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Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. \u00a9 1994 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540150811","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:06:06Z","timestamp":1104627966000},"page":"899-916","source":"Crossref","is-referenced-by-count":211,"title":["Cluster analysis of molecular conformations"],"prefix":"10.1002","volume":"15","author":[{"given":"Peter S.","family":"Shenkin","sequence":"first","affiliation":[]},{"given":"D. Quentin","family":"McDonald","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540110405"},{"key":"e_1_2_1_3_2","volume-title":"Algorithms for Clustering Data","author":"Jain A. 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