[chimerax-users] Density extraction

[Elaine Meng]

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 at 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