Tutorials: Structure Display

By default, a ribbon diagram will be loaded when a structure is loaded. To view a tutorial on changing defaults, please visit Preferences Tutorial.

The following tutorials on Creating and Displaying Structures will always begin from a ribbon diagram, and guide the user through methods of changing a structure, displaying backbone, trace, and redisplaying the ribbon diagram. They will also show how to render parts of the structure and to display only part of a structure.

1. Start a fresh copy of PKR Explorer
2. Options > Preferences
   Default Structure Display > Ribbon Representation
   Execute
3. File > Load from PDB
4. Select a PDB ID, or type the ID in the field.
5. The Status Bar should indicate that PDB file is being loaded. As a default, a colored ribbon structure of PKA will open in the Structure Viewer.  The sequence of PKA will open in the Sequence Viewer.  Helices are red, loops are green and beta strands are yellow by default.

First, choose OPTIONS > Common Coloring. 
By default, Common Selections is selected.  With this enabled, clicking a residue on the sequence or structure, highlights the corresponding residue on the structure or sequence.   With Common Coloring enabled, the a change of color on the sequence, changes the corresponding residue colors on the structure.

1. Options > Set Depth Perception.
   A menu opens that allows the user to set the degree of fog.

2. Choose Extent of Fading > Drag the scroll bar to the left to a value of 15.
   Notice the ribbon getting brighter (less fog).

3. Choose Extent of Fading > Drag the scroll bar to the right to a value of 70.
   Notice the ribbon getting faded (more fog).

4. Choose Extent of Fading > Set the value at 40.
   The view should look similar to that on the right.

5. Now, click on Set to Default. The Extent of Fading returns to 50.

6. Disable Depth Cueing. All fog disappears.
   Click on Disable Depth Cueing to verify that the structure appears very bright.

7. Before moving on to the next part of the tutorial, Choose Extent of Fading > Value 40.

1. Open PKR Explorer

2. Choose File > Load from PDB

3. Select or type into the field "1atp"

4. Display the Ribbon and Structure:
   View > Structure display... >
   Choose level of Selection: "Structure" >
   Click the structure window and make sure "Display" on the right is selected.

5. Click "OK"
   The structure will appear in addition to the ribbon.

6. Select Options > Ribbon /Structure Color >
   Disable this by un checking this option.
   If this option is checked, changing the color on a structure will change the ribbon color and visa versa.

7. Hide the ribbon:
   View > Ribbon display...> Ribbon Type: Rendered Ribbon > "Off"
   Click the ribbon > Click: "Execute"
   The ribbon is now hidden, the backbone is shown.

8. Display only a part of the structure:
   Click on the name of the sequence "1atp"
   Select residues 70-100.
   Click on residue 70, hold the shift down, and click 100.
   The selected residues should be colored yellow.

9. Structure Viewer > View > Structure display... >
   Level of Selection: "Selected" >
   Click: "Display only"
   Click "OK"
   The structure will disappear and only the selected portion will be shown.

10. Change the Depth Perception:
    Options > Depth Perception > Set to 70
    Notice that the depth perception can be seen as the part in the "front" is clearer than the part in the "back."

11. Color the Background White
    Options > Preferences > Structure Viewer > Background
    Click on the colored box next to "Background"
    Choose white on the colored palette> Click OK.
    Click OK in the Preferences Panel.

12. Options > Common Coloring: Disable Common Coloring
    (make sure it is un-checked)

13. Sequence Viewer > Display >
    Set Residue Color >
    Solid Color > choose Red > Click: "OK"
    This will allow the user to see which range of sequence is displayed in the Structure Viewer

14. Changing the Rendering Style:
    In the Sequence Viewer, Select Residue70.
    Hold the shift key and select on Residue80.
    In the Structure Viewer > View >
    Structure Rendering..>
    Currently Selected >
    Rendering Style: "Ball and Stick" >
    Rendering Quality: "Best">
    Click: "Execute"

15. Color a range of residues:
    With the same range (70-80) selected:
    Structure Viewer > View > Structure Color..> Currently selected >
    Custom Color: Red > Execute.

16. Change the Render style and Color of Selected Structure
    Select Residues 81-100 on the sequence.
    View > Structure Render..>
    Currently Selected >
    Rendering Style: "Space Filling" >
    Rendering Quality: "Best" >
    Click: "Execute"
    The space filling structure should be colored by default "bond color."

17. View the Ribbon:
    View > Ribbon Display...> "on" > Type protein name: "1atp"
    Execute

18. Change the Ribbon Color:
    With the ribbon now displayed:
    View > Ribbon Color..> Level of Selection: Structure > "1atp"
    Custom Color: Gray> Click: "Execute"

19. Export image:
    File > Export image
    Type of file: ".jpg"
    Choose a resolution: "dpi"
    Type name of file and choose location.
    Click: "Export"

20. To go onto other tutorials: Tutorial Home.