Hi Philipp,

  I suggest just using surface zone to show density around a helix.  An example of how to do that in ChimeraX is in the "Inspecting side chain density" section of this tutorial

https://www.rbvi.ucsf.edu/chimerax/data/stanford-jul2019/tutorial.html

Chimera has the same capabilities and is the predecessor of ChimeraX.  Commands are similar but not identical.

  Surface zone just hides the surface beyond the specified distance from the atoms.  The surface will look cutoff in some places where it extends beyond that distance.  That is a good thing so a person can see the density is cutoff.  Masking disguises those cuts by capping the cutoff density and is misleading, so I don't recommend it.

Tom



On Oct 18, 2021, at 6:14 AM, Philip via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Elaine,

thanks for suggesting the mask option!
For the latter, I use the estimated 0.143 cutoff FSC resolution of the density map (2.5 Å) to create a molmap of the helix:
molmap #1 2.5
and then use that map to mask the electron density:
mask #0 #1.1
However, the masked volume seems to depend on the contour level of the (intermediate) molmap.  I've set it to 3 σ, just like for the original density map.
Concerning the "zone" function, I think that although the contour level is not directly affected by the zone radius, the density is still clipped below a certain threshold.
I wonder which approach (zone or mask) leads to least artifacts when extracting the original density? I haven't tried "Segger" yet.

Best wishes

Philipp


-----Ursprüngliche Nachricht-----
Von: Elaine Meng <meng@cgl.ucsf.edu>
Gesendet: Samstag, 16. Oktober 2021 17:50
An: Selenschik, Philipp <pselensc@uni-muenster.de>
Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>
Betreff: Re: [Chimera-users] How to set the contour level correctly?

Hi Philipp,
The zone radius is independent of the contour level.  Think of it in two stages: first the contour level is applied, and then all the stuff beyond the zone radius is hidden.  If you want to mask the map by the contour surface, see the "mask" command instead.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

The sdLevel and rmsLevel options are in the help link below.  If either one fits your definition of sigma, then using the option with 3 would give contour at 3 sigma.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>

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




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