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

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