<div class="gmail_quote">I recently started using g_cluster and have a question. When I run g_cluster, the program asks me to select two groups. The output looks something like this:<br><br><span style="font-family: courier new,monospace;">Select group for least squares fit and RMSD calculation:</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Group 0 ( C-alpha) has 383 elements</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Group 1 ( active_site) has 2438 elements</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Select a group: 0</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Select group for output:</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Group 0 ( C-alpha) has 383 elements</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Group 1 ( active_site) has 2438 elements</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Select a group: 1</span><br><br>I have assumed that g_cluster aligns the trajectory by the first group selected, and then clusters based on the second group. Recently, however, someone told me that both the alignment and the clustering is performed only on the first group. Can anyone confirm this? If so, what's the purpose of the second group?<br>
<br>Thanks,<br><font color="#888888"><br>Jacob<br>
</font></div><br>