[Chimera-users] Chimera-users Digest, Vol 77, Issue 16

Ga=?ISO-8859-1?B?6w==?=l McGill mcgill at digizyme.com
Wed Sep 16 12:17:05 PDT 2009

Hi Andrew,

You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience
importing PDB data into Blender.

Here is her site:

Her e-mail:
Monica Zoppè <mzoppe at ifc.cnr.it>

Hope this is helpful,

Gaël McGill, Ph.D.

Director of Molecular Visualization
Center for Molecular & Cellular Dynamics
Harvard Medical School

President & CEO
Digizyme, Inc.
P.O. Box 1921
Brookline, MA 02446-1921

(617) 232-7676 (phone)
(617) 232-5623 (fax)
mcgill at digizyme.com

On 9/16/09 3:00 PM, "chimera-users-request at cgl.ucsf.edu"
<chimera-users-request at cgl.ucsf.edu> wrote:

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> Today's Topics:
>    1. Re: Exporting from Chimera to Blender - basic questions.
>       (Tom Goddard)
> ----------------------------------------------------------------------
> Message: 1
> Date: Tue, 15 Sep 2009 23:03:03 -0700
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic
> questions.
> To: "Waight, Andrew" <Andrew.Waight at med.nyu.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <4AB07F97.6080108 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Hi Andrew,
>   Chimera exports the surface vertex and individual atom and ribbon
> residue colors in the X3D and VRML output.   If you raytrace a scene
> with Chimera File / Save Image... it first exports X3D and then converts
> that X3D to input for POVray which does get all the colors right.  So I
> think your question calls for some expertise with Blender, to find out
> what color information it can handle when importing those files.  I
> don't know anything about Blender.
>     Tom
> -------- Original Message --------
> Subject: [Chimera-users] Exporting from Chimera to Blender - basic
> questions.
> From: Waight, Andrew <Andrew.Waight at med.nyu.edu>
> To: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Date: 9/15/09 10:31 AM
>> 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 experienc!
>  e !
>>  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
>> 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)? 
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