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Superimpose
Selecting Molecules and Setting Parameters
Make sure that both molecules are displayed.
Choose molecule 1 by clicking on a structure.
After selecting a molecule, the viewer zooms in and shows the molecule
in sticks.
Choose the type of alignment,
whether it be:
Note: C-alphas
(backbone-carbons) are more stable than the protein's floppy side-chains and
give a good indication of the protein's spatial conformation even though the
two proteins can be very different (e.g. the crystal structure has no hydrogen
atoms, or the proteins have different missing residues).
Note: If you chose the
heavy atom or the all atoms options, make sure that the two molecules have exactly
the same atoms.
As soon as everything is ready, press the Apply button.
Results
of Fitting
Molecule 1 does not change its coordinates, while molecule 2 changes its
coordinates to reach the best fit to molecule 1. This new object is named
"2 to 1".
You can see molecule 1 and molecule 2 to 1 on the display (Figure 56).
Figure 56 - Fitting
