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.

 

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2 Comments »

  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


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