Pi helix trick revisited

Started by infjamc

Tony Origami Lv 1

Thanks infjamc for your tips. It helps to turn sidechain view off as you have done in your picture otherwise it gets too confusing.

Tony Origami Lv 1

This little snippet of code seems to produce the bands for a pi helix - at least on this particular protein.

for x = 1, structure.GetCount()-5 do
band.AddBetweenSegments(x,x+5,3,1)
end

Is that correct?

beta_helix Staff Lv 1

We hopefully fixed the pi helix bug, please let us know if it still scores better than regular alpha helices.

infjamc Lv 1

To whom it may concern:

It seems to me that the pi helix is still artificially scoring higher than the standard alpha helix in symmetry puzzles:

Timo van der Laan Lv 1

Checked the segment scores of the helix in a very early stage, no straight bonds and not connected to the other one.
Total was then about 1060
In the shown picture it is about 1230

Not a big difference and can be explained by the extra bonding to the other one.

See the pictures with the segment scores of the first 10 segments.

If there is a bug it is not with the segment scores.

Timo van der Laan Lv 1

I just did an experiment on an early version.

I did my best to create one, succeeded and the score did went up a lot.
Made sure there was no interaction.

So I must conclude the bug is there. Of course I did not know about this before, thought it was a bonus for the better bonding with the other one.

Timo van der Laan Lv 1

A last remark:
The segment scores did not change by much about 50 because of other improvements.
Also the helix scored normal.

So the bug must be in the computation of the interaction bonus points.

infjamc Lv 1

Timo:

Thanks for taking the time to do the testing on your own. Your results are pretty much consistent with what my teammates and I have found– namely, pi helices score too high because their backbone hydrogen bonds are being given too much credit. If I remember correctly from the developers, this is because the backbone hydrogen bonds in the "n to n+5" case is being scored under the wrong category of hydrogen bonds.