Thanks for your answer, Eric:

perhaps you could describe why you want MSMS info in VRML format? There could be a better alternative available than writing the conversion routine.

I develop educational stuff--you might know one of my recent outings, "Lehninger Principles of Biochemistry 3e" (4e to appear in a couple months). I'm the development editor of that book for Freeman, and I'm branching out on my own into motion graphics to animate the things we talk about in the book. For molecular animations I convert pdb files into formats that professional 3D graphics programs can read. I can output b&s and vdW models into usable formats in a variety of ways, but right now the only route I know of for porting molecular surfaces into a 3D app is WebLab->VRML->3D app--imperfect for a variety of reasons (expensive, PC only, minimal access to surface parameters, etc). VMD exports VRML, but the output files are _gigantic_ and can't be read anyway by any 3D app I've tried. What I crave is a route that would let me tune a macromolecular surface with MSMS in a nimble app like Chimera, export it into VRML, and open it in any 3D app that reads VRML files (most of them). Possible? I'm afraid my programing skills are far too primitive to do this myself. So how can one get surfaces for enzymes--for the ribosome!--into a format that 3D apps can read? Your counsel will be greatly appreciated! Morgan

On Dec 15, 2003, at 5:24 PM, Eric Pettersen wrote:

On Friday, December 12, 2003, at 03:34 PM, Morgan Ryan wrote:

...

VRML seems to be a native internal format for (the magnificent) Chimera. Is it possible to export VRML models from Chimera? Or do you worldly folks know of a mechanism for converting msms output into vrml files? Thanks! Morgan Ryan, enthusiastic amateur

Hi Morgan, Although VRML is one of the model types that Chimera supports, we don't convert MSMS output into VRML. It is instead made into its own model type (MSMSModel) so that we can preserve information about the correspondence between surface points and atoms, which would be lost if we had used a VRML model. A Python routine _could_ be written that would convert the MSMSModel information into its VRML equivalent, but before "going there" perhaps you could describe why you want MSMS info in VRML format? There could be a better alternative available than writing the conversion routine.

                    Eric Pettersen
                    UCSF Computer Graphics Lab
                    pett@cgl.ucsf.edu
                    http://www.cgl.ucsf.edu

____________________ Morgan Ryan Development editor W H Freeman 209 Adams Way Chapel Hill NC 27516 phone: 919 942 4890 fax: 651 846 5265 mryan@whfreeman.com