Hi Dmitry, just for the records of the mailing list (as somebody have the same issue): Load map and model. Test your selection (this step is not needed, but helps if the selection includes multiple parts) # hide all atoms hide atoms # show your selection. The model is #2, you want to only select chlorophyll from chain A show #2/A:BCL This should display just your molecule/residue/ligand of interest. For the selection syntax: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html Now create a new map, just from your molecule volume zone #1 nearAtoms #2/A:BCL newMap true One can include also the range parameter (default 3.0), e.g. if the molecule placement is a bit unsure and you want to refine it in there. Now, just save the new map by save mapZone.mrc #3 If you try multiple volume zones, you might need to correct the id. Best Christian

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"Dmitry A. Semchonok via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> 02/08/22 12:42 PM >>> Dear colleagues,

I have a cryo-em map and a model. I would like to extract some the cryo-em density around certain fitted model. For example I have Chl molecule fitted into the correspondent cryo-em density. And I want to extract this certain Chl only out of the whole structure. How can I do that? Kind regards, Dmitry Sent from Mail for Windows _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users