Jmol/Storymorph

This is a draft documentation for File:Storymorph.spt, a suite of Jmol functions to help with superimposing and morphing between two structures representing different conformations of a molecule or molecular assembly. For more general information, see Jmol/Superposition and Morphs. If you load storymorph.spt into a Jmol session where no structures have loaded, it will run a demonstration superposition and morph based on calmodulin strutures. Most examples in this documentation are from this demo.

Loading the two structuresLoading the two structures

You can directly load two structures from the PDB into Jmol using the "load files" command, e.g. load files "=1prw" "=1cll"

In many cases, a single structure already contains two conformations, such as the two subunits of a dimer, mulitple models in an NMR structure, or multiple copies in the asymmetric unit. You can also assemble multiple structures into a single PDB file, designating them as different models (with the MODEL n and ENDMDL tags).

Defining the two structuresDefining the two structures

You need to define a variable (called "structures" in the examples) to select the two conformations. Structures is a list of two selections. The selections are enclosed in braces ("curly parentheses"), e.g. structures = [{1.1}, {2.1}]

Here, the selection is the first and the second structure loaded. For models in a single-structure file, you would use "1.1" and "1.2" instead. For subunits with different conformation, you would select by chain name, e.g. "chain=A" and "chain=B". More complicated cases are possible (chain B of the second model vs. chain A of the third model) but probably rare.

Defining the domainsDefining the domains

Often, conformational changes preserve the fold of entire domains but show differences in inter-domain orientation. Classical examples are the conformation states of hemoglobin or the flexible linker connecting domains of antibodies. For superpositions and morphs, it helps to identify these domains. In storymorph, the domains are collected in a list. Each list contains another list of three selections.