Flatten Icosahedron Flatten Icosahedron icon

Flatten Icosahedron rearranges the faces of an icosahedral virus capsid from Multiscale Models into a plane. This flat view can be saved as an image, printed, and folded into a paper icosahedron model.

Dengue virus 1k4r flattened
(larger version suitable for printing)
folded paper model

There are several ways to start Flatten Icosahedron, a tool in the Higher-Order Structure category.

The capsid subunit coordinates should first be opened in Chimera and the complete capsid generated with Multiscale Models using Icosahedral symmetry, xyz 2-fold axes (VIPER). This is done automatically when a structure is fetched from the Virus Particle Explorer database (VIPERdb) or a local VIPER file is read. This tool will not work on structures that are not multiscale models, even if they have the correct type of symmetry. All multiscale models present will be affected.

When Flatten is clicked, the twenty triangular faces of an icosahedral capsid are laid out in a plane. The orientations of the faces relative to the structure are assumed based on the known symmetry. Each chain is associated with the triangular face whose center is closest to the geometric center of the chain. To generate the planar arrangement, a common rotation and translation are applied to all the chains of a given face. The chains and faces remain three-dimensional; each face is simply repositioned relative to the others. Unflatten reverses the process. Close dismisses the Flatten Icosahedron dialog, and Help opens this manual page in a browser window.

Before saving an image, it may be desirable to adjust display parameters, in general (see the tips on preparing images) and in Multiscale Models. For example, when a multiscale model is first created, the original chains may not be shown as surfaces like the rest of the chains. To remedy this, select the chains with loaded atoms and change them to the surface style as well.


1m1c flattened 1m1c flattened and tiled

Tiling. Cutting and folding to make a paper model chops away parts of proteins that straddle triangle boundaries. Tiling the image allows parts of a cut protein to appear on both sides of the cut lines when taped together. Tiling is not necessary, but improves the appearance of the final model. Currently, Chimera cannot perform the tiling, so a separate image-editing program must be used. GIMP was used in the example shown here. Steps:

Known icosahedral symmetry. This tool uses the icosahedral reference frame where 2-fold axes are along the x, y and z axes, called Icosahedral symmetry, xyz 2-fold axes (VIPER) in the Multiscale Models dialog. To use a different reference frame requires a small change to the Python code. Specifically, you would change the '222' in file share/FlattenIcosahedron/__init__.py to '222r', or '2n5', or '2n3'. Refer to file share/Icosahedron/__init__.py for the definitions of these alternate reference frames.

UCSF Computer Graphics Laboratory / October 2007