[Chimera-users] Chimera output into Collada .dae file format

Eric Pettersen pett at cgl.ucsf.edu
Mon Jan 30 10:29:00 PST 2012

Sorry, these duplicate messages from Chris were accidentally approved  
by the list moderator (messages from non-subscribed addresses go into  
holding for approval).  Please ignore!


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Jan 28, 2012, at 11:07 PM, Chris Tomlinson wrote:

> Hello,
> Thank you very much for the information. The combination of Chimera  
> and Blender works quite well. I find that it is all too easy to  
> create models that are much too complex for the iPad however.
> Chris
> On Jan 29, 2012, at 9:28 AM, Evan Kantrowitz wrote:
>> Hi,
>> This is the way I got it to work, I exported  Chimera scene to VRML  
>> (.wrl).
>> Next you need blender.  You can download it from
>> http://www.blender.org/download/get-blender/
>> Then Open Blender.  In the upper right corner in the Scene section
>> right click on Lamp and delete it
>> right click on Cube and delete it
>> right click on Camera and delete it
>> Save this file so you don't have to do this every time.  I called  
>> mine empty_blender_file.blend
>> Either open empty_blender_file.blend or continue from above and  
>> read in the the .wrl file from Chimera
>> File -> import->X3D Extensible 3D (.x3d/.wrl)
>> this reads in the file
>> In Blender you need to delete the three lights that came in from  
>> Chimera called TOPO, TOPO.001 and TOPO.002
>> In the upper right corner in the Scene section
>> right click on TOPO and delete it
>> right click on TOPO.001 and delete it
>> right click on TOPO.002 and delete it
>> Now you need to move around the viewport to get it centered
>> In the upper right corner in the Scene section
>> click on the Viewport
>> then press number pad 0
>> Press the cube icon below the Scene section
>> Now in the transform section move the location x,y,z.  When you  
>> have it the way you want it is ready for export.
>> File->export->collada (.dae)
>> Done.  This file will read into iBooks Author and have somewhat  
>> uniform lighting.  By the way, .dae files can be opened an checked  
>> in Preview.  Its easier than going back and forth into the iPad,  
>> since you can rotate the image in Preview.
>> Here is a link to a .dae file of 1crn that you can import into  
>> iBooks Author or Preview
>> http://dl.dropbox.com/u/4300550/1crn2_mod.dae
>> Hope this helps, let me know if it works for you and if you have  
>> any suggestions.
>> Finally, someone needs to write a one step VRML and/or X3D to  
>> collada converter that will work with PyMol and Chimera etc.
>> PS It was a little easier from PyMol, if your interested see the  
>> post at https://discussions.apple.com/thread/3670156?start=0&tstart=0
>> PSS.  Okino Computer Graphics makes a .wrl and .x3d to .dae  
>> converter http://www.okino.com
>> Have fun!

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