Usually, a NMR structure represents the dynamics of a protein in solution. The NMR structure deposited in Protein Data Bank always contains 10 to 20 structures (states). It’s nice to generate a “tube (sausage) ” like structure to show how flexible each residue is.
MOLMOL is the best molecular viewer having this kind of function. Just load a NMR structure and run the standard macro called sausage.mac to make a sausage-view. Here is an example of 1PIT.pdb
PyMOL, however, doesn’t have built-in script to generate a sausage-view-structure. Cameron Mura in UCSD provides a nice pymol script to make this purpose. Just go to his pymol homepage (http://mccammon.ucsd.edu/~cmura/PyMOL/), download average3d.py and follow the instruction to generate a sausage-view-structure. Here is the result I made (also, 1PIT.pdb)