Update version file for the web site

commands/cascade-search.html

@@ -115,7 +115,7 @@ <h3>Precursor selection</h3>
   <li class="nobullet"><code>--max-precursor-charge &lt;integer&gt;</code> &ndash; The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
   <li class="nobullet"><code>--min-precursor-charge &lt;integer&gt;</code> &ndash; The minimum charge state of a spectra to consider in search. Default = <code>1</code>.</li>
   <li class="nobullet"><code>--precursor-window &lt;float&gt;</code> &ndash; Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>50</code>.</li>
-  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass / (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
+  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass * (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass * (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
 </ul>
 </li>
 <li class="nobullet">

commands/default.params

@@ -8,7 +8,7 @@
 #
 ################################################################################
 
-# Crux parameter file (generated by Crux version 4.2-e480be6-2024-04-15)
+# Crux parameter file (generated by Crux version 4.2-a3e1d9c-2024-07-02)
 # Full documentation available at http://cruxtoolkit.sourceforge.net/
 # comet_version 2016.01 rev. 1
 # Everything following the '#' symbol is treated as a comment.
@@ -133,8 +133,8 @@ precursor-window=50
 # to the peptide mass range using the precursor charge. For the
 # parts-per-million (ppm) window-type, the spectrum mass is calculated as in the
 # mass type. The lower bound of the mass window is then defined as the spectrum
-# mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
-# spectrum mass / (1.0 - (precursor-window / 1000000)).
+# mass * (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
+# spectrum mass * (1.0 - (precursor-window / 1000000)).
 # Available for tide-search.
 precursor-window-type=ppm
 

commands/pipeline.html

@@ -215,7 +215,7 @@ <h3>Precursor selection</h3>
   <li class="nobullet"><code>--max-precursor-charge &lt;integer&gt;</code> &ndash; The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
   <li class="nobullet"><code>--min-precursor-charge &lt;integer&gt;</code> &ndash; The minimum charge state of a spectra to consider in search. Default = <code>1</code>.</li>
   <li class="nobullet"><code>--precursor-window &lt;float&gt;</code> &ndash; Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>50</code>.</li>
-  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass / (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
+  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass * (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass * (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
 </ul>
 </li>
 <li class="nobullet">

commands/tide-search.html

@@ -109,7 +109,7 @@ <h3>Precursor selection</h3>
   <li class="nobullet"><code>--max-precursor-charge &lt;integer&gt;</code> &ndash; The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
   <li class="nobullet"><code>--min-precursor-charge &lt;integer&gt;</code> &ndash; The minimum charge state of a spectra to consider in search. Default = <code>1</code>.</li>
   <li class="nobullet"><code>--precursor-window &lt;float&gt;</code> &ndash; Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>50</code>.</li>
-  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass / (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
+  <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> &ndash; Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not available, then the mass is calculated from the precursor m/z and provided charge. The peptide mass is computed as the sum of the monoisotopic amino acid masses plus 18 Da for the terminal OH group. The mz window-type calculates the window as spectrum precursor m/z +/- precursor-window and then converts the resulting m/z range to the peptide mass range using the precursor charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as in the mass type. The lower bound of the mass window is then defined as the spectrum mass * (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum mass * (1.0 - (precursor-window / 1000000)). Default = <code>ppm</code>.</li>
 </ul>
 </li>
 <li class="nobullet">