[Chimera-users] Three-dimensional surface trace

Larsson, Per (pl6n) pl6n at eservices.virginia.edu
Thu Oct 18 13:25:24 PDT 2012

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?)

/Per Larsson, University of Virginia

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