[Chimera-users] detergent subtraction

[Daniel Asarnow]

Dmitry,
I assume you are working in EM. You may find it easier to use "reverse" or
"double" subtraction. Basically, create a mask using a higher iso-value
that captures the protein only. Then subtract the contents of this mask
from the original map in Chimera, or use it to subtract the protein from
your particle images and then calculate a reconstruction, which will
contain the micelle only.

Best,
-da

On Thu, Jul 16, 2020 at 9:30 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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