Downloading and Installation of Protein Explorer
- Print these instructions now!! The most common reason
people have problems installing Protein Explorer is that they
skip over the instructions below.
Protein Explorer is a
browser-based application. It does not have an automatic
installer like most programs have. After PE is downloaded
and unpacked (into over 900 separate files), "installing" it consists of
opening the correct file in a compatible browser, and then
creating a shortcut or bookmark that makes future use a one-click
- Download one or more PE Unzipper components.
It works fine to download it to your Desktop; or you may download
it to another location if you prefer. For current Protein Explorer version numbers and release
dates, please consult proteinexplorer.org.
Your download options are:
- PE 2.80 (May 14, 2007):
(Not available in smaller pieces.)
- Download PE-280-All-Unzipper.exe
(includes all components, including the Demo and the Atlas).
This includes the folder "my_molecules", a required component,
which contains the Presentation Template and Example PiPEs and
MolSlides. Installing it will automatically redirect your
existing PiPEs to the new version of PE, but otherwise will not
affect PiPEs or MolSlides you have made.
- Older Versions of Protein Explorer
Protein Explorer 2.72 or later included a folder my_molecules,
in the same folder as "Protein_Explorer_N.NN".
If you are upgrading from PE 2.72 or later,
it is crucial
that you now move your freshly downloaded PE-N.NN-Unzipper.exe file
to the folder that contains my_molecules and the folder Protein_Explorer_N.NN.
This ensures that when you unzip (next step), any PiPEs you have made
in the folder my_molecules\pipes
will henceforth run in the new version of PE.
If this is the first time you have installed a downloaded copy
of PE, you can leave the Unzipper file
on your desktop.
- Double-click the PE-Unzipper.exe
A WinZip Self-Extractor dialog will open. Click the
Unzip button (leaving all other settings unchanged).
When extraction has finished, click the Close button
in the WinZip dialog.
- The previous step creates two folders named "Protein Explorer N.NN"
(where "N.NN" is the current version number), and "my_molecules".
If this is the first time you have installed a downloaded copy of PE,
Drag these two folders to a permanent location of
your choosing (we recommend the C: drive, for example, C:\ProteinExplorer).
It is best
if you drag them to a permanent location now
-- this may avoid future complications.
The folder my_molecules MUST be in the same directory as the folder
Protein Explorer N.NN -- it is required for the operation of Protein Explorer.
- Double-click the new "Protein Explorer N.NN" folder to open it.
Inside you will find, among other things, a file named "How to Start PE.htm".
- Right-click "How to Start PE.htm" and select
Send To, then Desktop (create shortcut).
Do not drag it and drop it on the Desktop. This will not work!
- Click the Desktop Icon in your taskbar to minimize all open applications
and reveal your Desktop (or hold down the Windows key and press m).
- Double-click the new Shortcut to How to Start PE.htm on your
Desktop and follow the instructions there. (This should display the
downloaded instructions in your browser. If it doesn't, please
re-do the previous instructions carefully.)
-------------------- Now you can run your downloaded Protein Explorer!
- If you wish, you may copy the Shortcut to How to Start PE.htm
and paste it into other locations, or drag it and drop it into
another location. If you wish, you can drag it and drop it onto your
main Start menu.
- You may now delete the file PE-Unzipper.exe if you wish.
- If you are updating from a previous version of Protein Explorer,
optionally, you may delete the folder Protein_Explorer_N.NN
for the old version (deleting all of its contents, notably the folders
atlas, protexpl, pe_demo, and shared, and their contents), along
with your bookmarks/favorites to the OLD version.
(If you keep the old files and bookmarks/favorites, you can use either the
old or the new version as you wish.)
Do not delete the folder my_molecules which may contain
your own personal PiPEs and/or MolSlides! This folder is automatically
updated whenever you download and install a new version of PE.
- Never put any
your personal work in the "Protein Explorer N.NN" folder, of any of
its sub-folders, since they will be deleted when you update to a future