[Chimera-users] put outline box at the center of a marker

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 1 13:40:39 PDT 2017

Hi Dieter,
A marker is just a fake atom, so you can select the marker (Ctrl-click it) and use that atom box feature… at least, it worked when I tried it just now!

> On Aug 1, 2017, at 1:36 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Hi Elaine,
>  thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker.
> 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 01.08.2017 um 22:22 schrieb Elaine Meng:
>> Hi Dieter,
>> If you already had a larger map (or create one from scratch with “vop new” or from atoms/markers with “molmap"), you could use the Volume Viewer menu Features… Atom Box to crop out a box centered on a selected atom or marker.  Then use Volume Viewer menu Features… Data display options, "show outline box..." on the cropped data set.  You can move the slider so that no isosurface is shown for the map.  However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume.  I’m also not certain about whether the box would be EXACTLY centered on the marker… it might be slightly off due to rounding and grid-spacing of the original map.
>> If the original map is not in the right place, you can use the “A”ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately.
>> Maybe this is too many steps to be convenient, however.
>> vop new
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>
>> Volume Viewer, Features menu
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features>
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Aug 1, 2017, at 12:46 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
>>> Hi,
>>>    I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible?
>>> Thanks a lot for help, best, Dieter

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