Dear Elaine,

Thank you very much for the variety of solutions.

I believe you solved my issue!

I am sure that (1) will work best for my project!

Thanks again.

Kind regards,

Dmitry

From: Elaine Meng
Sent: Wednesday, November 9, 2022 7:05 PM
To: Dmitry Semchonok
Cc: ChimeraX Users Help
Subject: Re: [chimerax-users] Density extraction

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