[Chimera-users] Exporting from Chimera to Blender - basic questions.

Greg Couch gregc at cgl.ucsf.edu
Wed Sep 16 16:25:36 PDT 2009

On Tue, 15 Sep 2009, Waight, Andrew wrote:

> Hello all,
>       I have recently solved the structure of a novel membrane protein, 
> and have been using chimera quite a bit for my figures and analysis. In 
> my free time I have been playing around with the 3D animation package 
> Blender which I must say is a total blast, and makes fantastic movies 
> and animations. However exporting from Chimera to Blender is a little 
> tricky, in that when using VRML2 or X3D formats while the actual 3D 
> "mesh vertices" import quite well, the colors are not imported, and 
> imported items such as cartoon helices seem to have totally random 
> materials assigned to nonsensical segments (instead of materials 
> assigned by chain for example) . Ideally I would like to perform and 
> export the coloring operations using chimera because it's obviously an 
> order of magnitude easier to select residues, chains and monomers with 
> chimera. Or at least have the grouping of objects imported correctly. 
> This is really just for fun so I'd thought I'd ask if anyone here has 
> any experience ! with importing Chimera models into Blender. Of course I 
> have no idea how VRML2 actually works. Thanks all.
>                                                Andrew Waight
>                                                     Wang Lab
>                    Skirball Institute of Biomedical Sciences
>                                       NYU School of Medicine

This is more of a Blender question than a chimera question, in the sense 
that it is failing when you import the file into Blender, rather than when 
it is exported from chimera.  So normally, I would recommend that you ask 
in a Blender discussion group something like "Why does blender fail to 
import this VRML2/X3D file when it displays just fine in my browser?"

But the X3D importing that Blender 2.46b does is really bad.  It only 
tries to do the subset of X3D that corresponds to VRML97.  I can't tell 
why the surface colors are lost.

Matthieu Delanoe has a much much better X3D importer at 
<http://matthieu.delanoe.googlepages.com/blenderX3D.html>.  It needs to be 
updated for Python 2.6 by adding "# -*- coding: latin-1 -*-" as the second 
line to get it to work.  And again, the colors are lost even though there 
is code for them in the import script.

> P.S. Extra Credit: Does anyone have any idea how to export the 
> calculated electrostatic surface into UV mapping for a Blender Object 
> (the surface mesh obviously)?

If the surface has no holes (not true in general for molecular surfaces), 
then the mapping would be possible.  Not knowing Blender, can you say why 
you want the UV mapping?

 	-- Greg

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