Tutorial Puzzles
Comments18this wiki
Here you can see the original instructions of the intro puzzles.
Translations: Deutsch | Svenska | Español | German | Russian | Japanese
The information below is intended to provide basic tips and guidelines for the tutorial puzzles. If you have additional questions, you may either:
- Leave a comment below or
- Ask online in Fold.it chat either in the game client or using an external IRC client.
Tip: Try to complete the tuorials without help first. Experience has shown this results in deeper understanding of the game mechanics.
Tip: On the tutorials follow the instructions closely, don't overthink and do too much. Don't be afraid to reset and start again. Don't be in a rush to finish the level and move on, this is your opportunity to have a play with the tools and find out how they work.
Tip : read carefully the texts, press on button "tell me more", reset the puzzle after a few try and redo.
First puzzles video : http://www.youtube.com/watch?v=JW_Fd6blrLM
Contents |
Sidechains
Edit
Level 1-1: One Small Clash

Added by ForbisgarygYou can drag SIDECHAINS with the mouse. Get rid of the clash by clicking and dragging one of the sidechains away from the other.
Level 1-2: Swing It Around
Level 1-3 : Shake
You've earned the SHAKE tool! You can use shake to fix clashes for you! When you think SHAKE has done a good enough job, you can press it again to Stop.
Backbone packing
Edit
Level 2-1: When Backbones Collide

Added by MsuchardThis is the BACKBONE of the protein. Sometimes the backbone is too close together. Click and drag the backbone to pull it appart!
You can always Undo.
Shake will adjust the sidechains for you."
Level 2-2: Close the Gap
Ot
Added by MsuchardMadde's video: http://www.youtube.com/watch?v=WVJoyRfPbic Tips ; drag one helice closer to the other, theyhave to be paralell
Level 2-3: Wiggle
You now have access to a VERY powerful tool: the WIGGLE tool! Just like SHAKE tries to take care of sidechains, WIGGLE tries to let Foldit improve the backbone. WIGGLE gets stuck if it cannot increase the score. Click this button again to stop the tool.
Hydrogen Bonding
Edit
Level 3-1: Sheets Together

Level 3-2: Lonely Sheets
Time to matc
Added by MsuchardTip : put rubber bands between to two little sheets, wiggle, remove bands, shake and wiggle
Level 3-3: Sheets and Ladders
Thre
Added by MsuchardTip : put a rubber band at each end of the sheet with the end of the sheet above, wiggle, remove the bands, shake and wiggle. The step ladder are the sheets and the side the bands
Madde's video: http://www.youtube.com/watch?v=47Qco7fYa2k
Level 3-4: Lock and Lower

Added by Msuchard
Added by Msuchard</gallery>One of the sheets is out of place! Sheets like to be alongside each other. Remember, hydrogen bonds are great for your score. You can Freeze the sheets already in place. Hold shift and double click.
Tip : one sheet is over the row, freeze the 2 sheets on each side of it, double click on them, put the sheet between this two, rotate to see if the protein is flat, shake and wiggle,
Madde's video: http://www.youtube.com/watch?v=X7DPcTvz4Ns
Level 3-5: Rebuild

Added by MsuchardThis loop appears to be a problem. You can deal with problematic segments by using the REBUILD tool. Rebuild tests out different shapes for the protein. Right click (for windows) on the backbone to start a Rebuild. You can stop when Rebuild finds the shape you want. Shake and Wiggle will take care of clashes. This looks like a good shape! Try a Shake and Wiggle to clean it up. You can Wiggle a single section. Right click and choose Wiggle
Madde's video: http://www.youtube.com/watch?v=V-AiFAO_xgo
Hydrophobics and Hydrophilics
Edit
Level 4-1: Hide the Hydrophobics

Added by MsuchardBlue sidechains need plenty of space. They should point outward.
Orange sidechains should be kept surrounded. Hide it in the empty space in the protein's interior and move the blue hydrophilic away outside. Your score measures not only clashes, but also how well hydrophobics are hidden.
Tip : move the orange sidechain in the center.
Level 4-2: Turn It Down

Added by MsuchardThe helix has turned and exposed a hydrophobic!
Madde's video : http://www.youtube.com/watch?v=rafK-Z0dZs8
Level 4-3: Flippin' Sheets

Added by MsuchardLook for the sheet with the exposed hydrophobics, and click the new straight arrows on the Tweak tool to shift and flip it.
You're almost there! Try a Wiggle to finish up.
Shake and wiggle before then flip the sheet with oranges out in the right direction
LennStar's guide: This is one puzzle that really dislikes being mishandled. It took me at least 5 tries. This is how to do it: If you already have done anything to it, reset the puzzle. (Hint: You propably have to move the 4 sheets to the foreground, the one with the arrow pointing on with the short end to the left. You can also go back to puzzle menu to get the right view.)
Now right click on the one sheet where the arrow from the text points to. Click tweak. Now click one time on the straight arrow to the right. Now the sheet should flip. use shake and wiggle it. That should raise your score to the needed points.
Madde's video : http://www.youtube.com/watch?v=RDLNivggADE
Level 4-4: The Right Rotation

