Here we start the New Player Welcome Puzzle, with the screen from either starting or restarting the puzzle. As we make changes to the shape of the protein, we will be ignoring the score and concentrating on the shape instead.
By using the Structure Mode (key 2) we change some of the structure from loops to helices. Once done return to Pull Mode (key 1).
We add a band from the end segment into space - this is where we want the new helices to end. Then right click on the helices we just made and select Rebuild. Let the helices rebuild until it resembles something like the shape you can see here. Once it does stop the rebuild (space key). Remove the band (R key)
Shake (S key) and Wiggle (W key) then change the rotation of the model (Left click on the white space, and move mouse). This allows us to see the other end of the model, ready for the next part.
Place a band from segment 1 (Pressing the TAB key whilst pointing to a segment will give you info on that segment including the seg number), and place it in the top right hand corner. You can see I have frozen a segment (middle mouse button or "Shift" key and left mouse button), this is to point out the area to be worked on, separating the protein into two parts. Right click on the stretch of sheet and select Rebuild. Once the length of the model has stretched out, stop the rebuild (space key.)
Delete all the bands (R key) and now place two more bands, one from the end, downwards, and one from about the middle of the length, upwards. Using the Structure Mode, change the original sheet to loop and then make 2 new stretches of sheet, change back to Pull Mode.
Rebuild this stretch until it looks something like this image.
Add bands from one sheet to the other just as in the tutorials.
Remove the end band by clicking on the center of the band.
Rebuild this now double stretch until the sheets come together. Now would be a good time to turn on the "Show sheet bonds" in the View menu.
Remove the band in the middle and now on the end of the double sheet length. By right clicking on each of the sheets and clicking the Tweak tool, by pushing on the ball above the arrows, straighten the sheets.
Unfreeze any frozen segments (F key) and Shake (S key) and then Wiggle (W key).
Add a band from the end of the double length and attach it to the other end of the helices, ready for the next part of the structure design.
Use the wiggle tool to pull the sheets down to the helices. Space key to stop.
Shake the side chains and then Wiggle. The protein might bounce around a bit but it will settle down. Once it's settled stop the Wiggle and remove the bands (R key)
We can work on sections of the protein. By Freezing segments - either by clicking on them with the middle mouse button or Shift and Left button. We are going to work on the helices but by freezing segments either side of it we allow it to move. Right click on the helics and Rebuild. After a few movements, stop the rebuild (Space key). Open the Undo map and each change in shape will be stored on the Undo map. You can select any of those changes you want.
Shake and Wiggle.
Rotate the protein so the helics are easier to see.
Unfreeze all segments (F key), then freeze segment so we can work on the other helices. Now rebuild the second helices, again use the Undo menu tool.
Unfreeze all segments (F key) and then add a band between the two helices. The band stops the two helices coming apart.
Shake and Wiggle.
Now we're going to compact the protein. Place two new bands from the ends of the last helices to the ends of the sheet above it.
Using a very short Wiggle, bring the sheet towards the helices. Now rotate the protein to be able to work on the other sheet / helices.
Add two more bands from the ends of the helices and the sheet above it.
Again, use a very short Wiggle to bring the protein together.
Turn the bands off (D key). This is easier than deleting them and having to then replace them later if we need them again. Rotate and zoom in, point to the white area and either use the mouse wheel or hold down the middle mouse button (or Shift button and left mouse button) and move the mouse back and forth.
Shake and Wiggle, if the protein starts to come apart, turn the bands (D key) back on. After the Wiggle, remove the bands (R key).
Now it's time to start tweaking sheets. Right click on one sheet and select Tweak. Four arrows and a ball in the center of the arrows will appear. Click on the ball to straighten the sheet and the arrows that point perpendicular to the sheet to rotate the sheet. Press (Space key) to stop the tweak. Do the same for the other sheet. Then Shake and Wiggle.
Use the left mouse button to pull bits of the protein back to where you want them.
Use a long Shake and a long Wiggle.
This is just to demonstrate that bands can be used everywhere. Here we're going to change the shape of a helices.
Using a very short Wiggle we change the shape of the helices. The score does drop slightly.
Turn the band off (D key), Shake and Wiggle and we have a higher score than we did before we changed the helics shape. This is the main way of working on the protein by hand, changing the shape of sheets, helices and loops, whilst trying to make the protein more compact. If you turn the Voids on, you can see which areas of the protein need to be worked on the most.