# Scripts

/home/exec/utilities/python/clusterhead_mp.py d2gi_5A_cluster.out

• Clusterhead_mp provides the best representing model within each cluster.
• Clusterhead_mp requires only the cluster.out file.
• Important**:** The name of in the .out file must follow a very rigid naming format: '{system name}{diversity}cluster.out'
• Please refrain from using symbols and spaces in the system name and the diversity sections.
• If the .out file does not follow the proper naming format, rename it.
• output: The script creates directories that corresponds to the number of clusters. Each folder will contain soft links of pdbs to their appropriate
• Below is an example of 9 pdb files that are placed in 3 clusters:

1) Directory before clustered_mp

• This is how the directory should appear as before initiating clusterhead_mp. It must contain:

• all the pdb files obtained from VMD
• and the cluster.out file. (with the correct naming format)

2 ) Executing clustered_mp

• The script will display the amount of clusters found. Then prints out the pdbfiles that are assigned to clusters in the form of: (cluster number , [pdbfile(s)])

• Note: This is a very simplified version for tutorial purposes. Practically, you would have 10 or more clusters and a total of 1000 or more pdbfiles.
• Clusterhead_mp program is done when the "Processes finished" message appears.

3) Directory after Clusterhead_mp

• Clusterhead_mp creates new directories that corresponds to the number of clusters provided in the .out file.
• Each of these directories will contain the best representing model within a cluster.