- Initially, the sheets don't line up very straight.
- Freeze the sheets and start banding them.
- As the protein starts to fold, add more bands.
- Then make the helices.
How to get the helix to settle without upsetting the sheets while still getting the sheets to link up? Join sheets before making the helices: when the hydrogen bonds are made they'll become more stable. You can always freeze all the packs of sheets and the connecting loops to move the other side.
Try to have all hydrophobic amino acids (orange) inward-facing and hydrophilic amino acids outward-facing. Align the sheets so that the side with more orange faces the inside of the protein. As an exception, Tryptophan are orange have a mixed hydrophicity (often outside on blue side). Phenylalanine are often inside (orange).
[Edited from #global comments by itskimo and Marie]
Other ways to do this with cutpoints see the videos and the links provided in De-novo