Every object has an object matrix associated with it. The object matrix tells PyMOL whether the object coordinates are to be transformed before the object is displayed. The matrix is not a standard matrix in mathematical sense, it is something PyMOL-specific, also called TTT matrix: It is 4X4, with the upper left 3x3 forming a rotation matrix, the fourth column and row representing pre-rotation and post-rotation translation vectors respectively, and the 16th element always being 1.0. TTT stands for translation - transformation - translation.
Initially, the object matrix is the identity matrix, so no transformation takes place. It is changed during structure alignment (e.g. align and super). By hand, it can be changed with the commands rotate, translate, and origin.