[Chimera-users] Volume information from segmentation data

[Tom Goddard]

Hi Juleen,

  In our newer program ChimeraX there is the "mark connected" command that places a marker on each connected piece of a surface.

	https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html

I just added a "stats" option to output measurements for each blob including the surface area, enclosed volume, and number of holes.  This will be tonight's ChimeraX builds.

	https://www.rbvi.ucsf.edu/chimerax/download.html#daily <https://www.rbvi.ucsf.edu/chimerax/download.html#daily>

The mark connected command originally from this ChimeraX example code

	https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html

  Tom

> open 22000 from emdb
> volume #1 level 0.6903
> surface dust #1 size 10

> marker connected #1 stats true

Found 21 connected surface pieces
Surface #1.1 has 21 visible blobs
# id, center xyz, surface area, enclosed volume, holes
    1   154.58   152.55   149.36      108.7      43.23   0
    2   173.32   149.15   156.33      212.8      86.06   0
    3   156.96   165.48   158.25      320.1      148.3   0
    4   160.32   175.48   154.98       98.6      38.59   0
    5   143.37   151.62   162.12      77.07      25.17   0
...


> On Dec 14, 2020, at 7:58 AM, Juleen Dickson <jdickson6 at gmail.com> wrote:
> 
> Good Morning Everyone,
> 
> I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate.  Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help.
> 
> 
> Cheers,
> Juleen
> 
> "Never interrupt someone doing what you said couldn't be done."
> --Amelia Earhart,
> American aviator
> 
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> 
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> 
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