[Chimera-users] split segmented map

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 21 09:18:06 PDT 2011

Dear Gabor,
I don't know of a single step to create separate maps for all the separate segmentation regions, but below is how to do it for one region at a time.

You can use the "mask" command to extract the data within some surface, such as from segmentation. For example, if the original volume data is model #0 and you selected (Ctrl-click in graphics window) the segmentation surface of interest, the command could be something like:

mask #0 sel

... which would create a new volume model.

The mask command has several options, such as for inverting what you get or extracting a slab around the surface, see:

There is also a "segment" command with "exportmask" option to create a map in which the values are the identifiers of the segmentation regions:

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 Oct 21, 2011, at 5:04 AM, Gabor PAPAI wrote:

> Dear chimera team,
> I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that?
> Thanks in advance!
> Best regards,
> Gabor

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