[Chimera-users] Automate Segmetation

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 10 17:33:45 PDT 2017


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 <sgremesh at lbl.gov> 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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