[3dem] VolRover volume segmentation
Matthias Wolf
wolf at crystal.harvard.edu
Tue Jul 14 07:00:46 PDT 2009
Hi David,
you can alternatively use chimera to segment density: try the "color
zone" option together with "volume path tracer":
http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html
If you have an atomic model docked into the map it's even easier: Just
select the model parts you want colored, then use color zone with
appropriate radius and your density will be selectively colored.
In pymol you can do the same:
load map.ccp4
load model.pdb
isomesh full_map, map, 2.0
isomesh selective_mesh, map, 2.0, model//A//, carve=2.0
isosurf selective_surf, map, 2.0, model//B/210-234/, carve=3.0
color red, selective_surf
set transparency, 0.3
E.g., the last command creates an isodensity surface at 2 sigma level
around chain B, residues 210-234 and renders it at a distance of 3.0A
from the selected model atoms. Use set transparency, if you want a
transparent surface instead of wiremesh. Pymol produces very good
results. There is a 64bit version that can handle even the largest data
sets (if your machine has enough memory). Contact Warren DeLano about it.
Matthias
David Gene Morgan wrote:
> Hi,
>
> Has anyone recently used VolRover to segment a virus particle? I'm
> probably being an idiot, but I have tried several times over the past
> 6-8 months, and it doesn't seem to work. I have tried with my own data,
> and when that failed, I tried to follow the tutorial using the test data
> supplied with VolRover. That also fails miserably (the program crashes
> without leaving anything I find useful). I've tried to contact the
> developers but haven't got much help from those attempts.
>
> If other people are having more luck, I'd love to learn what they are
> doing that I'm not. Thanks.
>
> - --
> David Gene Morgan
> cryoEM Facility
> 005B Simon Hall
> Indiana University Bloomington
> 812 856 1457 (office)
> 812 856 3221 (EM lab)
> http://bio.indiana.edu/~cryo
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