Show neighbours in nglview

Nglview is a really nice Python library which encodes a widget to show a NGL viewport, a JS 3D protein viewer used until recently by the PDB. One annoying feature is that one cannot select neighbours as easily as say PyMOL's "select byres HEM around 3".  But it is possible and here is how.

Multiple poses in NGLView

As mentioned previously, most of my Pyrosetta operations are done in a Jupyter notebook run in a cluster node. As a result, I am heavily dependent on NGLView, an IPython widget that uses NGL.js. This is nice for some quick tasks, although admitted more limited than the PyMOL mover, which however requires another ssh to forward another port. My Michelanglo webapp uses NGL.js, so I cannot but say good things of NGL.js. However, one or two things in the Python module NGLView are not immediately clear, so I'll quickly cover dealing with multiple poses here.