Re: calculate phi psi angles

No.

According to IUPAC ( http://www.chem.qmul.ac.uk/iupac/misc/ 
ppep3.html ) the
angles are defined as the dihedral angles between the following four  
atoms:

PHI:  C(i-1), N(i), C(i)_alpha, C(i)
===
PSI:  N(i), C(i)_alpha, C(i), N(i+l)
===


with respect,
Boris



On 5-May-08, at 5:02 PM, Lapointe, David wrote:
> 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?
>
>
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