Examples

The first example reads the coordinates from two files into the main and comparison sets:

coordinates @set1.pdb
coordinates disposition=comparison  @set2.pdb

In the second example, the first set is least-squares fitted to the second (comparison) set using $C^{\alpha}$ atoms only. Note that all atoms are translated and rotated. Then the rms difference between the two sets is computed for backbone atoms and stored in the symbol $1. Finally, the individual rms differences are printed for all backbone atoms that show rms differences greater than 1 Å.

coordinates fit selection=( name ca ) end
coordinates rms selection=( name ca or name n or name c ) end
evaluate ($1=$result)
vector show ( b ) 
     ( attribute b > 1.0 and ( name ca or name n or name c ))

In the third example, the main coordinates are fractionalized, a translation and a rotation are applied, and the coordinates are orthogonalized again. The crystallographer will recognize the rotation and translation as the space-group operator $(-x,y+1/2,-z)$.

coordinates fractionalize
   a=30. b=40. c=20. alpha=90. beta=100. gamma=90.
end
coordinates rotate
   matrix=( -1 0 0  )
          (  0 1 0  )
          (  0 0 -1 )
end
coordinates translate
   vector=( 0 0.5 0 )
end
coordinates orthogonalize
   a=30. b=40. c=20. alpha=90. beta=100. gamma=90.
end

The final example shows how to rotate the coordinates using Eulerian angles:

coordinates rotate
    euler=( 10., 30., 2. )
end