[Molvis-list] Downloaded Protein Explorer/ConSurf in WinXP SP2

[Eric Martz]

The following issues apply only to Windows XP SP2 (hereafter referred to 
simply as "SP2"), and only when using Internet Explorer ("IE") to run 
Protein Explorer (proteinexplorer.org, "PE") or ConSurf 
(consurf.tau.ac.il). (None of these problems occur when you run PE in 
Netscape 4.):

Protein Explorer on-line (proteinexplorer.org) version 2.411 has been 
modified not to hide SP2's "information bar" (yellow bar that appears near 
top of the IE window), making it easy to access Internet Explorer's popup 
blocker and to give PE permission to popup new windows (which it requires 
in order to work). These changes to PE were released Sept. 10, 2004.

The version of Protein Explorer that is currently downloadable is 2.41. 
This is OK because SP2's popup blocker doesn't interfere with files you 
have downloaded.

However, SP2 by default blocks "active content" in downloaded files, which 
includes the javascript language in which Protein Explorer is written. 
(Details of the resulting behavior are below.)

SOLUTION ONE: Enable active content. In IE, open the Tools menu, select 
Internet Options. Choose the Advanced tab, and look for the Security 
section (last section at bottom). There, check "Allow active content to run 
in files on My Computer". Click OK. Now your downloaded PE will run in IE 
in SP2.

SOLUTION TWO: If you prefer not to enable active content, download Netscape 
4.8, install it, install MDL Chime in it, and use it only for Protein 
Explorer and ConSurf. Here are instructions for finding the Netscape 4.8 
installer: http://www.umass.edu/microbio/chime/netscape.htm (Netscape 4.8 
also has the advantage of full support for PE's Features of the Molecule 
control panel, unlike IE.)

I am working to get PE to work fully in Mozilla and Netscape 7 (current 
versions). I can't yet promise when or if.

Details of failure with "active content" blocked: When you try to run 
downloaded PE in IE, the information bar appears at the FrontDoor, and you 
must give permission before you can see the FrontDoor. When you try the 
QuickStart, you hear the telltale beep (information bar) but the 
information bar is instantly hidden when you see "One moment please -- 
Chime's installation is being checked in your Internet Explorer". 
Momentarily, you get an *incorrect* message that a popup blocker has 
stopped PE from working. Globally disabling the popup blocker has no effect 
because it is not the problem. (You cannot enter PE's local disk path into 
the popup blocker to give it permission because only Internet Zone URL's 
can be entered there. This is appropriate, because again, the popup blocker 
is not the problem for downloaded files.)

To find out if your Windows is XP SP2 (Service Pack 2), right click on My 
Computer (either on the Start Menu, or if you have set the Start Menu to 
Classic, on your Desktop) and select Properties.

------------------------------------------
Using ConSurf in SP2, IE:

ConSurf (consurf.tau.ac.il) colors each residue in a protein by its 
evolutionary conservation score, and does so completely automatically. It 
displays the colored protein in PE version 1.982.

When you try to start ConSurf's PE display in SP2 ("View ConSurf Results 
with Protein Explorer"), you see "The Protein Explorer should appear 
automatically in a few moments, if you are using a compatible browser.", 
and the information bar appears "Pop-up blocked". Click the information 
bar, and then "Always allow pop-ups from this site", then Yes. ConSurf will 
now work fine in SP2.

-------------------------------------------
The above instructions about "active content" will be integrated into a 
future downloadable release of Protein Explorer. The date cannot be 
promised because there are some other issues that we hope to resolve first.

-Eric


/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
       http://bioinformatics.org/mailman/listinfo/molvis-list

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
               http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */