oops, don't look at that.... stand by.... :)
Bob Hanson wrote: >Well, it works. I am so delighted with this Marching Cubes algorithm! >It turns out that the rendition of solvent-accessible surfaces using >isosurfaces is almost trivial. I just don't want to think how much time >first Miguel and then later I spent trying to do this other ways! > >see <http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm> > >One of the very nice consequences of doing solvent surfaces this way is that >they can then be colored using exactly the same methods being used for any >other isosurfaces. Examples: > > # First, just the surface. > load ch3cl.mol;isosurface solvent;show isosurface > > # Now mapped using electrostatic potential from a CUBE file > load ch3cl.mol;isosurface solvent color "ch3cl-esp.cub.gz";show isosurface > >(Note that the "show isosurface" command gives you the JVXL equivalent. > > # And the JVXL equivalent (19.5K) > load ch3cl.mol;isosurface "ch3cl-solvent.jvxl" > > # The color mapping can be adjusted to your liking > isosurface delete;isosurface solvent color absolute -0.01 0.01 >"ch3cl-esp.cub.gz" > > # solvent probe radius is set using the "set radius" command > load ch3cl.mol;set radius 3.0;isosurface solvent color "ch3cl-esp.cub.gz" > # back to the default: > load ch3cl.mol;set radius 1.2;isosurface solvent color "ch3cl-esp.cub.gz" > > # more examples > load C6H6.smol;isosurface _benzene mesh nofill solvent > load caffeine.xyz;isosurface _caffeine mesh nofill solvent > load 1crn.pdb;select 1-3;isosurface _pdb mesh nofill solvent > >--------------- > >I'm sure this will all see a bit of refinement as people express their >desires, but this is basically it. > >For those interested in the technical side of it, basically the key to >success was realizing that voxels can take values that express the >distance (positive or negative) to the nearest solvent-surface point, >and those points can be easily determined using simple geometry. Then, >with that "cube" data, the Marching Cube algorithm can interpolate >essentially perfectly to deliver the actual surface. The ones I am >seeing have a bit of bumpiness to them; this could be a bug. I'll play >some more with the algorithm to see if I overlooked something. (I can >think of one thing right now....) For now I'll call it a bit of >"texture". :) > >Bob > > > > > >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
