First, sorry that it has taken this long to write, but we have been incredibly busy with experiments.
The reason I am writing is that the models calculated by the I-TASSER server are not readable by the software we use. Primarily we use VMD, PyMol, and YASARA, neither can read the predicted secondary structures. Most critical is, according to VMD, PyMol, and YASARA, that beta-strands are nonexistent - helices are to some degree placed correctly. I have tried to manually add SHEET and HELIX data to the PDB file, but this approach does not yield significant improvement (YASARA and VMD still won't accept that the protein has beta-strands).
I hope you can help find a solution to this problem.
My target is http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S81014
Thank you!