Difference between revisions of "Task 10 (MSUD)"

From Bioinformatikpedia
(WEBnm@)
(WEBnm@)
Line 15: Line 15:
   
 
The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12.
 
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
   
 
===ElN&eacute;mo===
 
===ElN&eacute;mo===

Revision as of 17:16, 24 July 2013

Results

Lab journal

WEBnm@

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

ElNémo

Discussion