Locating atoms from angles-Help!

Rick Venable rvenable at deimos.cber.nih.gov
Mon Jun 5 14:54:08 EST 1995

On 5 Jun 1995 02:51:41 GMT Mr YC Yap pontificated:
> I wonder if someone can help me with a problem.
> I'm writing a protein folding program that uses
> a simplified representation storing only the amino
> acid sequence, C-alpha coordinates and the Phi and 
> Psi dihedral angles.

> At the end of the program, I need to reconstruct
> a detailed atomic model of the molecule. With the
> dihedral angles, I know the relative orientation
> of the backbone C, N and O atoms between one residue
> and its neighbour. But how do I get  the starting
> coordinates of the FIRST N atom? Once I get that,
> I can work out the rest of the atoms.

Assign the first atom to 0,0,0
Place the second atom along the positive X axis (X= N-CA bond, Y=0, Z=0)
Place the third atom in XY plane (Z=0); use CA-C bond and N-CA-C angle

Once the first 3 atoms are placed, the rest can be determined from bond
lengths, bond angles, and the dihedral angles.

The next step is often to align the molecular axes with the Cartesian axes,
so that the molecule's center of mass or geometry is at 0,0,0 and perhaps
the molecular long axis aligned with a Cartesian axis.

N.B.  I tried e-mail, but your addressed got garbled somewhere along the
way to my newsfeed.

Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \  /   |=|  / Not an official statement \
rvenable at deimos.cber.nih.gov       \/    |=|  \  or position of the FDA.  /

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