this crashes when mutating - no warning - just quits
not really playable - shame
Hi frood, thanks for the report, it would help us if you could open up a solution where the crashing happens and use the "upload to scientists" feature. In the description box you could type some info about how to make it crash (for example, just click mutate and wait, or what-have-you.)
Thanks!
I don't really understand the H-bond network filter.
In one example, I have 4 blue H-bonds in a row.
Serine-OH to Aspartate-O to Glutamine-NH to Aspartate-O to Arginine-NH
It says Interface HBonds: 3 (0 credited)
However, I only see two Glutamine-NHs from a neighboring protein have 2 bonds to two different Aspartate-Os.
All other residues are in one individual protein.
Polars Satisfied: 58.8235 %
I don't really understand how this odd number is calculated?
It would be more helpful if you could write something like "4 out of 13 possible atoms satisfied" into the filter
Yes, the H-Bond Network Objective is rather complicated, but that's because there are a lot of different aspects that make up a good H-bond network! You have probably already seen it, but there is a brief write-up about the Objective on the blog.
It's difficult to tell without seeing your solution, but it sounds like your network is below 75% satisfied so it will not receive any bonus. It does seem strange that it reports 3 interface bonds if you only see 2 bonds that span the interface. That could be a bug -- can you share your solution with scientists?
That is helpful feedback about reporting the raw numbers for the satisfaction calculation! I think we should be able to address that.
Thanks for the reply, Brian.
Unfortunately I did not have time anymore for the puzzle and will share my solutions with the next puzzles :)
Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).
Core Existence: Monomer (max +1600)
Ensures that at least 16 residues are buried in the core of the monomer unit.
Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.
H-bond Network (max +1800)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 9 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).
Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.
SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.
Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.
Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.