[Chimera-users] Volume information from segmentation data
goddard at sonic.net
Mon Dec 14 10:55:43 PST 2020
In our newer program ChimeraX there is the "mark connected" command that places a marker on each connected piece of a surface.
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.
The mark connected command originally from this ChimeraX example code
> 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.
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