Plot XPLOR NOEs in PyMOL
It is often useful when refining a structure with NMR distance restraints--or looking at someone else's refinement--to see the distance restraint connections on the 3D molecule itself. For structures refined by XPLOR-NIH there exists an excellent viewer for exactly this purpose: VMD-XPLOR. This software includes useful tools for the analysis of NMR restraints in structures.
However, if you prefer working with PyMOL, I've written a script that simply plots the XPLOR-formatted distance restraints on the molecular structure. The XPLOR file has the following format:
assign (residue 3 and name HN) (residue 4 and name HN) 2.0 0.2 0.2 # short-range
assign (residue 3 and name HA) (residue 4 and name HN) 3.5 0.2 0.2 # short-range
#assign (residue 3 and name HA) (residue 21 and name HB) 3.5 0.2 0.2 # long-range
Once in PyMOL, import the script using the following command:
PyMOL> import plot_noe
PyMOL> help plot_noe
The second command should explain how the function works. This PyMOL function does a simple parsing of the XPLOR restraints file, and the input NOE table will have to be modified by selecting individual members from atom groups.
Source Code
Demonstration
Once the NOE connectivities are plotted, the protein structure will look like this:
