In your file, each model has a different chain ID, so ChimeraX doesn’t find any residue of the second/third/etc. model to be the same as a residue of the first model, so creates one “trajectory” per model. I’ll try to improve this behavior and will update the ticket you created when I have something. My suggestion for now is to skip the combine/split steps: just guarantee the chain names are all the same after you do matchmaker (using the changechains command as needed) and then save as a multi-MODEL PDB file.

On Mar 8, 2026, at 6:56 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Ok, so I figured out how to make an aligned ensemble - matchmaker, combine then split - and I now have an aligned 100-member ensemble (pseudo-NMR-like).

However, when I try to analyze this using coordset (open ensemble.pdb coordsets true), nothing is displayed, and ChimeraX launches one instance of the coordset slider interface for each member of the ensemble! Is this the intended behavior, or am I doing something stupid?

Putting the same ensemble pdb into "old" chimera and running ensemble clustering seems to work fine, so I don't think it is an issue with the ensemble itself

Cheers
Oli

On Mar 8, 2026, at 9:20 AM, Oliver Clarke <olibclarke@gmail.com> wrote:

Looking at the daily builds, it seems like md cluster might do the trick, if the set of structures is opened as a trajectory - it is not exactly clear to me how to do that though, for a set of individual PDB files as opposed to an MD trajectory or NMR multi-model ensemble.

Also, the PDBs generated by alphafold are in arbitrary orientations. Is there a way to open, align and cluster a large set (100s) of structures in arbitrary orientations?

Cheers
Oli

On Mar 7, 2026, at 3:38 PM, Oliver Clarke <olibclarke@gmail.com> wrote:

Hi,

Are there any tools in ChimeraX suitable for clustering/analyzing conformational ensembles, e.g. as generated by AFSAMPLE2 (https://www.nature.com/articles/s42003-025-07791-9) or similar approaches?

The closest I could find was this:

https://www.rbvi.ucsf.edu/chimerax/data/simstruct-doc-oct2024/simstruct.html

The similarstructures interface looks great, but it seems like this can only analyze sets of structures generated in the tool - is there any way to use it to analyze an arbitrary set of structures?

Basically I would like a way to (for a set of say 200 input structures of the same sequence) quickly align them and then cluster them, to identify and group representative conformational states in the ensemble of predictions.

Cheers
Oli

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