Re: Helix tilt

From: Eduard Schreiner (
Date: Tue Jul 06 2010 - 12:27:50 CDT

Hi guys,

a quite simple solution in terms of post-processing of a trajectory
would be to calculate the inertia tensor for both helices and then
calculate the angle between the axes corresponding to the smallest
moment of inertia; this can be done in VMD.
For an ideal helix, this axis should correspond to the helix axis.
If the helix is bent, this correspondence does not hold anymore.
However, then the relative angle between two helices may be not the
proper descriptor anyway.


On Tue, Jul 6, 2010 at 11:48 AM, Nicholas M Glykos <> wrote:
>> how would one calculate the tilt between two helices along a
>> simulation in namd. I would like to know if there are any analysis
>> scripts written for it or tool or something like that.
> You are possibly posting to the wrong list. Having said that, calculating
> crossing angles for associating helices is not as straightforward as you
> may think. You would normally have to calculate the local helix axis for
> each helix, and then work your way from there. Once upon a time, there was
> a program called HELANAL (written in FORTRAN77(?), that's why I am using
> capital letters) which could do the trick (and much more). I bet there are
> more recent and automated programs available these days, but a quick
> search showed that HELANAL is still available. Needless to say that you
> probably can't do the calculation directly with your DCD file (save PDB
> files from the DCD and work with them).
> Nicholas
> --
>          Dr Nicholas M. Glykos, Department of Molecular Biology
>     and Genetics, Democritus University of Thrace, University Campus,
>  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>    Ext.77620, Tel (lab) +302551030615,

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078

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