[Chimera-users] Automate Segmetation

Soumya Govinda Remesh sgremesh at lbl.gov
Tue Oct 10 18:21:51 PDT 2017


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 at 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
>
>
>
>
>
> > 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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> >
>
>
>


-- 
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 at lbl.gov
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