[Chimera-users] Automate Segmetation

[Tom Goddard]

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

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> 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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