Don't use the Back button of your browser.
Because PE has multiple frames within a window, using the Back button
of the browser is not recommended. Use the PE Site Map to go
to any control panel in PE.
Turn off rotation to increase responsiveness.
The default rotation of the molecule consumes a large amount of
computer resources. All operations will be much slower when
rotation is on. It is recommended that you turn off rotation
except when gazing tranfixed by the beauty of the (rotating) molecule.
Let the Explorer catch up before proceeding.
Most problems with instability are induced by impatiently
clicking buttons and links
too rapidly. Never click over and over on the same item
-- click once and wait at least five seconds to see what happens.
before you see a response.
If you change your mind, let the process finish before you close the window
or click a different button.
will give you an impression of how long it takes
PE to complete various tasks on your computer. However, this mechanism is
not foolproof. If you rush ahead, clicking on links or buttons before PE has
finished the previous task, it is possible to induce problems such as
a permanent busy condition. If this happens, just close the window
and start over -- but operate PE at a more relaxed pace.
The Comparator has no "Ready/Busy" indicators but uses the
same internal mechanism. It is recommended that you use the one-molecule
flavor of PE enough to get a feel for how fast things work
before you use the Comparator.
In QuickViews, the pull-down menus (SELECT, DISPLAY, COLOR) won't
perform the same operation twice in a row, unless the second time,
you select (Repeat) near the top of each menu. For example, if
you DISPLAY Spacefill, then select something else, then
DISPLAY Spacefill again, nothing happens. Instead of the latter,
pick DISPLAY (Repeat) and the new selection will be spacefilled.
(This "feature" is not by design -- it is an annoying limitation of the HTML
selection menu implementation.)
If the structure disappears or slides out of view
when rotating, zoom down (click on the [-] button following [Zoom+])
and it will reappear. Keep the zoom lower when rotating.
Chime has a limited virtual space in which to rotate the
molecule. When large structures are at high levels of zoom, portions
of the molecule "hit the wall" of this space, pushing the centered
portion off to the side. Reducing the level of zoom recenters the
structure and reduces the problem. If you need to rotate a small portion
of a large structure at a high zoom level, the best solution is to
edit the PDB file to extract the structure of interest into a separate,
much smaller PDB file.
Do not attempt to resize the
window containing PE, or drag frame boundaries within it.
(Close PE and restart
it in a window of the desired size, using the menu labeled
size for new PE sessions on the FrontDoor.)
Resizing or frame boundary dragging may cause the browser to crash,
or if not (e.g. in Windows XP) cause PE to stop working correctly.
For example, in Windows XP, the browser usually survives
moving frame boundaries, but afterwards, the QuickViews help window
fails to display help appropriately, and the message window may fail
to update properly.
If a permanent busy condition ensues (evidenced in Comparator by
all buttons/commands being ignored), partial temporary recovery
can usually be achieved by clicking on the "Force Ready" link below the message
window. However, the only reliable solution is to close the window and
start a new session.
Expand/reduce the command/message frame? If you are typing
commands into the command-slot frequently, and if your screen is too
small to see the entire message box, you may prefer to increase the
size of the lower left frame. Just drag the top boundary of this
frame up to give yourself more room, and you'll be able to see the
entire message box. By dragging this frame boundary down, you can reduce
the size of this area, which may sometimes be useful in QuickViews to
expand the area for the middle help frame. However, pay attention to
whether PE works correctly afterwards -- particularly in Windows XP
or Internet Explorer,
dragging this frame boundary may cause failure to display appropriate
messages or help (see item above).
Be patient when loading large NMR PDB files.
Most NMR PDB files are several megabytes in size. While loading, there
will be a long period when Chime is blank and nothing seems to be happening.
Be patient -- eventually the aligned conformers will appear.
Windows: if clicks make beeps, tap the Alt key.
In Windows, sometimes an Alert message appears in a box and then
immediately gets put in the background before you even notice the box
has appeared. When this happens, clicking on buttons or links will
beep but otherwise be ignored, pending your pressing the "OK" button
on the (invisible) alert message. To get the message back into the foreground,
tap the Alt key once.
In Internet Explorer ONLY:
If two or more windows are opened containing Chime, when the
second Chime-containing window is closed, you may get a Plugin
Error alert. This can be avoided if you close the PE
window with PE's Quit link, rather than
by clicking on the X-button in the upper right corner of the
window. Sometimes the error, if it occurs, may crash the browser, or even
require a reboot.
A few of PE's functions work better in Netscape than in IE,
so we recommend Netscape over IE if you have a choice.";
Internet Explorer ONLY
has a behavior that can be quite confusing. Suppose you enter
a command in the command entry slot, then click the
[Bkg] button. There is still a flashing cursor in the
command entry slot, and if you type, letters appear in it.
However, the upper frame with the [Bkg] button still has focus.
This means that if you type a space or the Enter key, you re-execute
the [Bkg] button! You can prevent this bizzare behavior by clicking
in the command entry slot to focus it before you start typing.
If you have not pressed a button between entering commands, of course,
the focus remains in the command slot and this problem does not occur.
Intel Mac OSX: The tips below do not apply to Intel Macs,
where you must use PE in Windows. Please see
PE Compatible Browsers.
Browser Suddenly Disappers: Resizing a Netscape 4.8
window in OS X Classic sometimes causes Netscape to suddenly
disappear (crash, "vaporize") without warning. This happens
especially on the default page http://apple.netscape.com.
Workaround:Before you resize the browser window, change the
location to http://proteinexplorer.org. Now, change your default
starting page to proteinexplorer.org (open Netscape's Edit menu,
Preferences, Navigator, and set the Home Page to Current Page).
Resizing the Netscape window at Protein Explorer's FrontDoor
is much less likely to cause this problem. However, Netscape
may not survive resizing a PE session window
(with the three frames and the rotatable molecular image).
Therefore it is important to set the desired PE window size before
starting PE (using the Window Size menu on PE's FrontDoor).
Recurrent "Network Errors": Some but not all OSX computers
tend to complain
A network error occurred
while Netscape was sending data
Try connecting again
Sometimes, this "error" occurs repeatedly preventing the use of PE.
This can be prevented by rebooting, and running PE in Netscape 4.8 in Classic
as the only application. Running any other network-using application (such as Safari, Fetch,
etc.) before or concurrently with PE may induce the recurrent "Network
Downloaded PDB Files. When you download PDB files,
or copy them from Windows sources, OSX deems the PDB
files inaccessible by Netscape 4.8 in Classic. (It sets the type and creator
to be incompatible.) To make your PDB files compatible with PE in Netscape 4.8/Classic,
drop them on the PDB Conversion Droplet Program
This droplet can be
and it is included when
download Protein Explorer.