Excluding particles similar to an input volume

I am currently processing a dataset that contains a multi-protein complex in various stages of assembly; I am only interested in one of the stages. There is already a published structure of one of the later stages of assembly on PDB. If I were to import the corresponding map from EMDB, would there be a way to exclude any particles similar to that volume?

indirectly, use it as reference in heterogeneous refinement along with the other models and then select only particles which are not classified into that class. I don’t know of a way to not pick those particles, for instance.

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Another way is to use supervised 3D classification. If you have (low res) maps of your protein complex of interest, use that to classify against the map from EMDB. If you don’t have maps you could try using a LP filtered version of the map from the EMDB versus the map of the EMDB, or just a sphere vs the map of the EMDB. See what works best for you.

Good luck!