Hi Soumya, You can set the threshold level of a map (steps 1, 2, 3) with the volume command, for example, volume #0 level 0.011 As Elaine says there unfortunately is no command to run the Segger segmentation algorithm. That will be remedied in ChimeraX. But you can run a little Python script (attached) to do that open segscript.py To find the functions called in this script I looked at the Chimera Segger Python code which is part of your Chimera distribution in chimera/share/Segger/segment_dialog.py or on Mac Chimera.app/Contents/Resources/share/Segger/segment_dialog.py Tom
On Oct 10, 2017, at 5:33 PM, Elaine Meng wrote:
Hi Soumya, You can open map data with command “open” and set map contour level(s) with command “volume” (see the “level” option): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
However, there aren’t Chimera commands to do the segmentation stuff in your step 3. Theoretically “everything” could be done in python, but it may be unreasonably difficult and require a lot of programming expertise. Somebody else would have to comment on that issue.
There is a “segment” command, but to my understanding, it works with the output of Segment Map rather than doing the same thing as Segment Map. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 10, 2017, at 5:04 PM, Soumya Govinda Remesh wrote:
Hello Chimera Developers,
There is this repeated procedure that I have to do to get a Segmented map from my soft x-ray tomography maps. Here is what I want do:
1. open *mrc
put the map to Level 0.011
2. vop gaussian #0 sd 0.005
put Gaussian to 0.011
3. Go to: Tools --> Volume Data --> Segment Map
Segment the gaussian map
Smoothing step: 1
Step size: 500 voxels
Keep only regions at lease: 100 voxels
Save segments as an .mrc file
Go to: File (Segment Map) --> Save all regions to .mrc
Set Segment map to 0.011
4. Type: vop subtract #3 #0
#3 Corresponds with ID# of the segmented .mrc file
#0 Corresponds with ID# of the original file
5. sop split #0
#0 Corresponds with ID# of the original file
• Splits surface into disconnected parts The steps in bold are in command line. Is there anyway to have everything in a script format? Setting the levels, opening segmentation and setting values to specific Voxel values every time is quite time consuming. I would appreciate your help. Thanks
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