Checker searches for 3D (Z) coordinates.
Fixer offers:
cleaning the structures by 2D clean (clean);
setting the atomic z-coordinates to zero (removezcoordinate).
Example :
Three Dimension Checker (3d) | 
Warning: | Fix | |
|---|---|---|---|
Clean (clean) | 
Remove Z-Coordinate (removezcoordinate) | 
||
| Detect 3D coordinates |     ex_3d_ch | 
    ex_3d_f | 
    ex_3d_fz | 
   ex_3d_ch
   ex_3d_f
   ex_3d_fz