mine's broken - Mac Yosemite - the black cloud goes if I turn the isosurface off and it didn't crash, moving the ligand about doesn't fix it.
Thanks for all the bug reports relating to the "Show Isosurface" option! We'll try to reproduce these on our end and see if we can figure out the problem.
I'm sure you are also interested in different orientations of the vancomycin and the corresponding folds?
Clearly, we'd like players to focus on building a binding pocket on the concave side of the protein (where mutations are allowed).
But, by all means, experiment with different orientations of the ligand in the binding pocket to maximize packing and shape complementarity!
I know the comment says to look at other orientations, but if the ligand is completely outside of the pocket adjacent to the perimeter/arc of the protein I wouldn't expect to see a Complementarity score of +1459.2. Is that really right?!?
What is the maximum amount permissible for shape complementarity ?
In this puzzle, players can receive a maximum of 1500 points from the Shape Complementarity filter. But beware, there is a steep penalty if your shape complementarity drops too low, and the bonus will jump from 1250 to 250!
(Windows 7) The cloud appears or not when cliking on "Show Isosurface" depending on the solution I load. Even then , it sometimes arrounds also the ligan or not.
And I do not see any change when clicking on "show" for the new filter.
Here I see the cloud, but see on the left the strange black ligand
locked segments can be rebuilded, a bug?
and cut works too :-?
I have not found the cloud. That might be good. I would like a tool that lets me see sidechain links between the ligand and main protein only, not all sidechain links. If we have a lot of these puzzles, it would be very helpful. this is running slowly and the display is very jerky due to the large puzzle size.... simpler info of the right kind would be useful
Is turned on and off in the view menu, it is more of a translucent skin covering the bones to show the surface than an unattached cloud. We cant see hydrophobic bonds anywhere - not just about hydrogen bonds
If the purpose is to focus on and change (rebuild) the pocket - then why can't we idealize those segments?
I can't find "Shape Complementarity" in the return value for puzzle.GetPuzzleSubscoreNames. Is this intentional?
I noticed that it does appear in the notes.
not sure if this is going to work, team pattern is consistent, highest scores are outside the pocket,
after getting a good position with some side-chain interaction, shake side-chains and wiggle causes it to move away from the pocket,
tried running an idealized script, mutate no wiggle, c&ws early in order to stabilize the protean. it was better and will share to scientists if you like, but would not stay in contact.
I got good bonds down one side of protein (5, with both ends and 3 in middle). banded them. will share, but best score is to abandon the bonds. I have a smaller machine and team. I'm sure some bonds in the middle of the other side too might have helped. but this puzzle doesn't work as intended. any more like it seems like a waste of our time. perhaps scientists can post here after the close.
obviously 5 bonds spread out are not enough to hold over the clashing penalty. what is? need to rethink this.