An illustrative example of the difference in HPF1 and HPF2 is the difference between low-resolution methods and high-resolution methods for the scoring of hydrogen bonds. In HPF1 we used the strand packing score, now, for HPF2, we use the hydrogen bond score, you can see this score on the client window. In the HPF1 procedure backbone hydrogen bonding is scored indirectly by a term designed to pack strands into sheets that simply looks to see that strands are aligned. Hydrogen bonding in helices is not modeled and it is assumed that hydrogen bond are satisfied in helices. See the series of pictures below to see hydrogen bonds in proteins. This low-resolution method first reduces strands to vectors (ignoring helical secondary structure fragments) and then scores strand arrangement (and the correct hydrogen bonding implicit in this arrangement) via functions dependent on the angular and distance relationships between the two vectors. Thus, the scoring function is robust to a rather large amount of error in the coordinates of individual atoms participating in backbone hydrogen bonds (as large numbers of residues are reduced to the angle and distance between the two vectors representing the strands). In the high-resolution, refinement, mode of Rosetta an empirical hydrogen bond terms with angle and distance dependence between individual electro-positive and electro-negative atoms is used (Rohl, 2005). This more detailed hydrogen bond term has a higher fidelity and a more straightforward connection to the calculation of physically realistic energies (meaningful units, physicists wont make as much fun of us for using this one) but requires more sampling, as small changes in the backbone can cause large fluctuations in computed energy. Here is a small protein with the chain colored from N-terminus/start/blue to C-terminus/red.
Now I'll show just the two strands in this protein that are hydrogen bonded (a few hydrogen bonds) to each other:
Here is the protein if I color by atom type (C = green, N = Blue, O = red, S = yellow, H = white):
Here I've removed the fancy trace of the backbone everywhere but over the two strands:
And lastly I show the Hydrogen bonds as black zig-zags between the Nitrogens on one chain and the oxygens on another.
Here is another small protein that has no strands. Hydrogen bonds and help hold together the alpha helices.
Here it is with the helices drawn (same orientation, and colored by atom type):
And again, here is the protein with a few hydrogen bonds drawn as black zig-zags keeping the helix together: