[Chimera-users] excluded bilayer in chimera

Elaine Meng meng at cgl.ucsf.edu
Mon May 17 13:14:08 PDT 2021

Hi Yanhe,
I guess you mean you have no atomic structure fitted inside, only the map?  Zones are defined using atomic coordinates.

However, without any atoms, you can interactively  (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see:


It is in the menu, Tools... Volume Data... Volume Eraser. 

Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger.  

This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu:  Regions... Hide)  

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 17, 2021, at 1:00 PM, Yanhe Zhao <yanhezhao1990 at gmail.com> wrote:
> To whom may concern,
> This is Yanhe Zhao, from UT Southwestern Medical Center.
> I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information.
> Thanks a lot in advance for any input. 
> Best regards,
> Yanhe

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