Added by MsuchardMadde's video : http://www.youtube.com/watch?v=LX3qVcE4hlI
Level 4-5: Changing the structure

Added by MsuchardChanging the structure of the protein can help you see a solution better, and also affects Rebuild and Tweak. These three segments should be sheets. To enter Structure mode, click the Modes tab and choose Structure, or press 2. Right click a section of the protein while in structure mode to asign its structure from the three secondary structure types. Once you've done that, try using tweak to flip the sheet down. Use Shake and Wiggle to finish up. If the protein starts coming apart, you can use reset or undo.
Tip : click on pull mode, flip the sheet with the left arrow or rebuild the last part of the sheet.
Madde's video : http://www.youtube.com/watch?v=TfXeSc4AyA8
This puzzle is replaced in devprev by Structure and rebuild 4-5 Structure and Rebuild: http://youtu.be/x-l1aSl8QKg
Tools and Types
Edit
Level 5-1: Quest to the native (QTTN)

Added by Msuchard
Level 5-2: Movin' along
Sometimes you can MOVE whole pieces of the protein. Click on a piece to bring up the
Added by MsuchardTip : Click on the helix, then in the middle of the purple cross with the right button of your mouse (crtl on mac), then drag the helix on the shadow (if the helix rotates, you have not choose the right button), rotate the view to check then shake and wiggle. Dont use Align tools, if you have use it, go to intro puzzle menu then to movin along to refresh the view.
Madde's video : http://www.youtube.com/watch?v=Q2x03y6e4Kk
Level 5-3: Electron density

Added by MsuchardClick on the ELECTRON DENSITY button. These options let you control how the density surface is drawn. Adjust the THRESHOLD to change the thickness of the density region. At a good threshold, you can see shapes in the region that match parts of the protein. After moving the protein press ALIGN PROTEIN TO DENSITY to line up the surface with the protein. The alignment usually takes a few seconds to complete. Use Shake, Wiggle, and careful moving to fold the protein into the best possible shape that fits inside the predicted region.
Tip : wiggle, shake, wiggle, shake, then drag the end of protein inside the cloud with caution, skahe, wiggle. vidoe : http://www.youtube.com/watch?v=jDOY1QIGkog
Level 5-4: Exploration

Added by MsuchardMadde's video :http://www.youtube.com/watch?v=AAh3ThsxohQ
Level 5-5: Control over clashing

Added by MsuchardMadde's video: http://www.youtube.com/watch?v=TdC-9fmXdjY
Sequences
Edit
Level 6-1: Basic Threading

Added by MsuchardWhen you THREAD, your protein will try to fit onto the 3D template where the cylinders are. Click the little smiley to try threading. Now that you've threaded it, try a shake and wiggle!
In this puzzle, you'll just need to use the ALIGNMENT tool to thread, then wiggle and shake. Don't worry about making manual adjustments. In this puzzle, you'll just need to use the ALIGNMENT tool to thread, then shake and wiggle.
Level 6-2 : Cut and paste

Added by Msuchard
Level 6-3: Alignin' Sequences

Added by MsuchardVideo: http://youtu.be/TNi1b1HxEKE
Protein Design
Edit
Level 7-1: Intro to Design

Added by Msuchard
Level 7-2: Swapping Side Chains

Added by MsuchardNow some sidechains are too small, causing voids! Try replacing them with some large ringed hydrophobics.
You'll need to change to Design Mode.
Level 7-3: Mass Mutate

Added by MsuchardDont reset on this puzzle, go to menu/ intro puzzle and click on mass mutate.
Level 7-4: Insertion and Deletion
This red line is a CONSTRAINT, indicating that the segments it connects should be closer together. You can change the length of the helix by inserting or deleting segments. Right click a segment of the helix and use Insert Between. The blue blinking segments will show you where it will appear. The protein seems a little short now. You may want to undo or insert a segment. You can use wiggle and mutate sidechains to finish up. The protein seems a little long now. You may want to undo or delete a segment.
More molecules
Edit
Level 8-1: Ligand debut

Added by Msuchard
Level 8-2: Ligand constraints

Added by MsuchardThese are CONSTRAINTS. Red constraints are violated. Make the constraints become green! After moving the ligand closer, use WIGGLE SIDECHAINS to wiggle the sidechains and the ligand at the same time. Try and compare it to Shake Sidechains.
Level 8-3: DNA Pairing
Use Design Mode to find the correct match for the incorrectly paired sidechains. DNA sidechains pair according to color and size. Match sidechains of same color and opposite sizes to make lots of bonds!
Match sidechains of the same color and opposite sizes to form lots of hydrogen bonds! Look at this big yellow sidechain with a small yellow sidechain. Use Design Mode to find the right match for the incorrectly paired purple sidechains!
Level 8-4: DNA and Protein
DNA can hydrogen bond to protein. Mutate the proteins to form better bonds. Try adding a long hydrophilic here. Try a shorter, forked hydrophilic here