Starting Your Downloaded Copy of Protein Explorer (PE)
If something isn't clear, please email your suggestions
to me (emartz@microbio.umass.edu).
I. Choose a compatible browser.
Here is a
list of compatible browsers
(all free) and where to download them.
Windows:
see list at the above link.
Intel Mac OSX:
Use MS Windows (supported, for example, by
parallels.com).
PPC Mac OSX:
You must have Classic (OS9) to use PE.
PE requires the Classic application
Netscape Communicator 4.x (4.8 is recommended;
downloading instructions).
(No other browser works. Netscape 7 and 8 do not work.)
- When Netscape 4.8 is run in Classic under OSX, resizing the window
often causes it to suddenly disappear (crash) when the default Apple/Netscape
page is being displayed. After you have displayed Protein Explorer's FrontDoor
page, you can resize.
- To stop the annoying Netscape Messenger from popping up every time
you open Netscape 4.8, delete all files with "messenger" in their names
within the Netscape folders.
- See Tips for PE in Classic with OSX.
ALL PLATFORMS: If you're not sure whether your browser
is compatible, go ahead and try starting PE -- if you need a different
browser or version,
PE will explain how to proceed.
If you have already installed Netscape 7 or 8 and like it, it is perfectly
OK to install Netscape 4.8 in addition (just be sure to specify a separate
directory location). When installed in separate locations,
the two versions will not interfere with each other.
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Appearance of Protein Explorer after clicking
Quick-Start in a compatible browser.
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II. Verify browser compatibility.
Before you attempt to run your downloaded copy of Protein Explorer (PE),
make sure you can run Protein Explorer on-line from
http://proteinexplorer.org.
At the FrontDoor there, click the large Quick-Start link in the yellow
box near the top. If your browser is compatible, you will soon see
the PE's FirstView of 1d66, as shown on the right.
If your browser is not compatible, attempting to start PE
will automatically tell you how
make it compatible. It is best to get this resolved before attempting
to run your downloaded copy.
Seeing the 1d66 molecule (yeast Gal4 complexed to DNA) in PE, as
shown on the right, verifies that your browser is compatible.
After you have seen the molecule from PE running on-line, proceed
to start your downloaded copy as explained below.
If you think you have a compatible
browser but PE never displays the molecule, see
troubleshooting.
(If you do not have an Internet connection, go ahead and
start your downloaded copy as explained below.)
III. Start your Downloaded PE!
Generally, to see a molecule in PE, you must
- first open
a browser displaying PE, and
- next specify the molecule wanted.
There are a variety of ways to specify the molecule.
After you start PE, you will see them explained on the FrontDoor of PE.
Several methods you
might reasonably expect to work will not
work, such as double-clicking on a PDB file, or dragging
a PDB file and dropping it on a shortcut/alias to PE.
Here are several alternative methods for starting PE.
They are equally good -- use whichever is easiest for you.
- Windows XP Service Pack 2:
Give Permission for Active Content
- If you are not using
Windows XP Service Pack 2 (SP2)
please skip this section.
To find out which version of Windows you are using, right-click on
My Computer, then click Properties. If you do not see "Service Pack 2"
under "System", skip this section.
- In order to run a downloaded copy of PE in
Internet Explorer in
Windows XP SP2
you must give permission for "active content" (javascript) to
run from the downloaded HTML files that comprise PE.
While we can guarantee that the active content in PE is safe,
we cannot guarantee that active content in other files you might
download is safe. If you prefer not to enable active content,
the solution is simple: use
Netscape 4.8
(instructions) for PE.
You can still use
Internet Explorer
for all other purposes.
- Run
Internet Explorer (IE)
and open its Tools menu. Select
Internet Options. Choose the Advanced tab, and look for the Security
section (last section at bottom). There, check both
"Allow active content to run in files on My Computer"
and
"Allow active content from CDs to run on My Computer".
Click OK.
- For these changes to take effect,
ALL Internet Explorer windows must be closed before
you to re-open Internet Explorer to run PE.
Now your downloaded PE will run in IE
in SP2, either from hard disk or from CD-ROM.
- Method 1: Make a Desktop Shortcut/Alias to PE.
Windows:
- Open Windows Explorer (click Start at the lower left of your screen,
and pick Programs, Windows Explorer -- or hold down the Windows key
and press E).
- Find your newly installed folder
Protein Explorer N.NN,
where N.NN is the version number -- if you have several versions installed,
pick the highest number.
Open the folder to display the files it contains.
- Right click
the file "PE Startup.htm",
select the Send To menu, and click Desktop (create shortcut),
then OK.
Do not drag the file and drop it on your desktop -- this will
not work.
- Close Windows Explorer, and click on the Desktop icon in the Taskbar
at the bottom of the screen
(just to the right of the Start button). This simply minimizes all open
windows so you can see the Desktop. (You can also do this by holding down
the Windows key and pressing m.)
- On the Desktop, find the shortcut named Shortcut to PE Startup.htm.
Right click it, and select Rename. Change the name to Protein Explorer
(and press Enter),
or if you want to keep multiple versions, "Protein Explorer N.NN"
(substituting the version number for N.NN).
- Double-click the shortcut to Protein Explorer whenever you want to
run it.
This method invokes your default browser, normally
Internet Explorer.
If Protein Explorer doesn't work, see Troubleshooting.
