[MMTK] Deformation analysis

Konrad Hinsen research at khinsen.fastmail.net
Mon Nov 7 09:02:23 UTC 2011


On 4 nov. 2011, at 11:48, James Starlight wrote:

> 1) The molecule of the receptor cionsist of 7 alpha-helices domens 
> Could the NMA in general be suitable for investigation of the activation of the receptors ? In this case activation process is linked with the displacement of the some alpha-helices of the receptor. But as I've inderstood NMA is more suitable for the investigation of the displacement of the whole domains consisted of the specific monomer for instance.

NMA is fine for any size of subunit. It's the ENM that requires sufficiently large units to be valid. But there is no clear-cut limit; the larger the subunit you are looking at, the more reliable ENM predictions are.

> 2) As I understood the ENM doest require for the minimisation of my initial structure. But after some of my analysis some of the obtained modes were negative wich could indicate in case of NMA that my structure could not be minimised properly. Why negative modes might occur in case of ENM?

None. Some of the six zero-energy modes may be negative, but as long as they are close to zero, that's fine. If you see negative modes with an ENM and your input structure is reasonable, you can submit a bug report for MMTK. The only case I have ever seen was due to two C-alpha atom being much too close to be credible (about 1 Å).

> 3) Where I can obtain information about such deformation analysis if it possible via MMTK ? I found that  MMTK.Deformation module could be something that I need :) But Its not quite understood for me how to build deformation vector beetwen my structures.

It's just the difference between two configurations. Look at this example script:

	https://hg.python-science.org/MMTK/file/f6255150f538/Examples/NormalModes/conformational_change_analysis.py

> 4) Finally I want to compare def. vctor with the soft modes as well with the ensemble modes. So in first place I need in the directly comparison of the fluctuations along each  deformation direction. And in the second place I need in something like cumulative overlap beetwen def vector and the soft modes enssemble.  Would  this strategy  be correct?

What do you call ensemble modes? And what's "each deformation direction"?

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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