How to "see" a Molecule - Part 2

As I wrote earlier, Bragg had found a way to know the structure of a crystal. But as Venki Ramakrishnan writes in Gene Machine, Bragg’s method involved making guesses about the structure that would explain the observed pattern of concentration spots. This was not a practical approach as the number of types of atoms in a molecule increased.

 

Perhaps you are wondering:

“Couldn’t we just use X-rays with a lens to see images of molecules directly?”

Aha, writes Ramakrishnan, that’s not an option because:

  1. There is no lens that’s capable of making images of molecules based on X-rays;
  2. Worse, X-rays have a lot of energy, so they “damage the molecules they hit”. In other words, they end up distorting the very thing they observe.

 

Well, ok, can’t we solve Issue #1 above (no lens problem) by having a computer do the maths that a lens, had it existed, would have “done” to create the image? Not really, says Ramakrishnan, because a real lens combines both the amplitude and phase of the wave to create the image. Whereas what we would be feeding to the computer would only be the amplitude of the X-ray, and no phase info. Wait, it gets worse:

“(Amplitude) is the less important half because the image is much more sensitive to having the right phase than the right amplitude.”

This is called the “phase problem in crystallography”.

 

Arthur Lindo Patterson came up with one solution:

  1. Take the “image” you got via X-rays and use it to derive a function that would “allow you to locate the most prominent of the atoms in the structure”;
  2. Then calculate the phases that this calculated function would have produced and combine them with the image you had;
  3. This would result in some of the “missing” atoms from the first image show up as weaker concentration spots;
  4. Add these to the initial structure and re-do the calculations:

“You can gradually bootstrap your way to the final complete structure.”

 

But this, and other such ideas, still wouldn’t work for the molecules of biology: those were simply too large e.g. amino acids and proteins. And without knowing the structure, it was hard to even guess how those molecules did what they did in living things… but that’s a story that’s explained in Ramakrishnan’s book.

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