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Normal mode calculation and visualisation using Pymol

Normal mode analysis is a classical technique to generate functionnally relevant movements in biological macromolecules.

Here we use all atoms but we consider a highly simplified (and quadratic) potential energy between atoms, that are considered to be linked by a spring of universal strength provided that they are located less than 10 Angstrom away in the PDB structure. See the Tirion (1996) article in the References section. For low-frequency normal modes, which give the large-amplitude and collective modes, this Elastic Network Model gives excellent results.

The results will be returned both as a raw datafile with normal mode vectors, and as a series of PDB movies (structures separated by ENDMDL in a single file), one for each requested normal mode.
The frequencies will be in cm-1, using an aritrary elastic constant of 100 kcal/Mol/Angstr**2
If you load these in a program like PyMol you will get a nice visualization of the mode-induced movements.

Alternatively, you may download the movie with VMD.

The kind of simplified plot shown above describing the elastic network of your protein will also be calculated in this section, and will be available as a file loadable by Pymol 1GGG.pymol.

To proceed, simply read the trajectory file of a given mode with Pymol, using the File/Open menu options; then assign secondary structures in the Actions menu, then build a cartoon using the Show menu, then Hide the lines, then changes colours using the rainbow option of the Colour palette. Then play the Movie. You can rotate and translate the molecule while it is experiencing NM movements.
NB: It takes less than one minute to install Pymol (Linux, Mac OSX, Windows...) and the reward is immense... You have no excuse.

Here is a downloadable example, for Mode #7 of Citrate Synthase (6CSC), to be displayed with PyMol.
Here is a GIF-animated Movie of the same molecule.

This server calculates Tirion-style normal modes for a PDB file. By using cut-offs and sparse matrix representations it is possible calculate the first (lowest-frequency) dozens of modes (say n=100) even for very large systems - 30,000 atoms or more.

The normal modes will be calculated using whatever atoms you provide in the file. If you want a reduced representation you should edit the PDB file to only contain CA atoms. It is better not to include Hydrogen atoms in the PDB file.

Use the following two commands to generate a C-alpha trace movie with PyMOL:
1) pymol mode_1.pdb
Pymol>set cartoon_trace, 1
Pymol>show cartoon
2) Then change colors and play the movie...

The so-called "collectivity measure" is also calculated and reported, for each mode. This measure is defined in the Tama and Sanejouand (2001) paper (see References section).




  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 19:39 April 19, 2014.