I currently have a fifty point penalty on puzzle 971c under the Fragment Score section. When I check the box to show the affected residues, they appear on the main protein, and not on the twenty-five segment piece we are designing.
Is this a bug? Or are we supposed to design something that will deform the main protein enough to remove the penalty?
Not really that much of a bug. It's just a -50 point section that every player gets. No way to get rid of it, as the backbone is frozen at that point.
Frozen backbone=no moving=no fixing fragment.
Penalizing a player for something that he did not do, cannot fix, and cannot touch is definitely a bug.
Unless the dev's plan on releasing this puzzle later on and allowing us to work on the area of the main protein that would bind to our designs, perhaps?
The scoring part doesn't really affect anybody, since EVERYBODY gets the -50 points from the fragment. If everybody has the same -50 point filter, then the scores are equivalent. What bothers me is that the fragment filter is even taking into account the non-editable portion of this puzzle. This is likely one of the reasons for 971c's slowness.
Problems with 971c
Some of the segments in 971c are Locked not Frozen. Calling structure.IsLocked( seg ) and BB, SC = frozen.IsFrozen( seg ) can show this.
Wiggling and Shaking the Locked segments can change their segment energies and their segment sub-energy values. Some of the sub-energies come out as zero even though the segment energy is not zero.
I went through the procedure of resetting puzzle 971c and then running a program seg_tot_not_tot v 1.1, which prints the segment energies and the sub-energies. It also checks and prints out the results for structure.IsLocked( seg ) and BB, SC = frozen.IsFrozen( seg ). I then set wiggle power to medium, did shake and wiggle until the score reached a maximum, and ran the program again. The full results for each run are appended.
Reset and ran the program
38 l Leu 13.977254718244 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 13.977254718244
39 n Asn -1.1297687999634 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 -1.1297687999634
40 l Leu 36.312977148015 H Helix
locked,
clashing -8.14734078
packing 43.30009768
hiding -4.35330886
bonding 10.53348571
ideality -0.57393302
backbone 1.75360353
sidechain -2.20101618
reference -6.02328000
other 2.02466906
41 e Glu -12.551003864246 H Helix
locked,
***** seg engy not equal tot of seg subengy 0 -12.551003864246
This segment of output after the puzzle had been shaken and wiggled shows that the segments are locked but not frozen. Each of the segment sub-energies is zero. The segment energy for that segment is not zero.
38 l Leu 13.977254718153 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 13.977254718153
39 n Asn -1.1297687999636 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 -1.1297687999636
40 l Leu 36.646099347351 H Helix
locked,
clashing -8.14734078
packing 42.89730938
hiding -3.55821967
bonding 10.53348571
ideality -0.57393302
backbone 1.75360353
sidechain -2.20101618
reference -6.02328000
other 1.96549037
41 e Glu -12.550954583835 H Helix
locked,
***** seg engy not equal tot of seg subengy 0 -12.550954583835
The sub-energies for segment 38 and others come out zero. For segment 40 and others, the packing, hiding, and other sub-energies are different for a just reset puzzle and one that has been wiggled and shaken.
Problems with 971c
Some of the segments in 971c are Locked not Frozen. Calling structure.IsLocked( seg ) and BB, SC = frozen.IsFrozen( seg ) can show this.
Wiggling and Shaking the Locked segments can change their segment energies and their segment sub-energy values. Some of the sub-energies come out as zero even though the segment energy is not zero.
I went through the procedure of resetting puzzle 971c and then running a program seg_tot_not_tot v 1.1, which prints the segment energies and the sub-energies. It also checks and prints out the results for structure.IsLocked( seg ) and BB, SC = frozen.IsFrozen( seg ). I then set wiggle power to medium, did shake and wiggle until the score reached a maximum, and ran the program again. The full results for each run are appended.
Reset and ran the program
38 l Leu 13.977254718244 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 13.977254718244
39 n Asn -1.1297687999634 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 -1.1297687999634
40 l Leu 36.312977148015 H Helix
locked,
clashing -8.14734078
packing 43.30009768
hiding -4.35330886
bonding 10.53348571
ideality -0.57393302
backbone 1.75360353
sidechain -2.20101618
reference -6.02328000
other 2.02466906
41 e Glu -12.551003864246 H Helix
locked,
***** seg engy not equal tot of seg subengy 0 -12.551003864246
This segment of output after the puzzle had been shaken and wiggled shows that the segments are locked but not frozen. Each of the segment sub-energies is zero. The segment energy for that segment is not zero.
38 l Leu 13.977254718153 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 13.977254718153
39 n Asn -1.1297687999636 E Sheet
locked,
*** seg engy not equal tot of seg subengy 0 -1.1297687999636
40 l Leu 36.646099347351 H Helix
locked,
clashing -8.14734078
packing 42.89730938
hiding -3.55821967
bonding 10.53348571
ideality -0.57393302
backbone 1.75360353
sidechain -2.20101618
reference -6.02328000
other 1.96549037
41 e Glu -12.550954583835 H Helix
locked,
***** seg engy not equal tot of seg subengy 0 -12.550954583835
The sub-energies for segment 38 and others come out zero. For segment 40 and others, the packing, hiding, and other sub-energies are different for a just reset puzzle and one that has been wiggled and shaken.