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

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 20 07:59:02 PST 2017


Hi Dieter,
The first model number in the command should be the map, and you can specify the marker by selecting it (Ctrl-click) and using “sel” as the atom specification.  So if your map is #3 and you already selected the marker, something like the following should work:

vop boxes #3 sel isize 50

<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 20, 2017, at 4:26 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> 
> 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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