We are also releasing new tools in the update posted today. They are in the "Tools 2" tab, marked as new.
Pull Tool The Pull Tool unifies many of the existing tools and adds some useful new features! You can use it as follows:
Left click and drag to pull on the protein. This is similar to the Drag Tool. However, the effects of the pull will be localized and only affect the area which turns purple.
Right click to lock/unlock the protein. On sidechains this is just like the Lock Tool. You can now lock the backbone structures as well, so that when pulling other structures, they will not move. This can be used like the Backbone Tool or Pivot Tool.
Right click and drag to add a rubber band. This is similar to the Rubber Band Tool. You can now add bands that pull to any location in space! If they get close to the backbone, they will snap to it and act like the previous rubber bands.
Double left click to optimize the protein. The effects will be localized as well.
Keeping the pull effects local can let you focus on one part of the protein without worrying about undoing your work on other parts. For example, if you just want to move a helix around, lock structures on either side of it -- but not the ones directly neighboring it, to give it room to move.
The rubber bands still have effect while you are pulling! So if you want to pull in two places at once, try placing a rubber band into space for one, then when you start pulling the other, the rubber band will pull as well.
Bands and locks added with this tool will remain when switching to other tools, but may not affect them. They will also be saved and loaded with your solution.
We have left all the previous tools in, although they might not all quite work together yet. Notably, the bands used by the Rubber Band Tool are completely separate from the bands added by this tool.
We hope to post a video soon demonstrating the use of this new feature!
Auto All This will automatically wiggle and shake the protein to improve it. It will be affected by locks and bands added by the pull tool.
Please try out these new tools and give us feedback in the forum! Your comments will help us improve their usefulness.
We have posted 2 new competition puzzles, one of which is the complete pig prion protein. The Bio 200 puzzle we posted last week was a smaller version of the prion protein, now you can compete on the whole thing!
Congratulations to out top players on last week's puzzles 22 (mummiebrain, feet1st, hugothehermit, spvincent, and labraticmp3) and 23 (feet1st, spvincent, zzaltz, hugothehermit, and labraticmp3). Of our three new puzzles for this week, two are a new kind of puzzle in which you can see the optimal solution. The challenge is to use the tools to match this solution. We're hoping these puzzles will serve as a test of our tools, as well as help users understand what kind of structures really occur in real proteins. There will be considerable competition in these new puzzles as we have added a large set of computer science grad students to the pool of players. May the best folder win!