Hi all, I need a quick hack for the following problem:
I have a protein structure (generated by i-Tasser) in PDB format. I would like to transform the 3D model into a linearized form representing only the secondary structure, as a long flat chain of secondary structures from C to N terminus along the linear backbone. Of course, contained helices and sheets should still be rendered correctly. So this might be called reversing the 3D-folding of the structure.
The output would preferentially be in PDB format again. Is there possibly an easy way to do that?
Please let me know if the description of the task is unclear.
Background: I wish to create a little protein movie in Chimera using its morph tool, where the 2D cartoon structure morphs into the 3D ribbon structure. I tried to quickly flatten the structure manually, but that is not really convenient. I also have the i-Tasser output, if that helps.
The structure, just in case you need it.
Here is a little movie trying to explain what I want to achieve. As you can see, the linear model is far from perfect.
And here is the final movie.