[Chimera-users] How to set the contour level correctly?

[Elaine Meng]

Hi Philipp,
The "mask" command just masks the first map by a surface (not caring that the surface is for another map), so yes, it does depend exactly on that contour surface.  Using some specific sigma may not be that meaningful, instead you may want to contour the molmap far enough away from the helix to include whatever density from the first map that you think should be included. I don't know what you mean by "artifacts."

"mask" command
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

As I understand it, zoning is not for editing the data so much as for visualization; it just hides the density rather than deleting it.  For deleting/zeroing density see masking, cropping, and/or volume eraser.

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




> On Oct 18, 2021, at 6:14 AM, Philip via Chimera-users <chimera-users at 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 at cgl.ucsf.edu> 
> Gesendet: Samstag, 16. Oktober 2021 17:50
> An: Selenschik, Philipp <pselensc at uni-muenster.de>
> Cc: chimera-users at cgl.ucsf.edu List <chimera-users at 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
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>