  PbTaSe$_2$ is a unique topological material, in which the number of nodal
lines is expected to change at the structural transition between the lower
temperature/pressure "L" phase and the higher temperature/pressure "H" phase.
We report the anomalous Nernst effect attributed to the Berry curvature of
nodal lines and its change with the structural transition. In the L phase, the
Nernst coefficient ($S_{yx}$) shows the step-like magnetic field dependence
reminiscent of the anomalous Nernst effect of nonmagnetic Dirac/Weyl
semimetals. By applying hydrostatic pressure, we discovered that the amplitude
of the anomalous component significantly decreases at the transition to the H
phase, which might correspond to the partial annihilation of nodal line
structures.
