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

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 1 13:22:11 PDT 2017


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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