Chimera output into Collada .dae file format
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! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz@bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------
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! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz@bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 -------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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!
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! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz@bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 -------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Chris Tomlinson -
Chris Tomlinson -
Eric Pettersen -
Evan Kantrowitz