[Chimera-users] Three-dimensional surface trace

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 18 13:50:46 PDT 2012

Dear Per Larsson,
I would recommend instead calculating an occupancy map of the loop atoms over the trajectory.  That will produce a 3D grid (map) of values reflecting how often the atoms occupied that location, and you can then display the map at different isosurface levels.

See the MD Movie documentation (go to the "Occupancy Analysis" section):

And for an example, see the "Trajectory and Ensemble Analysis" tutorial, part 2.  The figures near the bottom show isosurfaces of occupancy maps.  The figures show mesh, but you could alternatively use "surface" display (non-mesh).

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 18, 2012, at 1:25 PM, Larsson, Per (pl6n) wrote:

> Dear Chimera-users
> I have a problem that I'm not sure can be solved in Chimera, but I thought I'd put the questions out there. Have search the archives, but couldn't turn up anything really relevant.
> I have a set of pdb-structures (snapshots of the same protein from a molecular dynamics simulation). The protein sits in a membrane and has a bunch of floppy loops that protrude into the solvent region. My aim is to be able to make a plot (in 3D) of the space explored by these loops over the entire simulation, essentially to see if some regions of space are preferred over others. 
> What I thought of doing was to calculate the surface regions traced out by the loops projected on the half-sphere formed by the membrane in the x-y-plane and z>0. I hope that makes sense!
> Is something like this even possible in Chimera, or should I look elsewhere for a solution (perhaps inventing my own method?)
> Thanks
> /Per Larsson, University of Virginia

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