Multiple global helical axes in one structure, how to calc?

[ramon989]

Hi,

I have a single structure consisting of two helices seperated by some sort of hinge.
The problem is to find the angle between the two helices.
If I look at the [pdbname].out file, which results from
find_pair [pdbname].pdb stdout|analyze
There is not gobal helix axis defined.

What I want is four HETATM lines in the outputfile, defining the begining and the ending of the global helix axis for both helices.
Can I only obtain this by cutting the PDB in parts and then analyze these parts seperately, and append the HETATM lines to the original PDB file ?


Greetings,
Ramon

E.G. structure looks like this (very schematically):


 |--|
 |--| Helix I
 |--|
 /  
 |   | Non-helical hing-area
   /
 |--|
 |--| Helix II
 |--|

I want the angle between helix I and II

[xiangjun]

This question deserves as a FAQ now. Indeed, in the coming 3DNA Nature Protocols paper (anytime soon!), there is an example which involves quantifying the bending angle between two relatively straight helix regions in a DNA-RNA junction structure.

To answer your question now, yes, you need to analyze the two helical regions separately to get the helical axis vector for each, and then to calculate the angle between them. The "analyze" program always takes each structure fed to it as a whole, and outputs a ls-fitted global linear axis if the structure overall does not deviate significantly from a regular helix.

You might also want to play with Curves, which outputs a bending angle as part of its global analysis. As you know, this method is quite frequently mentioned in the literature.

HTH,

Xiang-Jun