Fwd: Tools for clustering conformational ensembles?

[olibclarke@…]

Attachment available until Apr 7, 2026
Hi,

I tried to submit the below as a bug report but the bug report server was unavailable:

Trying to analyze the attached ensemble with `coordest slider` or `open ensemble.pdb coordsets true` leads to unexpected results.

In the former case, it launches 100 copies of the coordset slider UI, with one frame per copy. In the latter case, only 51 of the 100 frames are shown in the model panel, the log says that 150 structures are loaded, and the slider UI does not seem to work as indicated in the docs. Am I doing something wrong? I have attached the input ensemble in case it is helpful.

Cheers
Oli

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21.8 MB

> Begin forwarded message:
> 
> From: Oliver Clarke <olibclarke@gmail.com>
> Subject: Re: Tools for clustering conformational ensembles?
> Date: March 8, 2026 at 9:56:49 AM EDT
> To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
> 
> 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
>> 
>