What is the maximum number of structures I can cluster using XCluster?
All memory used by XCluster is allocated dynamically therefore the only limit on the number of structures which can be clustered should be the amount of memory available in your machine. However in practice, calculating the pairwise distance matrix for more than a couple thousand structures is very slow (extremely slow if symmetry is involved). Also the “Map” display is limited to displaying a map with a minimum of one pixel per structure. On most monitors this means that Maps < 1000 pixels are the only ones which can be viewed in their entirety (Version 1.4 (First Qtr 1997) has a scroll-bar which removes this limitation). Note that if clusters do exist they will usually show up in a subset of the data. If you have too many structures to comfortably cluster then build a subset by sampling randomly from the data file and run on that. Q9.
