Volume information from segmentation data
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*
"Friends... they cherish one another's hopes. They are kind to one another's dreams."
*-- Henry David Thoreau* *“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene*
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@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
"Friends... they cherish one another's hopes. They are kind to one another's dreams."
-- Henry David Thoreau “Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Juleen Dickson -
Tom Goddard