[Chimera-users] box cut out is not a cube!

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 19 09:09:43 PST 2017

Hi Dieter,
There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”):

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

> On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Dear all and Elaine,
>       I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
> Thanks for help, best, Dieter

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