Hi Abhi, The ChimeraX "volume zone" command will do this. For example, open 8orh open 17125 from emdb volume zone #2 near #1 minimalBounds true save asym_unit.mrc model #2 open asym_unit.mrc Here we open a PDB of the asymmetric unit for an EMDB map, then show the map just near the atomic model and use the "minimalBounds true" option so it crops the map bounds to contain that asymmetric unit. Then save that cropped part of the map to a new MRC file. The volume zone command will show just the map surface near atomic model, but the saved map will contain the full cropped box of map data and will preserve alignment with the original map. Tom 
On Apr 23, 2024, at 1:57 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density.
Thanks in advance for any guidance. Abhi _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
