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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Wed Dec 20 10:10:11 PST 2017


That was it! Thanks so much!

------------------------------------------------------------------------
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 20.12.2017 um 16:59 schrieb Elaine Meng:
> 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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