SEQUEST Browser Run Summary Bug Fix
Overview: This SEQUEST tip describes how to fix a bug that effects some of the buttons in the SEQUEST Summary view of the SEQUEST browser. Our experience is that the bug only shows up when using MS Internet Explorer. Netscape (v 4.7) browsers appear to work fine. The fix is simple to implement and only involves careful editing of a text file. The fix is only required on Xcalibur 1.2 Bioworks. If you are running the initial release of the Sequest browser, you may not be seeing this problem.
The Problem: Some of the buttons on the Summary page in the SEQUEST browser do not work in Internet Explorer. When you click on the  button, you should then see another series of buttons, as shown below:
  
If you've been running Internet Explorer, you may have noticed that the All-None-Inv-Execute buttons do not work. These buttons are highly useful since they allow you to select or deselect OUT and DTA files and either delete them or copy them to a new directory (aka, clone a directory). This is useful if you want to select only the good hits from a SEQUEST search and copy those to a new directory, for example.
Ok, get on with it, show me the fix: In order to fix this problem, we need to add a line in the microchem_var.pl Perl script. An undefined variable is what is causing the buttons not to work.
Here's what to do:
- Locate your Website Pro directory, or wherever you've installed the Website Pro server software. This is usually C:\Website. Look in the etc subdirectory (e.g., C:\Website\etc). There should be a file called microchem_var.pl. This is a Perl script which sets a bunch of initial variables for the SEQUEST browser. (Note: I suggest making a backup of this file in case you muck something up by mistake and you can go back to the original). Use a notepad to open this TEXT (ASCII) file. Near the top of the script, you should see some text which looks like this:
#############################################################################
###################### system-dependent information #########################
# unfortunately, much of the time we need to keep track of files twice,
# once by real location and once by the URL
$htdocs = "C:/WebSite/htdocs";
$Harvard_Microchem = "0";
- Add the line in bold red text exactly as shown above. Note: the "0" is a zero.
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Save the file microchem_var.pl. Make sure to save the file as a text file and that it is in the correct /etc directory. (Also, make sure you backup the original with a different name first!)
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Try it out. Go to your SEQUEST Browser Summary page and try using the Show, All, None, Inv selection buttons. They should now work. (You may have to hit reload or refresh in your browser to get them to work initially).
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