Hi Pranav, The Place Object Chimera plugin places STL models (surfaces) at particles positions in a tomogram that were used for subtomogram averaging. You probably don't want to mask the tomogram to those surfaces since the nearby density is also important. If you did this subtomogram averaging then you should already have the extract density for each particle. The Chimera "vop boxes" command can extract a box from the tomogram around markers, but you would need to place a marker where each of these STL surface is. Tom

On Mar 17, 2022, at 9:05 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Pranav, Sorry, I have not used that plugin and don't know the answer to your question. Maybe you could ask somebody in the Briggs group?

Maps can be simulated from atoms (see command "molmap"), and parts of an original map that are inside a surface model can be extracted (see command "mask") but perhaps neither of those apply in the case of objects created by the plugin.

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Mar 17, 2022, at 4:58 AM, Pranav Shah via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Elaine, Is it possible to convert object instances generated by the Place Objects plugin developed by the Briggs group into mrc maps? Best, Pranav

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