Disclaimer: I'm taking a class to get some experience with structural informatics and this question is related to an assignment for that class.
Given a PDB file, I have written a program that will calculate various lengths and angles from the atom coordinates provided in the file. I now need to select a certain amino acid, set its phi and psi angles to 0, recalculate the atomic coordinates for all affected atoms, and check for steric clashing.
I'm struggling conceptually with how to recalculate atomic coordinates. What types of concepts do I need to understand to tackle this type of question?