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chase.smith Author

Level 1

10 points

How to create Protein or Chemical structures in .pdb or .mol format for use with iBooks Author. Please help.

Dear Community,

There are a large variety of software packages used by Chemists and Biologists to view and manipulate Protein and Chemical structures in 3D. They typically have formats such as .pdb, or .mol. I have looked around and none of the software packages that I currently use allow me to export to the COLLADA (.dae) format.

Does anyone have any idea where to begin to allow me to do this. I would like to try and put in some of the 3D objects into the iBook Author program.

Thank you. Chase

Mac OS X (10.7.2)

Posted on Jan 20, 2012 11:02 AM

Top-ranking reply

Sjazbec

Level 4

1,674 points

Posted on Jan 22, 2012 5:16 AM

ibooks Author accepts exported collada models from Poser Pro very fine, even with texture and lights. This program also allows to make animated Quicktime Movies from your models, and thus you can use these movies alongside free rotatable dae models also in ibooks autor. It is a nice workflow it seems ( and I am only experimenting as we speak ) .. :

these models in iBooks Author ( they can be zoomed, rotated, fullscreened on iPad ) :

View in context

18 replies

ChB_Fr91

Level 1

8 points

Nov 4, 2013 9:38 AM in response to chase.smith

Dear Chase

I made a test with hemoglobin (F variant), which is not a small molecule. It is OK on ipad 2. The problem is that DAE file size increases very fast with complexity of molecules: for glucose, number of vertices is 5496 and number of faces is 10724; for HbF, number of vertices is 105792 and number of faces is197340. There may be problems with "old" ipads.

With ibooks on OSX Mavericks, there is no problem. Even, if you export from Chimera in HTML, display on OSX will be possible (not very nice), BUT NOT on IOS (does not support WebGL). May be in the future??

Rgds

Christian

Jan 20, 2012 9:07 PM in response to chase.smith

I have not had a chance to play with it, so I do not know if it will import the correct files for you, but try Blender. it's a3d modelling program for mac.

Hope this helps, not sure if it will.

Shawn

Jan 21, 2012 4:19 PM in response to chase.smith

Google Sketchup is free and supports export to CAE, but it of course doesn't support importing .pdb or .mol files.

How to create Protein or Chemical structures in .pdb or .mol format for use with iBooks Author. Please help.