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 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 ( rmsd ) ( attribute rmsd > 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 .
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