On completion, clusterPca will display a graph of the clustering results. This graph will also be saved to clusterPca.png unless flgPdf is true. (Prior to 1.10.1, pdf was the default, but this proved excessively slow for large datasets). If more than 3 features were used, the clusters will be projected down to the space spanned by the first 3 features for viewing. 3D plots can be rotated for better visibility using the toolbar, and can be saved manually in a variety of formats using the plot's File menu.
An IMOD model for tomogram <T> with particles from class I in object I will be saved to a file named class_tom<T>_<fnModParticle>.mod, where <fnModParticle> is the name of model corresponding to tomogram <T>. Objects nClusters+1 and nClusters+2 will be associated with particles flagged as duplicates and unclassified particles, respectively. These models are intended for viewing (e.g. with 3dmodv) only, and will not be compatible with the either the input or output motive lists, since particles will have been re-ordered and dispersed among multiple objects.
Finally, output motive lists with the assigned classes stored in column 20 of the motive list will be written to files named pca_<basename>_MOTL_Tom<T>_Iter<I>.csv, where <basename> is the specified output name, <T> is the tomgram number, and <I> is 1 plus the iteration number used to generate the alignment. Subvolume averages corresponding to an individual class can be generated by backing up the original output motive lists (i.e. without the "pca_" prefix), replacing them with the new ones, and then running averageAll with selectClassID in the prm file set to the desired class number. Typically, one would also set lstThresholds to a single, large number to avoid generated multiple averages for each class.
NOTE: like pca, this program is potentially memory intensive. 32 GB or more of ram may be required for typical applications (e.g. approximately 600 particles of size 140x140x140 voxels). Binning or single-precision computation may be required for larger data sets or systems with insufficient memory. See the pca man page for additional details.