If you need a quick workaround right now, and you aren't dealing with models linked to EM maps - or 100s of models per sequence, then I'd suggest trying out Jalview for this, since it handles 1 sequence -> many models naturally. The workflow we've found useful is to create sequence features in Jalview, open the linked models for each sequence in ChimeraX, and use the Jalview ChimeraX dropdown menu to write the features to ChimeraX as attributes. You can then construct expressions to select those regions from the ChimeraX command line.

Dear ChimeraX team,

Two selection-related questions:

I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection.

Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections.

Cheers,

Esa-Pekka Kumpula, PhD

Senior Postdoctoral Researcher

Laboratory of Structural Biology

Institute of Biotechnology

Helsinki Institute of Life Science HiLIFE

University of Helsinki