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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