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***  ams8 ca4 before md  ***

elNémo ID: 19073111072652752

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)

B-factor analysis

Correlation= 0.039 for 476 C-alpha atoms.

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)

PDB-filePerturbationAnimationCA-variRMSD<R2>CA-strain
mode 7 for download-100 (20 ) 100 small/largeXn/a<R2>X
mode 8 for download-100 (20 ) 100 small/largeXn/a<R2>X
mode 9 for download-100 (20 ) 100 small/largeXn/a<R2>X
mode 10 for download-100 (20 ) 100 small/largeXn/a<R2>X
mode 11 for download-100 (20 ) 100 small/largeXn/a<R2>X

(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 VMD, Chime, RASMOL or 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 19073111072652752.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.

MODE= DQMIN= DQMAX= DQSTEP=

generate animated gif images



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.

MODE1= DQMIN1= DQMAX1= DQSTEP1=
MODE2= DQMIN2= DQMAX2= DQSTEP2=





If these results do not correspond to what you expected, take a look at the elNémo log files


If you find results from this site helpful for your research, please cite one of our papers:

elNémo 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.