Recycling Corner/Center Of Mass

Center of mass

Jmol centers the model around its geometric center, i.e. the center of the boundbox. If you are interested in the mass center of the molecule:

1. Run or define or load from a script file this content in JmolScript:

function CoM(atomSet) {
  if (atomSet=="") {
    print "Warning: there are no atoms in the provided set. Using all atoms in the model."; 
    atomSet = {*}; 
  }
  var n = atomSet.size;
  var mx = 0; var my = 0; var mz = 0;
  for (i=0; i<n; i+=1) {
    mx = mx + atomSet[i].x * atomSet[i].mass;
    my = my + atomSet[i].y * atomSet[i].mass;
    mz = mz + atomSet[i].z * atomSet[i].mass;
  }
  var m = atomSet.mass.sum;
  mx = mx / m;
  my = my / m;
  mz = mz / m;
  return {@mx @my @mz};
}

function drawCoM(atomSet) {
  draw ctr diameter 0.9 color translucent yellowTint @{CoM(atomSet)};
}

function axesCoM(atomSet) {
  axes center @{CoM(atomSet)};
  axes on;
}

2. after that has been executed, you can

• retrieve the coordinates of the center:

c = CoM(); // using all atoms
print @c;
c = CoM( {_C},{_O} ); // just the carbon and oxygen atoms
print @c;

• draw a sphere in the center of mass:

drawCoM();
drawCoM( {_C},{_O} );

• place axes in the center of mass:

axesCoM();
axesCoM( {_C},{_O} );

Contributors

AngelHerraez