[Chimera-users] segment map & mesh view

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 4 10:12:17 PDT 2015

Hi Dmitry,
The output of Segment Map is a set of segmentation surfaces or “regions", which (as you may know) are different than a density map.

If you mean just deleting a region and saving the remaining region surfaces to a segmentation file, it can be done by selecting the region(s) you want to delete (Ctrl-click, Shift-Ctrl-click on them in the main window) and using the Segment Map menu:  Regions… Delete selected, File… Save segmentation as.

However, maybe you instead mean you wanted to make a copy of the input volume (density map) where the part inside the segmentation surface is erased, values set to zero.  In that case you could select the region(s), then use Segment Map menu: Regions… Subtract selected from map.   This will create a new map, automatically open in Volume Viewer, and you can save it to a file using the Volume Viewer menu: File… Save map as.

The segmentation surfaces are triangulated, but not on the rectangular grid of the map.  Thus I don’t think it is possible to make the meshes match exactly.  However, you can change the meshing on the volume data in Volume Viewer, Features: Surface and Mesh options, see subdivision, smoothing, etc.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 4, 2015, at 7:14 AM, Dmitry <semchonok at gmail.com> wrote:
> Dear Colleagues,
> Does anybody know how to:
> 1. Delete selected segment from segment map and save the result.
> 2. Change the mesh view properties - because for the volume the mesh size is different then for the segment map.
> Sincerely,
> Dmitry

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