[Chimera-users] Exporting VRML, Using Blender

Lydia Jablonski lydka at uoregon.edu
Mon Oct 30 14:47:06 PST 2006

Jonathan and Greg-

Thank you for your suggestions. I wanted to at least try them before I responded.

Exporting VRML: I did try the export to VRML from version 1.2304 and it is good to know that it works for ribbons now. Unfortunately, the imported VRML meshes don't seem to respond to the mesh smoothing in 3ds max. With the .pdb --> .pov --> .3ds --> .max  workflow I'm able to get a completely smooth surface on the ribbon. With the imported .wrl (VRML) I am able to see the triangulation on the surface, especially with shiny materials. Increasing the subdivision quality in Chimera makes these triangles smaller, but they are still visible. 

Blender: Can you explain more the advantages of Blender for rendering/animating molecular models? I've been using 3ds max for quite a while (since the DOS days) so I feel very comfortable with it. But the need to work with molecular models is new so I'm still bumping around trying to figure out what all the possibilities are. If another 3D animation program would work better with exported .pdb files I'd be willing to pick it up.

Any more pointers would be much appreciated.


On Fri, 27 Oct 2006 16:39:39 -0700 (PDT), Greg Couch <gregc at cgl.ucsf.edu> wrote:
> A couple of things:
> 3DS Max supports importing VRML (.wrl) files, so you'd be better off
> using the latest chimera, 1.2304, and exporting VRML for direct import 
> into 3ds Max.
> As for biopython/blender, I believe you'd be better off using chimera to 
> export to blender using the X3D format.  Chimera understands PDB files 
> better than biopython, generates ribbons and molecular surfaces, deals 
> with volume data easily (see http://www.cgl.ucsf.edu/chimera/ for 
> details), and blender can do wonderful animations and other 
> postprocessing.  It's a more powerful combination.
>  	Greg Couch
>  	UCSF Computer Graphics Lab
> On Fri, 27 Oct 2006, Jonathan Hilmer wrote:
> > Date: Fri, 27 Oct 2006 14:09:12 -0600
> > From: Jonathan Hilmer <jkhilmer at gmail.com>
> > To: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
> > 
> > Although this does not relate to your question on licensing, is there
> > any particular reason you're using such a complicated workflow?
> > Chimera can be used to generate basic geometry (sphere/cylinder) from
> > PDB files via povray, but so could any import system you have for the
> > 3D modeling software.  You would also lose the benefit of
> > chemistry-centered structure for manipulation or selection: chains,
> > residues, etc.
> >
> > I've been using Blender to handle complicated chemical models for a
> > while now, and it wasn't that difficult to implement the import of
> > various data types.  With BioPython pdb files become trivial, and
> > volumetric data sets are (very) difficult but possible.
> >
> > Jonathan
> >
> >
> >
> >> Hello-
> >>
> >> Do any of you have an idea of how much a single commercial license for 
> >> Chimera would cost?
> >>
> >> I'm a 3D artist/animator/biology student that works at in the art dept. 
> >> of a biotech company. I'm interested in the exporting .pdb files to 
> >> .pov, then converting to .3ds to import to 3ds max.
> >>
> >> Thanks,
> >>
> >> Lydia Jablonski
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
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