[Biodevelopers] calculate phi psi angles

[Lapointe, David]

Actually the problem is to determine the dihedral angles between two
planes, one plane being the peptide bond ( on the N side of the
alpha-Carbon, or the C=0 side of the alpha carbon), and a plane defined
by the N-(alpha-c)-(beta-c) for example. So consider 4 atoms
cb-ca-c-O, where cb is the first atom in the R group, then the alpha
carbon, then the carboxyl carbon and the oxygen in the carboxyl group.

cb-ca-c define a plane, ca-c-O define a plane  and the dihedral angle is
the angle between these planes or the rotation of cb and o around ca-c,
in this case psi. So given the x,y,z coordinates of four atoms, form 2
planes and determine the angle between them. Do that twice for each
alpha carbon ( phi-N side  , psi- C=O side) that is not a terminal
residue to get the phi-psi angles. In a peptide bond the C, O, and N are
co-planar, the other plane defined by cb-ca-c ( or n). 

See also http://en.wikipedia.org/wiki/Dihedral_angle for some math.

David
> 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...
>> _________________________________________________________________
>> Back to work after baby-how do you know when you're ready?