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

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

Best,
Soumya Govinda Remesh, Ph.D.
Postdoctoral Fellow at Advanced Light Source
SIBYLS group: http://sibyls.als.lbl.gov/ 
Lawrence Berkeley National Laboratory

1 Cyclotron Road   MS 6R2100
Berkeley, CA 94720
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