I would like to know how do I get the invariant points of 2 PDB structures because i need to superimpose them and program it in JAVA. Eg. How do I know what is the origin and so on.. How do I read the invariant points from the txt file? Is there any specific/ most used point for this?
The invariant points can be any points that you choose. In protein superposition you read in the two structures and extract xyz coordinates (typically those of the alpha-carbon atoms). Then, you use some iterative procedure along these lines:
Select points from each structure that you don't want to move (termed fixed or invariant)
Superpose those points
Allow other points to move around (within limits imposed by bonds and steric clashes)
Calculate some "goodness of fit" score (typically RMSD)
You may start with these related questions: