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

[Elaine Meng]

Hi Dieter,
I believe that the box is already drawn along the same axes as the original map, so it's automatically in the same orientation.  You can save the region with the “volume” command, specifying the region bounds and any other file-saving options you might want:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>

The region bounds are shown in the VV dialog as described below.

Yes, if you just have one atom or marker selected, it would make the padding value the side-length of the cube centered on that point. If your data is in Angstroms (e.g. not nanometers) the size will be in those units. However, there is still the caveat of it not being exactly centered, depending on the grid size of the original map and the position of the marker.  If I choose padding 2 or some other small size relative to the spacing, I can see that the marker isn’t  exactly in the center or the box isn’t exactly a cube.

You can check region bounds (VV menu Features… Region bounds) to see if it’s really a cube and even change the values to make it so, but that might put the point farther from the center.

You can go back to the full-sized original map  with VV menu Features… Subregion selection, clicking the “Full” button.
Best,
Elaine

> On Aug 1, 2017, at 1:47 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> 
> Hi Elaine,
>    yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume?
> best, Dieter