Dear colleagues, Fast questions. 1. How to segment the selected segment? So I have a) segmented the map using the segment map tool b) selected 1 piece. b) I want to segment that selected piece on the smaller parts 2. how to increase the threshold of the segmented map? Thank you Kind regards, Dmitry
Hi Dmitry, You select the segmented region you want to split by ctrl-click on it. Then you press the Ungroup button in the Segment Map (aka Segger) panel. If it does not split it and the log says "Ungrouped to 0 regions" then that is the finest granularity Segger computed. The algorithm finds a segment for each local maximum of the smoothed map, so the region probably had just one local maximum. If you want to split you could try segmenting with different smoothing or grouping options. There are examples using Segger and a paper from its author Greg Pintilie if you want to learn more about how it works. https://people.csail.mit.edu/gdp/segger/docs_segmenting.html Tom
On Mar 17, 2022, at 1:24 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Fast questions.
1. How to segment the selected segment?
So I have a) segmented the map using the segment map tool b) selected 1 piece. b) I want to segment that selected piece on the smaller parts
2. how to increase the threshold of the segmented map?
Thank you
Kind regards, Dmitry
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Hi Dmitry, For your question part 2, the blobs you get from segmentation are only surfaces (not maps), so you can't adjust the threshold level on those. If you look in the Model Panel (and in Volume Viewer) you will still have your original map. You could adjust the threshold on your original map before creating the segmentations. Or if you mean you want to get just the map region inside a specific segmentation surface (after which you can adjust its threshold), you could select the surface and use Segment Map menu: File... Save selected regions to mrc file. Then you can open the newly saved mrc file, change its threshold, etc. There is a menu option to extract densities directly to create a new map without saving/opening, but that is only implemented in Chimera's Segger tool (menu: Regions... Extract densities...), not yet in ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 17, 2022, at 10:45 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry,
You select the segmented region you want to split by ctrl-click on it. Then you press the Ungroup button in the Segment Map (aka Segger) panel. If it does not split it and the log says "Ungrouped to 0 regions" then that is the finest granularity Segger computed. The algorithm finds a segment for each local maximum of the smoothed map, so the region probably had just one local maximum. If you want to split you could try segmenting with different smoothing or grouping options.
There are examples using Segger and a paper from its author Greg Pintilie if you want to learn more about how it works.
https://people.csail.mit.edu/gdp/segger/docs_segmenting.html
Tom
On Mar 17, 2022, at 1:24 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Fast questions.
1. How to segment the selected segment?
So I have a) segmented the map using the segment map tool b) selected 1 piece. b) I want to segment that selected piece on the smaller parts
2. how to increase the threshold of the segmented map?
Thank you
Kind regards, Dmitry
participants (3)
-
Dmitry Semchonok -
Elaine Meng -
Tom Goddard