Before we start, let’s go to the movies!
James Holton (interview), while at Berkeley, produced a number of movies that demonstrate the importance of resolution, amplitudes and phases for the quality of the resulting electron-density map. James has kindly given permission to incorporate a couple of his movies into this practical.
Hopefully, the movies make you aware (if you weren't already) of the importance of having experimental data, but also of its variability. High-resolution maps are usually easier to interpret than low-resolution ones. But even at the same nominal resolution, the quality and interpretability of two maps can differ substantially. What's more, even inside a map there will be regions that are much poorer and harder to interpret than others.
The effect of resolution
Click here to start the movie. "This movie displays a calculated electron density map, contoured at 1 sigma, as the resolution limit is adjusted slowly from 0.5Å to 6Å. [...] The phases are perfect, and so are the amplitudes (R-factor = 0.0%) for all the resolutions displayed. Note that, even for a perfect map, you expect side chains to poke out of density at 3.5Å."
The importance of amplitudes
Click here to start the movie. "This movie displays the effect of calculating a map with "wrong" amplitudes. [...] The images in this movie represent the slow changing of all the amplitudes to a different set of randomly selected values while holding the phases constant. It is interesting to note that the map hardly changes at all until the R-factor gets higher than 30%. The maximum R-factor you can get for two random data sets is 75%, which is the end of the movie. Kinda spookey how it still looks traceable, isn't it? The resolution here is 1.5Å, and the phases are always perfect."
The importance of phases
Click here to start the movie. "This movie displays the effect of calculating a map with "wrong" phases. The "figure of merit" (cosine of the error in the phase) is displayed as "m". The images in this movie were calculated by merging a perfect calculated map with another map, calculated with the same amplitudes, but with phases obtained from a model with randomly positioned atoms. Merging these two maps always preserves the amplitudes, but changes the phases slowly to a new set of values. At what point do you think the map becomes untraceable? The resolution here is 1.5Å, and the R-factor is always 0.0%."
