 AM, Hsueh, Vincent via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Good morning UCSF ChimeraX Support Team,

My name is Vincent Hsueh and I'm a P1 Pharmacy Student at Champan University.

I'm a new member to the lab and it seems no one, currently with the lab, has prior experience to using ChimeraX. So far, I have isolated the Human ACE hAChE (PDB: 3LII) in the .csx file attached to the email.

My PI gave me the task to superimpose to proteins, Human AChE (PDB: 3LII) colored in Beige and hTg ChEL (PDB 6SCJ) colored in Gold, but I'm having issues learning how to do it on my own. I'm trying to isolate Chain #B from PDB: 3LII with PDB: 6SCJ to see which part of 6SCJ is adjacent to 3LII prior to isolating both chains.

I tried reading the ChimeraX user guide, and created the attached "in-progress(super-imposed)_final.csx file, but I'm still not sure how to do it properly.

So far, I've opened my isolated PDB: 3LII model in ChimeraX, opened the PDB: 6SCJ file, used the matchmaker command, highlighted the corresponding sequences in SequenceViewer, but my PI has told me that the resulting model still has minor issues.

Hopefully, I can gain some guidance in this effort to learn ChimeraX on my own, for my lab, and for future lab members!

Vincent Hsueh PharmD Candidate Class of 2028 Chapman University School of Pharmacy vhsueh@chapman.edu

<Screenshot 2026-01-07 at 12.53.25 PM.png><in-progress(super-imposed)_final.cxs><Human ACE hAChE (PDB 3LII_highlighted_completed.cxs>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/