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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Wed Dec 20 04:26:50 PST 2017

Hi Elaine,

    sorry, but I still do not understand the syntax. I am trying to make 
a box around marker 1 within marker set 1. I tried

"vop boxes #1 marker 1 isize 50" but this does not work. I have to give 
an atom definition of one of the markers in marker set #1. If I mouse 
over it it tells the name: "#1 marker 1" whereas its name in ModelPanel 
is "marker set 1". How do I translate this in an "atom specification"? 
Furthermore, it does not recognize "isize" but this might be due to an 
error earlier in the command!

Can you please give me an example of the command!

Thanks again, best wishes, 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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