Editing Cluster mols (section)

== GUI Options ==
[[File:cluster_mols_screen_1_desc.png|200px|thumb]]
[[File:cluster_mols_screen_2_desc.png|200px|thumb]]

In the 'Compute Similarities' tab, there are options for selecting a new ligand and for specifying how many CPUs you want to run the similarity calculation on. Clicking the 'Compute Similarity' button will start the similarity calculations. If you check the 'Ignore saved results?' box it will ignore any saved intermediate results files. This could be useful if you change the contents of the original input file while keeping the file name the same.

Depending on how many compounds there are, the similarity calculations may take between 1 and 10 minutes.  If you launched PyMOL from the command line, you will be able to see the progress printing out in the console. The similarity results are saved to a file so if you want to re-cluster the same input file, you do not need to wait to recompute the similarities.


The first option on the Cluster Compounds tab defines how the clusters will be sorted. The default is to sort by the 'minimizedAffinity' which is inserted into the output sdf file after minimization with 'smina' (An enhanced version of AutoDock Vina. Available at: http://www.smina.sf.net). You can also sort the clusters by any SD tag that exists in the input file, or by the Title (alphabetically) or by the size of the cluster.

The second option is the height at which the hierarchical clustering tree is cut. The units are arbitrary, but a higher number leads to a small number of large clusters of less similar compounds, and lower cutoffs lead to more small clusters of more similar compounds. Play around with the cutoff until you get a clustering that you like. The third option is a check box for whether to group clusters with only one compound into one ‘singletons’ cluster. The forth option enables the show_contacts tool that is described below. There is also a field to enter a PyMOL selection string to compute the hydrogen bonds to. Finally, there is a button to create the clusters and load them into PyMOL.