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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Wed Dec 20 02:19:42 PST 2017

Hi Elaine,

     thank you for the hint! I believe that is what I needed!

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 19.12.2017 um 18:09 schrieb Elaine Meng:
> Hi Dieter,
> There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”):
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
> I hope this helps,
> Elaine
> -----
> 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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