My software notes

July 5, 2011

[software] MaxCluster

Filed under: softwares and scripts — kpwu @ 10:42 am
Tags: , ,

I was searching online for some scripts/macros that I can use them to superimpose and compare the RMSD of two proteins (same sequence) based on my calculated results. I know PyMOL and MOLMOL provide such tools however I have tons of protein candidates to be compared.

Before I start to write the script by myself, I checked online and saw this software “MaxCluster” developed by the “Structural Bioinformatics group in Imperial College London” . This program can do all atom or backbone RMSD calculation (superposition/alignment too) as well as ensemble clustering. It works pretty FAST!! I used many times recently. To compare more than 3000 structures, it returns me the results in one minutes.

Good for try.




  1. Hi tahnx fr the info. im using this maxcluster version in windows, and may i know how to process one to all rmsd calculation. means i need the command. and moreover where shoul i keep all my model .pdb files i.e., in the folder????

    Comment by varul — July 3, 2012 @ 1:27 am | Reply

  2. I don’t run it in windows but if the commands are same as in Mac, you should put all pdb in the same folder and run something like:
    “maxcluster -h” to see the available arguments. Also the official site gives you very detailed tutorials. What you need to do is make a list file and run “maxcluster -e exp_pdb -l list.txt”

    Comment by kpwu — July 3, 2012 @ 9:58 pm | Reply

  3. it is not assesible for downloading. what to do?

    Comment by Sonam — June 19, 2017 @ 5:54 am | Reply

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