Physics. The human body has in it a beautiful instrument for detecting light. Our eyes, in conjunction with our nervous system, have been evolving for 451 million years[1], and have been crafted into a system that detects what you and I know as light. Light, the Almighty Light, which physicists have identified as electromagnetic waves pervades and powers the world around us and we, as humans, have molecules (see Box 1.0) in our eyes that respond to the waves with wavelengths of anywhere between 400 and 700 nanometers.(Figure 1.0) Since our visual systems are designed to interpret only wavelengths of this size, we can say that this is our resolution. The wavelength of the light that is interacting with the observed object determines what resolution is achievable. """We can see the chairs and trees around us just fine because the lightwaves which we use is of a smaller length than tree."""
In order to see the atoms that make up proteins, we need wavelengths that are orders of magnitude shorter than visible light. (10,000 times shorter OR 5 orders of magnitude shorter OR 1x10^5 OR 1E5 shorter). Let's say that an atom is about .1 nanometers. When we gather data about atoms' positions in proteins we must use X-rays, whose waves are .01 to 10 nanometers in length.

Figure 1.0. Electromagnetic Spectrum

Box 1.0 Three-dimensional structure of bovine rhodopsin. The seven transmembrane domains are shown in varying colors. The chromophore is shown in red. Biology. The chromophore absorbs a photon of light resulting in a conformational change in the protein. This, through a series of interactions with subsequent proteins ultimately opens a channel in the membrane, allowing the influx of Na+ and Ca2+, which depolarizes the cell causing an action potential which is the means for communicating with the subsequent neuron on the signals path back to the visual cortex in the back of the brain, before it gets processed into what we call vision.