The red lines indicate constraints.
Constraints are used in some puzzles to hold parts of a protein or a ligand in place. Constraints are similar to bands, but are a permanent part of a puzzle. Players can't add, delete, or disable constraints or change a constraint's length or strength.
Constraints are normally used in design puzzles which have a specific target. For example, in the aflatoxin puzzles, constraints may be used to hold the aflatoxin molecule (a ligand) in place.
Constraints are often invisible. They appear as thin read lines when the piece being held is moved out of place. Constraints normally disappear when the wiggle tool is applied.
Persistent Constraints
Sometimes on a puzzle, there will be one or two constraints which simply will not go away on their own. Though infrequent, they are quite troublesome. A visible constraint may reduce your score by 100 points or more. It is in your best interest to do all within your power to eradicate them from your puzzle. Normally even persistent ones will go away before mid-game, however for those that do not a couple of effective strategies for removing them are as follows:
- Try tracing the constraints with a rubber band. Sometimes all they need is a little extra incentive to push themselves where they need to go. Once you have the band(s) over the constraint, wiggle. If the constraint does not go away, try working as normal for a little while, leaving the bands in place.
- Try pushing the sidechains in the immediate vicinity of the constraint around a bit. Make them clash with one another, or pull them as far away from the constraint line as possible. Wiggle it out again, and see if it goes away.
- If the banding and sidechain techniques do not work, sometimes it is helpful to look at the backbone structure of the section with constraints. If the section in question is a loop, it can be helpful to change it to a helix, and use the straighten and rotate tools to contort it where it should be. If the segment is folded over on itself, changing it to a sheet and straightening it may cure the problem. If the segment is already one of these two, than these tools should also be effective at removing the constraint.
- Finally, if you simply cannot remove the constraint, you may wish to consider ignoring it for a while. Focus on the rest of the puzzle, often through working the backbone, the constraint will disappear on it's own. Just keep in mind while it is there, that it is generally an indicator of a section of the backbone being out of place.
Constraints in Rosetta
Foldit is based in part on Rosetta. The Rosetta tools include several types of constraints.
Some constraints are defined in a constraints file, as described here:
http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/file_constraints.html
Player research at the time indicated the constraints in puzzle 480 were of the harmonic type. Unfortunately, the details that led to this conclusion have not been documented.
Rosetta also includes other constraints, such as constraint to a point in space (similar to a spaceband, which can't be defined in a constraints file.