[Chimera-users] excluded bilayer in chimera

[Yanhe Zhao]

Hi Elaine,

Sorry for my delay as I was trying the ways you described above. Thanks a
lot for that.
I have another question as below:
How can I have color gradient along the map dimensions? For example along X.

Thanks and best,
Yanhe

Elaine Meng <meng at cgl.ucsf.edu> 于2021年5月17日周一 下午3:14写道：

> 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:
>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html
> >
>
> 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.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html
> >
>
> 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
> -----
> 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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