0

Hey guys, I seriously need some help here.

I have no idea why but after undergoing the Rotation phase I lost

coordinatesRotZ[a][0],coordinatesRotZ[a][1]. The value appears to be 0.0

However coordinatesRotZ[a][2] has values stored in it.

so the output looks something like that after printing:

coordinatesRotZ[a][0] coordinatesRotZ[a][1] coordinatesRotZ[a][2]:

0.0 0.0 13.44

0.0 0.0 14.85

Thanks in advance!!

```
//---------------------------Translation---------------------------------------
for(int a=0; a<coordinates1.length; a++) {
for(int b=0; b<3; b++){
for(int c=0; c<3; c++){
X = coordinates1[1][0]/coordinates2[1][0]; //alpha c coordinate
Y = coordinates1[1][1]/coordinates2[1][1];
Z = coordinates1[1][2]/coordinates2[1][2];
double [][] Translation1={ {X,0.0,0.0}, {0.0,Y,0.0}, {0.0,0.0,Z} };
coordinates2T[a][b] = coordinates2[a][c]*Translation1[c][b];
//-------------------------Rotation & RMSD Cal----------------------------------
//Uses Leohard Euler's angle of rotation theorem
//5 degrees in rad.
double [][] Rotz={ {Math.cos(0.087266463), Math.sin(-0.087266463), 0.0},
{Math.sin(0.087266463), Math.cos(0.087266463), 0.0},
{0.0, 0.0 , 1.0} };
double [][] RotX={ {1.0,0.0,0.0},
{0.0,Math.cos(0.087266463), Math.sin(-0.087266463)},
{0.0,Math.sin(0.087266463), Math.cos(0.087266463)} };
double [][] RotZ={ {Math.cos(0.087266463), Math.sin(0.087266463), 0.0},
{Math.sin(-0.087266463), Math.cos(0.087266463), 0.0},
{0.0, 0.0 , 1.0} };
coordinatesRotz[a][b]= coordinates2T[a][c]*Rotz[c][b];
coordinatesRotX[a][b]= coordinatesRotz[a][c]*RotX[c][b];
coordinatesRotZ[a][b]= coordinatesRotX[a][c]*RotZ[c][b];
}
}
}
for(int a=0; a<3; a++){
R1=0;
for(int b=0; b<3; b++){
R1 =Math.sqrt((Math.pow((coordinates1[a][0]-coordinatesRotZ[b][0]),2)
+Math.pow((coordinates1[a][1]-coordinatesRotZ[b][1]),2)
+Math.pow((coordinates1[a][2]-coordinatesRotZ[b][2]),2)));
R2 = R1 + R2;
// if(coordinatesRotZ[b][a] !=0.0)
//System.out.println(Translation1[a][0]+"\t"+Translation1[a][1]+"\t"+Translation1[a][2]);
//System.out.println(R2);
}
}
RMSD_Final = R2 / 3.0;
for(int a=0; a<3; a++){
for(int b=0; b<3; b++){
if(coordinatesRotZ[a][b] !=0.0)
System.out.println(coordinatesRotZ[a][0]+"\t"+coordinatesRotZ[a][1]+"\t"+coordinatesRotZ[a][2]);
```