[Chimera-users] detergent subtraction

[Elaine Meng]

Hi Dmitry,
There are related tools but they all require your input/judgement, rather than identifying the detergent shell automatically.

If you already have atoms fitted into the remainder, a few possible different ways:

- use Color Zone (split map button) to get a new map retaining only the parts close to the atoms
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

- show surface for atoms, e.g. molecular surface (or surface of map derived from atoms with "molmap") and then "mask" the original map by that surface
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

- semiautomated segmentation approaches to segment out only the part(s) you want
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>

If you don't have atoms fitted:

- Volume Eraser for you to do it "manually"
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>

There are also several kinds of map filtering that may also be relevant, see Volume Filter (or "vop" commands):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html>

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

> On Jul 16, 2020, at 1:30 AM, Dmitry A. Semchonok <semchonok at gmail.com> wrote:
> 
> Dear colleagues,
> 
> Is there a way to subtract the detergent shell from the cryo-em map in chimera?
> 
> Thank you
> 
> Sincerely,
> Dmitry