Changes: Rebuild

Revision as of 01:03, 8 August 2008

Rebuild is a notoriously difficult tool to use. It is not covered in the tutorial, and virtually no documentation is provided on how to make it work. It can, however, be the key to significant scoring breakthroughs, particularly in the Middlegame.

Documentation

The explanation given by the Baker Lab for how to use this tool runs as follows:

You can access rebuilding through the ctrl/right-click pie menu in pull mode. Rebuild will search through completely new shapes for the protein's backbone. Use locks and bands to control the rebuild!

Notes

Using rebuild without locks or rubber bands produces a wide variety of different shapes, most of which will score very low due to clashes. This phenomenon is not completely random, although it will probably appear that way, even to very advanced users. Player Fugofish recently visited the developers and asked specifically about this effect. Here is her description of the response:

When you select an area for Rebuild, Foldit scans a local database for the relevant sequences, as well as the structure you have given that sequence. So, when rebuilding a helix, for example, Foldit tends to cough up helix solutions more often than random loop sequences. Useful to know.

It is important to watch the progress of rebuild, however, as a player with good intuition may recognize that one of these low-scoring shapes nonetheless has great potential if the clashes can be resolved. A player with a good idea of where an element "needs" to go can also use rubber bands to constrain a rebuild in that direction. In either case, following a rebuild, it will usually be necessary to resolve sidechain clashes, to local Wiggle the rebuilt shape, and then to global wiggle or Nudge the protein in other ways to reach a satisfactory Score.

Previous rebuilds are saved in the undo list, and you may return to them by clicking back through it. This is often useful, as the rebuilds can cycle through very quickly otherwise.

Feet1st has provided a useful YouTube video giving some idea of how Rebuild works, although its functionality has changed somewhat in the meantime.

Rebuild Techniques

One effective rebuild technique is to normalize a Helix, then Lock just that helix. Next, global Wiggle the protein. It will adjust into place around the normalized helix. Complete this combination after the structure has reached Stability by unlocking the helix and doing another global wiggle. You may get even more points. This technique works best if the helix is deformed to begin with, and if correcting it will result in a global score gain.

Cheese's Notes

Rebuilds are much more useful if you can follow these tips. Trust me, I thought Rebuilds were just a pain, but if you do them then you can get a ton of points. First you view coloring to see where the red is. Then, you lock two sections so the red is in the middle of the locks, or in any random spot you want to rebuild. Next, you right click and Rebuild. Stop the Rebuild right away so you aren’t loosing 1000’s of points. If the Rebuild is too fast then you can always undo it and go back to the spot you like. After that, you do a Global Wiggle, not a Local Wiggle. Then, you do a Global Shake. Lastly, you do a Local Wiggle after the Shake. Hopefully this helps, and if you need any other tips on Rebuilds, please contact me (cheese) on Fold It. I have a ton of more strategies with Rebuilds so contact me for more!

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 ==Notes==
-Using rebuild without locks or rubber bands produces a wide variety of different shapes, most of which will score very low due to [[clashes]].  It is important to watch these, however, as a player with good intuition may recognize that one of these low-scoring shapes nonetheless has great potential if the clashes can be resolved.  A player with a good idea of where an element "needs" to go can also use rubber bands to constrain a rebuild in that direction.  In either case, following a rebuild, it will usually be necessary to resolve sidechain clashes, to local [[Wiggle]] the rebuilt shape, and then to global wiggle or [[Nudge]] the protein in other ways to reach a satisfactory [[Score]].
+*Using rebuild without locks or rubber bands produces a wide variety of different shapes, most of which will score very low due to [[clashes]].    This phenomenon is not completely random, although it will probably appear that way, even to very advanced users.  Player Fugofish recently visited the developers and asked specifically about this effect.  [http://sites.google.com/site/zoranvisit/ Here is her description of the response]:
+:When you select an area for Rebuild, Foldit scans a local database for the relevant sequences, as well as the structure you have given that sequence.  So, when rebuilding a helix, for example, Foldit tends to cough up helix solutions more often than random loop sequences.  Useful to know.
+It is important to watch the progress of rebuild, however, as a player with good intuition may recognize that one of these low-scoring shapes nonetheless has great potential if the clashes can be resolved.  A player with a good idea of where an element "needs" to go can also use rubber bands to constrain a rebuild in that direction.  In either case, following a rebuild, it will usually be necessary to resolve sidechain clashes, to local [[Wiggle]] the rebuilt shape, and then to global wiggle or [[Nudge]] the protein in other ways to reach a satisfactory [[Score]].
 Previous rebuilds are saved in the undo list, and you may return to them by clicking back through it.  This is often useful, as the rebuilds can cycle through very quickly otherwise.