The animation shown here of the conformational change of IRP1 is a molecular morph. The purpose of molecular morphing is to smooth the visual transition between two molecular conformations, making it easier to see and understand the structural differences between them. In contrast, predicting the actual trajectory through which a conformational change occurs is rarely, if ever, the goal of a morph.
The morph can be viewed from any perspective, while animating, by rotating it with the mouse. It can also be zoomed to examine details. The display and color scheme can be changed easily.
Chemically possible (also sometimes called chemically plausible, semi-plausible, or chemically reasonable) means that, at the least, correct covalent bond lengths and angles are maintained, and that atoms are constrained not to pass through each other. This type of morph requires sophisticated software, but luckily that is freely available and easy to use at the Yale Morph Server. The server does the structural alignment of the starting PDB files, and then does a linear interpolation followed by some energy minimization to render each frame chemically possible.
Credits and Notes
1. Molecular Morph: Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis, molmovdb.org, developed by Mark Gerstein and coworkers at Yale University, USA.
2. "About this animation," above, is drawn largely the excellent resource page on morphs by Eric Martz, in Proteopedia.
3. Careful viewing of this morph reveals that part of the structure is present only in the first model in the series (PDB ID 2B3X). The parts of the protein that are not present in models 2-10 (residues 126-146, 499-511 and 623-629) were not resolved in the crystal structure of IRP1 bound to the IRE (PDB ID 2IPY).
To measure distances, double click on the structure. Now, as you touch other parts of the structure, the distances will be shown on a pink line. Double click to fix the distance report in black.
For easier measurements, turn on the spacefill representation (a requirement for accuracy when surfaces are displayed).
To cancel without fixing a distance report, simply move the mouse outside of the Jmol rectangle. To remove an already fixed report, double click on each of the two atoms again. To remove all distance reports, click the original radio button to refresh the molecular view.