Agilent Spectrum Mill 3.0.015 Patch Installation Guide (23 September 2003)
Agilent Technolgies Inc.

This software patch fixes the following known problems (KPRs) noted in the Agilent Software Status Bulletin (SSB) and Patches public website (http://www.chem.agilent.com/cag/servsup/softdocs/ssbmain.html#):
#62, 140, 144-151, 153, and 161.

Following installation of this patch the homepage will display the A.03.015 patch designation

Instructions for installation:
==============================
The list of files shown in the "Files updated:" table below will be updated as part of the patch installation.  The defects fixed by this installation are listed in the "Defects fixed with files replaced:" table below.

Spectrum Mill A.03.00 must be installed first.

Step 1:  Download the self-extracting zip file "sm3.0.015-patch.exe" to a temporary directory on your Spectrum Mill server.  This file is available on the SSB and Patches website.

** WARNING! **
If you have customized any of the following files, make a backup copy so that you can include your customized changes in the updated files:
 
msparams_mill\urlsAccessionNum.txt
msparams_mill\terminiCarboxy.tsv
millhtml\sm_js\protChem.js

Step 2:  Double-click on the "sm3.0.015-patch.exe" in Windows Exlporer.

Step 3:  Extract the files to the Spectrum Mill directory on your server (default is E:\SpectrumMill).

Note:  If any of the files fail to update, make sure that those files are not read-only. After making the files writeable, re-run the patch program.


Files updated:
==============
millhome.htm
millbin\mstagpara.cgi
millbin\sherenga.jar
millbin\viewMaster.jar
millbin\xtractorAgilent.cgi
millbin\xtractorGeneric.cgi
millbin\xtractorsciex.cgi
millhtml\summarypp.htm
millhtml\summarysherengaframe.htm
millhtml\SM_js\protChem.js
millscripts\sherengaReport.pl
millscripts\libSpecMill\lsmViewerParams.pl
msparams_mill\terminiCarboxy.tsv
msparams_mill\urlsAccessionNum.txt


Defects fixed with files replaced:
==============
KPR#62  Gray Sequence Tag results section in Sherenga De Novo Summary is not aligned. 
- millscripts\sherengaReport.pl
- millscripts\libSpecMill\lsmViewerParams.pl
KPR#140 Accession number link in Summary only takes user to database main website.
- msparams_mill\urlsAccessionNum.txt
KPR#144 Neuropeps c-terminus search parameter doesnt work.  
- msparams_mill\terminiCarboxy.tsv
- millhtml\sm_js\protChem.js
KPR#145 De Novo Summary spectrum view too large 
- millhtml\sherengasummaryframe.htm
- millscripts\sherengaReport.pl
- millscripts\libSpecMill\lsmViewerParams.pl
KPR#146 Agilent Extractor hangs with combined profile and centroided data file 
- millbin\xtractorAgilent.cgi, xtractorGeneric.cgi
KPR#147 File not found error when clicking link in Protein/Peptide summary with two directories 
KPR#148 In Protein/Peptide Summary, unchecked directories get rechecked when mode is switched
- millhtml\summarypp.htm
KPR#149 b/y fragment ion assignments for 3+ precursors not always assigned
KPR#150 Coverage map wrong if N-term peptide or if coverage starts at second residue 
KPR#151 Different scores for spectrum with no amino acid substitutions in Identity vs. Homology modes 
- millbin\mstagpara.cgi
KPR#153 Sciex Extractor hangs if more than 8 experiments in data file
KPR#161 Extracting data from a Sciex QStar (.wiff file) sometimes fails with large (>200Mb) data files.
