Task 10 (MSUD)
The informations that are provided on the results page include:
- deformation energies and eigenvalues for the lowest-frequency non-trivial modes
- atomic displacement and fluctuation plots
- mode visualization with Jmol and vector field represention of modes
- correlation matrix for motions between Calphas
- overlap analysis for different conformations of the same protein
For the calculation of normal modes, WEBnm@ takes only Calpha atoms. The mass of the whole residue is assigned to its Calpha atom for the analysis.
The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12.
Vector representations of modes 7 and 9:
<gallery widths=500px heights=250px perrow=2"> File:MSUD_mode7.png| Normal mode 7 of 2BFF, alpha and beta chain move against each other. File:MSUD_mode9.png| Normal mode 9 of 2BFF, end of alpha chain moves strongly. </gallery