I am learning how to use the Library MCS program and the clustering seems to work fine. Is there a way to get the original structure names to appear in the dendrogram or output? I'm inputting a SDF files with 60 structures and can't figure out how I can identify which structure goes with which cluster!
I'm afraid that the dendrogram viewer cannot display names and other properties. However, if you move the mouse over the nodes in the dendrogram an information window pops up and it displays all data associated with the structure. The grid view below the dendrogam also shows all property values (this is not the standard view though, to get there either press CtrlM or click the icon with the benzene, or use the menu, Display->Mode->MarvinView.
Does this help at all?