Hi Oli, The ChimeraX Similar Structures capability is intended for looking at large sets (hundreds or thousands) of distant homolog structures found by FoldSeek structure-based searches. It offers clustering that uses x,y,z coordinates of specified residues (defaulting to the top several conserved residues) using UMAP. Because the intended use was with large numbers of homologs it uses both sequence alignments, and is optimized to use C-alpha coordinates provided by Foldseek instead of trying to load a thousand full structure models. In theory this could be used for your much simpler case of structures all having the same sequence. But currently there is no code to convert a trajectory into the data structures with sequence alignments and C-alpha coordinates that are currently used. It wouldn't take much code to adapt to your case. I'm not sure how useful it would be because it requires you to figure out which residues to use for clustering conformations. Using UMAP to reduce to reduce a high dimensional set of residue x,y,z coordinates to 2D was an experiment. It is not even clustering, just reducing to 2D for visualization. So I'm not sure this experimental approach designed for distant homologs is the best for your case where I guess many clustering algorithms have been developed. Tom
On Mar 7, 2026, at 12:38 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> 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 _______________________________________________ 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/