Expert mode can be selected as a preference. Preferences survive between sessions. The link to Preferences is below the message box.
Expert mode can also be forced in a hyperlink that invokes Protein Explorer by using a query parameter, "x=1".

When Expert Mode is off, if ten commands are entered into the command entry slot, a window opens informing you of the existence of the Expert Mode preference.

Expert Mode has the following effects:

Startup
1. When Expert Mode is selected in Preferences, the molecule does not start out spinning, water is hidden in the initial image, and identification reports for clicked atoms are abbreviated to one line. However, these are also individual preferences, so you can set any of them as you wish while keeping Expert Mode on.

2. A molecule can be loaded in either of two ways: (i) pre-specified (in the link to PE or in the slot at the FrontDoor), or (ii) starting Explorer or Comparator Empty, and then using PE's Load Molecule control panel. After a molecule has been loaded, when Expert Mode is off, PE automatically changes the control panel to FirstView. When Expert Mode is on, if the molecule was prespecified, PE starts at Features of the molecule (instead of FirstView). If the molecule was loaded from the Load Molecule control panel, in Expert Mode or Comparator, there are links to FirstView and QuickViews, but the control panel does not change automatically.

3. When Expert Mode is on, and when the PDB file contains an ensemble of two or more models (e.g. from NMR):
   1. PE does not display the alert announcing the existence of multiple models.
   2. The initial view shows all models, instead of only the first model.
   3. Upon entering QuickViews, an alert is shown reminding you that QuickViews controls the display of the first model only.

4. At startup, the command entry slot will be blank (instead of containing the comment "# Commands May Be Entered Here"), and the message box will be empty (instead of containing "MESSAGE BOX: Messages will appear here, including identities of atoms clicked with the mouse.").

   Convenience Buttons

5. When the PDB file contains an ensemble of two or more models (e.g. an NMR result), and when Expert Mode is off, the first time the [Water] or [Ligand] button is pressed, an alert is shown warning that only the water/ligand for the first model is displayed. In Expert Mode, all models are shown, these buttons toggle water/ligand for all models, and these alerts are suppressed.

6. Pressing Quit closes PE immediately. When Expert Mode is off, confirmation is requested before the session is lost.

   Control Panels

7. When Expert Mode is off, after loading a molecule in the Load Molecule control panel, PE automatically changes the control panel to FirstView (unless in Comparator mode). This automatic change is suppressed when Expert Mode is on, and links to both Advanced Explorer and QuickViews appear. (Only the latter link appears when Expert Mode is off.)

8. Entering the NMR Models/Animation control panel with Expert Mode off triggers an offer to display all models colored by N->C Rainbow. In Expert Mode, the latter is the initial view, so the offer is not made.

   Atom Identification

9. Clicking an atoms reports its identity in the message box. A preference "Explain ID's of clicked atoms" controls whether the basic one-line report is interpreted. When Expert Mode is off, for only the first report in a session, you are warned that in unusual cases, the explanation may be incorrect. When Expert Mode is on, and explanations are enabled, the warning is not shown.

   PE Recorder

10. The PE Recorder is controlled by a cluster of buttons beneath the message box. In expert mode, an additonal option appears, "Edit Script ..", which enables experts to examine or edit the recorded command script.

11. In expert mode, the PE Recorder help button displays the PE Recorder Help Index. With expert mode off, it displays the PE Recorder Introduction (on which Index is a link, among others).