Jacob Durrant wrote:
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:
Select group for least squares fit and RMSD calculation:
Group 0 ( C-alpha) has 383 elements
Group 1 ( active_site) has 2438 elements
Select a group: 0
Select group for output:
Group 0 ( C-alpha) has 383 elements
Group 1 ( active_site) has 2438 elements
Select a group: 1
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?
I agree that "output" is ambiguous. g_cluster -h is also silent on both
the need to provide these groups and what they're used for. Perhaps an
improvement to the documentation is in order.
Mark
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