[chimerax-users] Automating Map segment

[Tom Goddard]

Hi Sam,

  I did an initial port of Segger from Chimera to ChimeraX (also called Segment Map) but that code was written by Greg Pintilie and he has not worked the ChimeraX version so there is no new command to run it in a script.  It would probably not be too hard to write some Python to run it.  The Chimera script mentioned in the mailing list is attached to my message about it. 

	https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013979.html

That won't work in ChimeraX, but here I attach the equivalent for ChimeraX.

  Segger was developed to segment molecules in EM maps, so I have doubts that it will do much good for your light microscopy.  But you can decide that by running it by hand on some time steps and see if you like the result.

  Here is a different approach we used to quantify protrusions of crawling neutrophils in light sheet microscopy by placing markers that might be of interest.

	https://www.cgl.ucsf.edu/chimera/data/protrusion-sep2015/protrusions.html

  Tom




> On Jul 29, 2021, at 3:24 PM, Sam W Marchant via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013980.html> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me?
> Thanks,
> Sam Marchant.
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