Hi Dmitry, I don't know how you plan to figure out which part is for one subunit if you don't have a structure. Some vague ideas are: (1) segmentation, e.g. see "Segment Map" <https://www.rbvi.ucsf.edu/chimerax/docs/index.html> (2) if you can picture the part that you want, manual erasing, e.g. see "Map Eraser" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html> (3) create a surface that includes the part you want, e.g. some geometric shape with the "shape" command, and then use that surface in "volume mask" <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> You could also try fitting a homologous structure (if any is available), or get an AlphaFold prediction for your structure and fit that, then limit the density to what is surrounding the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 9, 2022, at 1:15 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I have a 3D map of the helix.

1. Do you know how can I extract 1 subunit?

2. Also, if there is no x-ray structure available.

Thanks in advance.

Kind regards, Dmitry