Thank you Elaine and Tom. At least some part of the process can be done with a script. That is good for now. Looking forward to segmenting in ChimeraX. Thanks again On Tue, Oct 10, 2017 at 5:58 PM, Tom Goddard <goddard@sonic.net> wrote:

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

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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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-- 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 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh@lbl.gov