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Level 1

8 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

18 replies

ChB_Fr91

Level 1

8 points

Nov 4, 2013 2:25 AM in response to chase.smith

Chase

The very last (2013-11-02) Chimera beta version (http://www.cgl.ucsf.edu/chimera/download.html) allows export directly to collada format and the files are compatible with IBA. I did a test with HbF (dae file is 13,8 Mo): it is OK and can displayed on ipad2, with colors.

Regards

chase.smith Author

Level 1

8 points

Nov 4, 2013 4:18 AM in response to ChB_Fr91

ChB_Fr91,

Thank you for the heads up on this. I had given up on an easy way to get this accomplished.

Do you happen to know if this can also be done with larger macromolecules also?

Thanks, Chase

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

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