[Biodevelopers] calculate phi psi angles

[Mike Marchywka]

> Guys does anyone know the algorithm with which I can calculate phi and psi
>> angles out of a pdb archive? Not necessarily a source code -although a perl
>> source would pe appreciated- but the algorithm itself... plz help...

I'm still not sure what you are asking. There are only two issues AFAIK.
1) Definition. This is easy to find, even if the angle assigments are not uniform. 
Using the angles here,

http://en.wikipedia.org/wiki/Protein_structure

would probably work.

2) Calculation. The pdb files contain coordinates for each atom. It would seem
the problem here is then trigonometry. Try a search on wikipedia for
terms like "dot product" as this should get you the relevant cosines.
Then, you just need an inverse cosine call. Of course, you may need to convert radians
and degrees too :)




> Date: Sat, 3 May 2008 00:22:19 +0530
> From: skhadar at gmail.com
> To: biodevelopers at bioinformatics.org
> Subject: Re: [Biodevelopers] calculate phi psi angles
>
> Did you tried PerlMol or bioruby ?
>
> On Wed, Apr 30, 2008 at 5:01 PM, JONATHAN BLACK 
> wrote:
>
>>
>> Guys does anyone know the algorithm with which I can calculate phi and psi
>> angles out of a pdb archive? Not necessarily a source code -although a perl
>> source would pe appreciated- but the algorithm itself... plz help...
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