VMD plugins at WMC Physiology & Biophysics

Cluster: Clustering Tool

Description | Usage | Download | Installation | Author

Description

Features include:

• Import results from:
  • NMRCLUSTER (link doesn't work anymore).
  • Xcluster.
  • R hierarchical clustering.
  • Gromacs clustering utility g_cluster.
• Color conformations by cluster.
• Selection of clusters and/or conformations to display.
• Multiple levels of clustering.
• Custom representation.
• Join single member clusters in a separate cluster.

Usage

To use the Cluster plugin you need:

1. Load a trajectory of the conformations used for clustering into VMD.
2. Define the atom selection and molecule to use as representation in vmd.
3. Generate the clusters with one of the following external utilities and Import the results into the plugin:
   • NMRCLUSTER: import the "Cluster.log" file. Only a level (0) will be available. Outliers will be splitted in different clusters. Use the Join 1 member clusters to cluster them together.
   • Xcluster: import the ".clg" file. All levels of interest must be saved in order to display them in VMD (look in the Xcluster manual for the Writecls command).
   • R:
     1. Obtain the rmsd between structures. You can use the iTrajComp plugin for and easy way of doing this (I suggest writing the results in matrix format).
     2. Load the data into R and use one of the available functions in R to do hierarchical clustering (hclust, agnes, diana, ...). If you used the iTrajComp plugin to create the rmsd matrix, the following should work in R (see the documentation of the individual commands for further options):

                data = scan('/path/to/rmsd.mat')
                rmsd = matrix(data, nrow=sqrt(length(data)), ncol=sqrt(length(data)))
                library(cluster)
                cluster = agnes(rmsd, diss=T)
              

     3. Cut the tree into groups (levels) using cutree. You can cut into one or more groupings. For example

                levels = cutree(cluster, k=2:5)
              

        will output the cluster membership of each object for levels 2 to 5.
     4. Write the results to a file to input into the Cluster plugin:

                write.table(levels, file='levels.dat', quote=F)
              

     5. Import the file into the Cluster plugin.
   • Gromacs (g_cluster): import the "cluster.log" file. Only a level (0) will be available. g_cluster timesteps are automatically mapped into VMD frames. Thanks to Andrea Carotti for all his help with the testing.
4. Managing the GUI:
   • Select the level you want to see. The list of clusters will be updated together with the colors of the conformations. All clusters will be displayed when you change the level.
   • Select/Deselect clusters to activate/deactivate them.
   • Select/Deselect conformations to activate/deactivate individual conformations.
   • All and None turn on/off all the clusters and conformations.
   • Activate Join 1 member clusters to display all single member clusters in a separate cluster (outl).
   • The atom selection to represent can be changed in the atom selection box. Click the Update Selection button to apply the changes.

Download

Installation

1. Download the plugin from here to the directory where you store your VMD plugins.
2. Add the following to your .vmdrc startup file (or create one) (for unix the path should be $HOME/.vmdrc, and for windows %USERPROFILE%\vmd.rc):
   1. For VMD 1.8.3 and up

      lappend auto_path {/path/to/your/plugins/directory}
      vmd_install_extension clustering clustering "WMC PhysBio/Cluster"
      

   2. For VMD 1.8.2 and down

      lappend auto_path {/path/to/your/plugins/directory}
      if { [catch "package require clustering" msg] } {
        puts "VMD Cluster package could not be loaded:\n$msg"
      } elseif { [catch {menu tk register "Cluster" clustering} msg] } {
        puts "VMD Cluster could not be started:\n$msg"
      }
      

   Remember to correct the path to your plugins directory; i.e, if you saved the plugin in /home/user/myplugins, write that same path in the auto_path line.

   Note: If you created the .vmdrc file, remember to add menu main on to get the main menu back.

3. Start VMD. The Cluster plugin should be accessible from the Extensions menu.

Author

Send comments and feedback to Luis Gracia.