[Chimera-users] detergent subtraction

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 16 09:28:19 PDT 2020

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

- 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

- semiautomated segmentation approaches to segment out only the part(s) you want

If you don't have atoms fitted:

- Volume Eraser for you to do it "manually"

There are also several kinds of map filtering that may also be relevant, see Volume Filter (or "vop" commands):

I hope this helps,
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

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