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Calculate Normal Modes Overlap Coefficient

Needs 2 superimposed PDB struct.

Given two conformations of the same molecule, the program will calculate the overlap between the difference vectors of the two forms and each set of eigenvectors of lowest frequency mormal modes.

See Tama and Sanejouand (Ref) for definition of overlap and more details. The code is from Y.-H. Sanejouand, interfaced for the web.
The program assumes that you have previously aligned the two structures.
The program will output a postscript file for each case:
i) first conf. vs 2nd conf. and ii) vice versa.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters, no space)

PDB File of the first form of the molecule (CA)
Ex: PDB_file

PDB File of the second form of the molecule (CA)
Ex: PDB_file


  • The PDB files should contain only CAs and be already superposed by e.g. Profit.
    They should have exactly the same number of residues!!!
    If you are unsure about gaps or insertions between the two files you can i) extract the sequence form the PDB file (here) and ii) align the sequences (here).
    The calculation will not work properly in case there are more than about 3000 (CA) atoms. In this case, one should resort to the RTB method and work with Blocks of residues (see YHS web site). Go and visit Elnemo for a web-interface of this (See Related links).

  • The output files will consist of 2 postscript files showing the overlap coefficients (dot product) between the eigenvectors of the first 100 lowest-frequency modes and the set of difference vectors between the two forms. As a check, the contribution of the first 6 modes should be exactly zero, if the superposition has been done correctly. The calculation is done twice: once while using the first form to calculate the normal modes and another time using the second form to calculate the normal modes.
    N.B. The cumulated score is also shown.

  • The job title is for internal use only, but note that it will show up in the public job queue (but your results will not be public).
    Avoid using a blank line here, otherwise the second plot will not be named properly and you won't be able to retrieve it.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 17:03 May 15, 2017.