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

[Selenschik, Philipp]

Hi Elaine and Tom,

thanks for your patience and help! I got it now :)
What I meant by "artifacts" in my previous mail were parts of the volume that are shown due to non-ideal parameters (either radius for (surface) zone or contour level for the mask approach). 
All the best

Philipp

-----Ursprüngliche Nachricht-----
Von: Elaine Meng <meng at cgl.ucsf.edu> 
Gesendet: Montag, 18. Oktober 2021 19:15
An: pselensc at wwu.de
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] How to set the contour level correctly?

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