structure calculation
D M Webster
bssdmw at bath.ac.uk
Wed May 17 04:01:42 EST 1995
In the referenced article, chan at bioch.ox.ac.uk writes:
>Hi there,
>
>Can anyone tell me is there a software that can calculate the phi and psi
>angles of each amino acid residue from pdb files. The reason is that I
>want to know which strach of amino acid is alpha-coil, beta-sheet, turn
>and random coil _calculated_ from the pdb files. That means, not
>prediction. I have try to extract the molscript file from rasmol, but the
>result is not very good.
>
>Thanks in advance!
>
>
>
>
>**********************************************************************
>* 2 * Christopher Chan *
>* CCCCC * Dept. of Biochemistry *
>* C * University of Oxford *
>* C * Oxford *
>* C * U.K. *
>* CCCCC * Tel.: 0865-(2)75239 *
>* * E-mail: chan at bioch.ox.ac.uk *
>**********************************************************************
>----- PGP public key available upon request -----
>
>
You could easily write your own. Below is the IMPLEMENTATION module
of a Torsion module written in Modula-2. You should have no trouble
converting it to a language of your choice.
P.S. I havn't included any of the IMPORTED modules but they are pretty
much self explanatory. If you don't know what DotProduct etc is then
check out any standard graphics text.
David Webster
IMPLEMENTATION MODULE Torsion;
(*=================================================================
Version : 1.00 Thu Oct 6 1994
Author : Dr David M Webster
Rights : Southern Cross Molecular Ltd
Compiler : Modula-2
Component : Torsions
COPYLEFT
Copyright (C) 1994,1995. Dr David M Webster.
Southern Cross Molecular Ltd.
No claim is made as to the validity of the code in this module.
No warranty is granted or implied.
Users of this code do so at their own risk.
Permission is granted to freely copy, distribute or modify
this module, provided that
1. this header section is left intact.
2. that no charge is made for the modules distribution or
distribution of any modified copy.
3. Modifications to this module should be entered under the
revision history and the name of the author stated.
4. All of the above warranties and permissions be included in
any distribution of this module, modified or not.
THE ABSTRACTION
NOTE
All routines return results as radians
ROUTINES
- Dihedral calculates the torsion angle of a set of four atoms v1-v4.
The dihedral angle is the angle between the projection of
p1-p2 and the projection of p4-p3 onto a plane normal to
bond p2-p3.
To calculate Phi, Psi, Omega, Chi or Cad pass as parameters to
Dihedral as follows
Psi : p1 = previous [n-1] carbonyl carbon
p2 = nitrogen
p3 = calpha
p4 = carbonyl carbon
Phi : p1 = nitrogen
p2 = calpha
p3 = carbonyl carbon
p4 = next [n+1] nitrogen
Omega : p1 = previous [n-1] calpha
p2 = previous [n-1] carbonyl carbon
p3 = nitrogen
p4 = calpha
Chi : Sidechain E.g. Lys
Chi1 Chi2 Chi3 Chi4
p1 = nitrogen calpha cbeta cgamma (CG)
p2 = calpha cbeta cgamma cdelta (CD)
p3 = cbeta cgamma cdelta cepsilon (CE)
p4 = cgamma cdelta cepsilon czeta (CZ)
Cad : p1 = [n-2] calpha
p2 = [n-1] calpha
p3 = [n] calpha
p4 = [n+1] calpha
- Angle calculates the bend angle between adjacent atoms
E.g. for adjacent calpha atoms
p1 = [n-1] calpha
p2 = [n ] calpha
p3 = [n+1] calpha
REVISION HISTORY
v1.00 Thu Oct 6 1994. Initial implementation.
=========================================================================*)
IMPORT
B := BIOPT,
C := Constants,
Math,
LM:= LongMath,
V := Vector3D;
(*
Dihedral calculates the torsion angle of a set of four atoms p1-p4.
The dihedral angle is the angle between the projection of p1-p2 and
the projection of p4-p3 onto a plane normal to bond p2-p3.
*)
PROCEDURE Dihedral ( p1,p2,p3,p4 : B.PointType ) -- in
: LONGREAL; -- out
VAR
p12,p43,p23 : B.PointType;
a,b,c : B.PointType;
u,v,dihedral : LONGREAL;
BEGIN
V.Subtract(p1,p2,p12);
V.Subtract(p4,p3,p43);
V.Subtract(p2,p3,p23);
V.CrossProduct(p23,p12,a);
V.CrossProduct(p23,p43,b);
V.CrossProduct(p23,b ,c);
u := V.DotProduct(b,b);
v := V.DotProduct(c,c);
dihedral := C.pi2;
IF (u > 0.0) AND (v > 0.0) THEN
u := V.DotProduct(a,b)/LM.sqrt(u);
v := V.DotProduct(a,c)/LM.sqrt(v);
IF (u <> 0.0) OR (v <> 0.0) THEN
dihedral := Math.arctan2(v,u);
END;
END;
RETURN dihedral;
END Dihedral;
PROCEDURE Angle ( p1,p2,p3 : B.PointType ) : LONGREAL;
VAR
u,v : B.PointType;
dot : LONGREAL;
BEGIN
V.UnitVector( p2,p1,u );
V.UnitVector( p2,p3,v );
dot := V.Dot( u,p2,v );
IF dot > 1.0 THEN
dot := 1.0;
ELSIF dot < -1.0 THEN
dot := -1.0;
END;
RETURN LM.arccos(dot);
END Angle;
(*--------------------------------------------*)
END Torsion.
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