The native is all in loops.
To align the guide on a section of the protein, put the part you want to align on a structure like : a segment loop, a segment sheet and a segment loop,
- on old interface, right click on the sheet and align but dont work well
- on selection interface, select the section (double click on the sheet), align.
Hints from infjamc :
- You might notice that the protein has an unusually high number of glycines. The lack of side chain in glycine is critical for the flexibility in the backbone configuration for this protein.
- If a segment scores poorly relative to the guide despite that its backbone score is okay, check to see if it is a glycine. If so, consider rebuilding a short segment containing the glycine and its neighbors, with a zero-length band added to the glycine to keep it in place. (The idea is to see if flipping the backbone atom configuration would do the trick, e.g. via the formation of new hydrogen bonds.)
- The starting configuration for that puzzle was intentionally made incorrect. The correct structure has sheet-like extended segments, but the hydrogen bonding pattern is more complex. The pattern involves bonding to adjacent pieces in "3D" rather than "2D"-- more like "one to the left, one to the right, one below," etc.
- When starting this puzzle, you might want to set the entire structure to sheet and then straighten out the protein entirely. This ensures that the incorrectly-formed hydrogen bonds in the starting configuration (a "giant helix") would not re-form easily and may make it easier to reshape the structure manually.
- If you use the Ctrl+Shift+V full-atom mode, the atoms on the same side should go "red, then two whites," or "white, then two reds" as opposed to the "one red, one white" pattern in a standard beta sheet.
colors of AA here http://jmol.sourceforge.net/jscolors/