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Normal Mode Analysis for ID EXAMPLE1
conformational change will be analysed
The following table indicates for every normal mode
its frequency (black, normalized relative to the lowest mode frequency) and its collectivity (magenta).
If a second structure was submitted, the cummulative overlap
between the normal modes and the conformational change is computed
(red). The corresponding amplitude (dq) is then also given (green).
Click on the mode link to obtain a visualization of the mean square displacement
<R2> of the C-alpha atoms associated to each mode.
WARNING: there are 2 low-collectivity modes among your first 5 modes (see below)!
The degree of collectivity indicates the fraction of residues that are significantly affected by a given mode.
While low-frequency modes are expected to have collective character, computed ones sometimes happen to be localized.
In such cases, they correspond to motions of some extended parts of the system, as often observed
in crystallographic protein structures for N- and C-termini.
[HELP on collectivity]
[HELP on overlap]
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.