A virus capsid from one protomer

Read a molecule, draw its backbone, color it by a property of its atoms, and draw it 60 times with the icosahedral symmetry of the capsid.

PDB entry 2PLV is poliovirus (type 1, Mahoney strain). The file holds one protomer of the capsid (the four proteins VP1 to VP4) placed in the icosahedral frame: the 60 rotations of an icosahedron build the whole capsid from it. Open start here (its folder holds 2plv.pdb).

Read and draw the molecule

  1. With Libraries…, load Molecules and 3D Visualization.
  2. Drag a Read Molecule node (Molecules > Input) and choose 2plv.pdb with its file widget. Right-click its mol output and choose Show data to see what it sends: a MolKit2 molecule (Vision's introspect data showed its fields too).
  3. Drag a Select node (Molecules > Filter), connect the molecule to its nodes input, and type name CA C N: the backbone atoms. (Select takes ProDy's selection language, or MolKit's.)
  4. Drag a Lines node (Molecules > Mapper) and connect the selection to its atoms.
  5. Drag a Viewer node (3D Visualization > Output) and connect Lines' lines to its geometries. A 3D panel opens under the network, and fits the molecule in its view.
In Vision this was the Lines Macro, a macro that computed the bonds, selected the atoms, built the lines and made a geometry; its nodes were inside it, and coloring or copying the lines meant opening it and connecting inside. Here Lines is one node, with inputs for the colors, the opacity and the copies.

Color by the x coordinate

  1. Drag an Extract Atom Property node (Molecules > Input), connect the selection to its atoms, and choose the property coords[0]: the x coordinate of each atom.
  2. Drag a Color Map node (3D Visualization > Mapper) and connect the property values to its values. It turns each value into a color, from blue (the smallest) to red (the largest).
  3. Connect Color Map's colors to Lines' colors. There are as many colors as atoms, so each atom gets its own.
  4. Connect Color Map's legend to the Viewer: the color bar and its range appear over the view. Drag it where you want it; right-click it for its options (see Color maps and legends).

The capsid

  1. Load the SymServer library and drag Icosahedral1 (SymServer > Macro). It outputs the 60 matrices of the icosahedral group.
  2. Connect its Merge_outMatrices to Lines' instanceMatrices. Lines draws one copy of the backbone per matrix: the whole capsid.
The mol2plv network and the poliovirus capsid colored by x, with its legend
The poliovirus capsid. 60 copies of the protomer's backbone, each atom colored by its x coordinate in the protomer: the copies show the same pattern turned by the symmetry.
Checkpoint mol2plv: poliovirus with icosahedral symmetry

Inside Icosahedral1

Icosahedral1 is a macro of the SymServer library: double-click it. The 5-fold axis makes 5 matrices, and the 3-fold axis turns them into 15. Three 2-fold axes then turn these 15 about three perpendicular axes (one of them also keeps the 15 it got), and Merge collects the 60.

The inside of the Icosahedral1 macro: 5-fold, 3-fold, three 2-fold nodes and Merge
Icosahedral1, opened in a tab. Each symmetry node's axis and angle are its widgets; select one to see them.
The saved tutorial network (mol2plv_net.py) also changed the inside of Icosahedral1, adding a translation driven by an iterate node to pull the copies apart frame by frame. The importer does not carry over changes made inside a library's macro; it reports them. The checkpoint network is the one this page builds.
← Indexing a list; macrosAn icosahedral cage →