In this example, we choose the alpha carbons of the respective active sites, but other choices are possible. the distances of which pairs of atoms should be minimized. You have to choose which sets of atoms should be superimposed, i.e. The model command determines which model will be displayed (0 means all). (If you want to superimpose different parts of a single structure, for example the two subunits in a dimer, you just load one structure, and access the subunits via the chain identifier - examples will follow). The number before the decimal point refers to the two structures, while the "1" after the decimal point refers to the first model in the respective coordinate set. Once they are loaded, you refer to them as "1.1" and "2.1". In the following, the related structures with the PDB IDs 3HG5 and 3H54 are loaded: The "load files" command accomplishes that. If you want to see superpositions in the context of a Proteopedia page (and look at the underlying Jmol scripts), take a look at Garman lab: Interconversion of lysosomal enzyme specificities and Schubert lab: bacterial InIC disrupts human Tuba complexes.īefore you can superimpose two structures in Jmol, they have to be loaded at the same time. Instead, you minimize the root-mean-square of the distances (RMSD) to achieve a compromise.
Because the two structures are different, not all equivalent atoms can match at the same time. Superpositions (or overlays) are a way to compare two structures by moving them on top of one another so the "equivalent atoms" are close to one another.
#JMOL OVERLAY PDB HOW TO#
This page is a tutorial on how to superimpose two structures in Jmol and show them in Proteopedia.
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