[Chimera-users] unit for the diameter of the erase sphere

[Elaine Meng]

Hi Dieter,
Hmmmmmm, good question!  Two ideas below… I’m not the primary expert on maps, however, so there may be a better answer:

(1) duplicate original map (volume viewer File menu).  In one copy, limit display to the box, show box-map at lowest contour to display it as a rectangular-box surface, use “mask” command to mask the full map by the box-map surface with “invert true” to zero inside the surface instead of outside:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>   

I tried this and it seemed to work, but it was hard to see exactly the shape of the hole.

(2) duplicate original map. In one copy, limit display to the box, save box region to file (volume viewer File menu), open the file, and use “vop subtract” to subtract the box-map from the original map.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

If I find a better answer, will let you know.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 2, 2017, at 11:31 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> 
> Hi Elaine,
> 
>   thank you! May I ask one more question: How can I erase a box from a density map? I have tried 'Box' from within Volume Viewer. I can cut out the density within this box but I cannot erase this density so that the original map has a cubic hole?
> 
> Dieter
>