Expert Mode in Protein Explorer (PE)
Expert mode can be selected as a preference. Preferences
sessions. The link to Preferences is below the
Expert mode can also be forced in a hyperlink that
invokes Protein Explorer by using a
query parameter, "x=1".
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:
is selected in
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.
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),
(ii) starting Explorer or Comparator
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.
When Expert Mode is on,
and when the PDB file contains an ensemble of two or more models (e.g. from NMR):
- PE does not display the alert announcing the existence of
- The initial view shows all models, instead of only the first model.
- Upon entering QuickViews, an alert is shown reminding
you that QuickViews controls the display of the first model only.
- 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.").
- When the PDB file contains an ensemble of two or more models
(e.g. an NMR result), and when
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
all models are shown, these buttons toggle water/ligand for all
models, and these alerts are suppressed.
- Pressing Quit closes PE immediately. When
is off, confirmation is requested before the session is lost.
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
- Entering the NMR Models/Animation
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.
- 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.
- The PE Recorder is controlled by a cluster of buttons beneath
message box. In expert mode, an additonal option appears,
"Edit Script ..", which enables experts to examine or edit the recorded
- 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).