Partial threading is used to copy the position of a section of the protein from a different model rather than doing it manually. It may introduce cut points which you will need to close and repair.
Puzzles with an active Alignment Tool usually have 5-10 models as starting points.
Reset the puzzle to choose the model you want to use as your base model.
Tip: Rainbow colour (view menu) can make it easier to compare models.
1 Show Alignment
Show Alignment Tool
Show the Alignment Tool (main menu) your base model will be in the top row and shown in the display window with a 'ball and stick' overlay.
Your base model will also be shown in the first row of models highlighted with a white X to the left of the panel. Use the green and red arrows to move any or all of the models in and out of reserve.
2 Choose the model
Choose the model you want to use
Put an X next to each model to see the ball and stick views move as you change models. You can rotate and zoom the protein to get a better view and use scripts, shake and wiggle but can't move any of the parts by hand.
3 Select segs to be threaded
Select the area to be partially threaded.
Hover over the letters in the top row to locate the area you want to partially thread, they will be highlighted on the protein and the segment number and the name of the amino acid will be displayed.
Tip: If you drag the letters spaces will appear, use the yellow undo button to remove them.
In the very top row, click the first letter of the section you want to partially thread, then shift click the letter at the end of your chosen area. The section will be highlighted by a green box.
4 Set the selection area
Set the selection area
Click the white rectangle at the top right to set the selection area. If you use the selection interface the selection will turn blue.
Your chosen model and the selected segments will be highlighted.
Click the far right white box to deselect.
5 Thread the segments
Thread the section
Click the white triangle at the left of the top row to thread the selection to the new position.
You can repeat steps 2-5 for other areas of the protein you want to partially thread using the same or different models.