- To run PE in a non-default browser,
on your Desktop, drag the
Protein Explorer shortcut and drop it onto a
shortcut for the desired browser.
(If there is no shortcut to the desired browser
on your Desktop, find that browser
on your Start menu, right click and
Send To Desktop.)
- Instructions for making a shortcut that will start PE directly in
Firefox, Netscape, or Mozilla are
below.
- Optionally, you may copy the shortcut to Protein Explorer and paste it
into other locations, or drag it and drop it in another location. It
can be dragged and dropped into the Programs submenu of the
main Start menu. Shortcuts will work
from any location, as long as the original file "PE Startup.htm" remains
in the "Protein Explorer N.NN" folder.
Macintosh PPC:
- (If you have an
Intel Mac, PE will run only
in
MS Windows [supported, for example,
parallels.com]. This
section does not apply to
Intel Macs.)
- Open your new folder Protein Explorer N.NN,
where N.NN is the version number -- if you have several
versions installed, pick the highest number.
- Select the file PE Startup.htm.
Make an
alias.
(Finder's File menu, Make Alias, or in OS 8/9 Apple m, or in OSX
Apple l).
- Drag the new
alias
to your Desktop, or another convenient location if you prefer.
Do not drag the file itself to the Desktop -- this will render it useless!
- Rename the alias to "Protein Explorer"
or "Protein Explorer N.NN"
(substituting the version number for N.NN).
- Double-click the alias to Protein Explorer whenever you want to
run it. It should automatically start in Netscape.
(If by any chance it starts in Internet Explorer or another
incompatible browser, then drag the
Protein Explorer alias and drop it onto Netscape to force it to
start in Netscape.)
If Protein Explorer doesn't work, see Troubleshooting.
- Optionally, you may drag
the alias to Protein
Explorer (or a duplicate of it) into any convenient folder you wish.
Aliases will
work from any location, as long as the original file "PE
Startup.htm" remains in the "Protein Explorer N.NN" folder.
- If you would like Protein Explorer to be listed on your Apple menu,
drag an alias into Macintosh HD:System Folder:Apple Menu Items.
- Method 2. Make a bookmark/favorite to PE in your browser.
- Display PE's FrontDoor in your browser
using the shortcut/alias prepared in Method 1.
Firefox, Netscape, or Mozilla:
- Open the Bookmarks menu near the upper left of the Netscape window
(Macintosh: top of the screen),
and click Add Bookmark or Bookmark This Page.
- From now on, after you open Netscape, you can start PE from the Bookmarks menu
(look for Protein Explorer FrontDoor).
- Optionally, you can rename the Bookmark to indicate that
it runs your local downloaded copy of PE, not PE on-line.
Choose Edit Bookmarks in the Bookmarks menu.
Select the desired bookmark, then right click it, and select Bookmark
Properties. Change the Name and click OK.
Internet Explorer: (Windows only)
- Open the Favorites menu at the top of the IE window,
and click Add.
- From now on, after you open IE, you can start PE from the Favorites menu
(look for Protein Explorer FrontDoor).
- Optionally, you can rename the Favorite to indicate that
it runs your downloaded copy of PE, not PE on-line.
Choose Organize Favorites on the Favorites menu.
- Troubleshooting.
- No FrontDoor. Does Method 1 above display the
Protein Explorer FrontDoor page in your browser? This is
the same page you see on-line at proteinexplorer.org.
If you do not see the downloaded FrontDoor, you probably
skipped some of the instructions above. Please try following the above instructions
more carefully.
- FrontDoor, but No Molecule. When you click the large Quick-Start link
near the top of the FrontDoor page, a new browser window should open
and display 3 frames. The frame on the right should display a molecule,
as shown in the figure above. If you see the 3 frames, but no molecule ever
appears, you may have a problem with your Chime installation.
Please follow the suggestions in
Troubleshooting Chime and Protein Explorer.
- How to make a Netscape shortcut
to PE in Windows.
(This procedure can also be used for
Firefox, substituting "Firefox" for
"Netscape" below.)
- This procedure is needed
only when your default browser is
Internet Explorer. If Netscape is your
default browser, you can simply double-click on the "Shortcut to Protein Explorer"
that you created in Method 1 above.
- Click the Desktop icon in the taskbar to reveal the Desktop
(or hold down the Windows key and press m to minimize all windows).
- Right click the Netscape shortcut on your desktop, and
select Copy.
- Right click on an empty space on your Desktop and select
Paste Shortcut.
- Right click the new Netscape shortcut, and select Rename.
Name it "Protein Explorer in Netscape" (it needs
to have a different name from your existing "Protein Explorer" shortcut
that starts PE in IE).
- Right click your shortcut to Protein Explorer (created
in Method 1 above) and select
Properties. Block the Target pathname, right click on the
blocked target, and select Copy. Click Cancel.
- Right click the "Protein Explorer in Netscape" shortcut you made above,
and select Properties. Click in the Target slot, and press the End key.
Type a space, then right click and select Paste. (This should
add the pathname of "PE Startup.htm" to the end of the Target command.)
Click OK.
- Double-click this shortcut to Protein Explorer in Netscape whenever you
want to run PE in Netscape.
- The shortcut to Protein Explorer in Netscape can be copied or dragged
to any convenient location, including the Programs submenu of the main
Start menu.
END OF INSTRUCTIONS.