Superpose and Sort

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What is it?


Superpose and Sort (SnS) is a tool for automatisation of superposition of multiple macromolecular structures. It is also an AppleScript applet that uses superpose program (distributed with CCP4 package) to automatically superpose many query structures on a target structure. It writes superpositioned target and query structures as one PDB file and orders them according to RMSD. It also writes a log file with RMSD values for all performed superpositions.



How does it work?

Diagram above illustrate basic idea behind this applet. After SnS is launched it will:
1. Locate the superpose binary (if superpose cannot be found, it will ask user to show where superpose is).
2. Ask user for query PDB files (it will choose only files with .pdb, .ent and .brk extensions).*
3. Ask user for a target PDB file.
4. Make folder „results” inside the folder containing query PDB files, where all output files will end up.
5. Use superpose program to do all hard work.
6. Score results according to RMSD and write output PDB files and a log file with RMSD values.

* - SnS will change file extension of .ent and .brk files to .pdb, it will also give an option to process just selected files or all files in the folder.


Limitations

  • Superpose and Sort requires superpose to be installed.
  • As Superpose and Sort is written in AppleScript it can be only used on Macs.


  • Download


    You can download Superpose and Sort HERE.



    Acknowledgements and disclaimer


    I am grateful to Martin Moncrieffe and Hernani Leonardo Silvestre for constructive criticism and applet testing. The applet icon was made using PyMOL.

    Superpose reference: E.Krissinel and K.Henrick (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. D60, 2256-2268.
    Superpose home page: http://www.ebi.ac.uk/msd-srv/ssm/

    While I have made every effort to make the applet free of any errors, I cannot guarantee it is free from defects. Therefore use the software on your own risk. Under no circumstances I shall be liable for direct, indirect, incidental, or consequential damages resulting from the use, misuse, or inability to use this software.