[3dem] VolRover volume segmentation

[Matthias Wolf]

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