Viewing Structures with the integrated Jmol Viewer

  1. Close all windows and load the alignment at

  2. Right-click on the sequence ID label of FER1_SPIOL to open the context menu and select 3D Structure Data. A Structure Chooser dialog box opens for the sequence, listing available PDB structure data. Select 1a70 from the list and click Open new structure with JMOL.

    Note: The Structure Chooser dialog presents available PDB structures by querying the EMBL-EBI’s PDBe web API. Extra information can be included in this window by checking boxes in the columns of the Customise Displayed Options tab.

  3. By default, the Jmol structure viewer opens. Rotate the molecule by clicking and dragging the mouse in the structure viewing window. Zoom with the mouse scroll wheel.

  4. In the Jmol viewer, placing the cursor over a part of the structure to bring up a tooltip indicating the name and number of that residue. In the alignment window, the corresponding residue in the sequence is highlighted in black and residue information is show in the status bar in the lower left-hand corner.

  5. Roll the mouse cursor along the FER1_SPIOL sequence in the alignment window. If the residue in the sequence maps to one in the structure, the residue molecular shape is visible in the structure viewer.

  6. Clicking the alpha carbon in the Jmol viewer toggles the residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence.

  7. In the structure viewer menu, select Colours $\Rightarrow$ Background Colour. . . and choose a suitable colour. Press OK to apply this.

  8. Select File $\Rightarrow$ View Mapping from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.

  9. In the Jmol window menu, select File $\Rightarrow$ Save as $\Rightarrow$ PDB file and enter a filename to save a PDB file. Once the file is saved, open the location in your file browser and drag the PDB file that you just saved onto the Jalview desktop. (Or load it using File $\Rightarrow$ Input Alignment $\Rightarrow$ From File). Verify that you can open and view the associated structure from the new alignment window using the sequence ID context menu.

  10. In the Jmol window, right-click the mouse on the background to open the Jmol menu options. Explore this, for example by Select (n) $\Rightarrow$ All (where n is the number of residues selected), and then the Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick command.

For more information on this topic go to section 7.1 of the Jalview manual.
 This exercise can be viewed in the 3D Molecular Structure Jmol and UCSF Chimera viewers video.