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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Mon Oct 2 14:46:11 PDT 2017

Hi Elaine,

    thanks very much for the hints! At first sight, it seems that (2) 
worked for me! I put a marker, selected it and used "Box around selected 
atoms with padding 40", which cuts out a box of, I suppose, 80 A. I 
saved the boxed density, re-opened it and subtracted it from the 
original map. The result is a map with a rectangular hole!

I also tried (1) but do not understand the syntax and/or where to enter 
"invert true"! I cannot find it in the GUI. There is only "Zone" "No 
Zone" and "Mask". Do I have to enter it in the command line?

Best, Dieter

Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: dieter.blaas at meduniwien.ac.at

Am 02.10.2017 um 23:19 schrieb 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

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