Should you encounter any unexpected behaviour,
please let us know.
***  GENE REGULATION/RNA 27-FEB-04 1SI3  ***
|Overall normal mode analysis (collectivity, overlap)|
click here to view the properties of the normal modes
(Displays the collectivity of the normal modes and the
overlap between the modes and a conformational change
when two models are submitted)
%Bfactors-Wn> 0 negative values found in the B-factors column of pdb file.
(CHARMM units assumed for eigenvalues)
Bfactors> Normal end.
click here to compute predicted B-factors
(Computes the B-factors from the normal modes and compares them to the B-factors in the model)
|Individual normal mode analysis (animations, RMSD)|
(The PDB-files for download contain several models separated by MODEL/ENDMDL.
Shift-Click on the mode you wish to save to your local disk.
If your browser has a plugin for PDB files, such as
Swiss-Pdb Viewer, just click on the mode you wish to display.
The perturbation indicates the amplitudes that were applied in the normal mode perturbation as DQMIN(DQSTEP)DQMAX.
Small animations (GIF-format) are about 300kB, large animations are 3Mb.
CA-vari computes the distance fluctuations between all C-alpha atoms.)
The (best) RMSD is computed with respect to the second conformer.
<R2> gives a visualization of the mean square displacement
of all C-alpha atoms associated with a given mode.
|All NMA perturbed models (download)|
SHIFT-CLICK HERE to save to disk
(This zip'ped file can be read under Unix with 'tar xfz 220814071015109309.tgz'
Windows/Mac users use WinZip.)
|Compute additional perturbed models with elNémo|
Here you can request additional normal mode computations, or change the amplitude range (DQMIN/DQMAX)
for an already existing mode. When the calculations are finished, the new mode will apear in the list above.
|Compute models for molecular replacement (bi-modal screens)|
Here you can request models that are perturbed in the direction of
two normal modes at the same time.
This kind of computation is of interest when using NMA
for molecular replacement in X-ray crystallography diffraction
data phasing. Enter the two modes and the perturbation range below.
Please note that computations are limitted to 200 models per job.
If you find results from this site helpful for your research, please cite one of our papers:
is maintained by Yves-Henri Sanejouand.
It was developed
by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: October 18th, 2018.