Hi Nick, If you are referring to the Matchmaker tool, or to the matchmaker command, or to the align command, the is deterministic and gives the same result for the same input... there is no random number involved, nor does it depend on the starting position. <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> If any result is different we would expect it to be because some input parameter and/or the input structure is different. All I can say is to make sure you are really using exactly the same set of parameters. Note that if you change values manually in some dialog, some of the settings are "sticky" and may remain changed in a future session even though you didn't change them manually again. When you use the Matchmaker tool it shows the command in the Log. So it you get two different results, take a careful look at the two commands that generated them. If you can provide an example where you got a different result from exactly the same input, please use menu: Help... Report a Bug and include any description needed to reproduce the problem, including attaching a session or some data, and your email address if you want feedback on it. 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 Nov 4, 2024, at 10:15 AM, Christman, Nick via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

My name is Nick Christman and I am a microbiology PhD student at Indiana University. I am using ChimeraX to visualize and compare some small proteins (minor pilins) and it has been working great. I have run into an issue that I am hoping you can help me resolve. I want to use the match function to compare various different minor pilins. Each minor pilin has a somewhat unique structure, and I am trying to make the case that certain minor pilins from one organism are homologous to other minor pilins from a different organism. I have noticed that the match function provides different results from session to session. This concerns me and makes me question how much I can trust the results provided by chimeraX. Along with different spatial matching, the calculated RMSD values differ greatly. Is there a way I can make these matches more consistent? Like dictating a set starting point for matching?

Thanks for your time!

Nick Christman (He/Him) Dalia Lab Indiana University