I'm studying protein crystallography now and I reached an inevitable point where I had to deal with the phase problem. Well, my problem is, that I'm not exactly sure what the phase is because no book really explains that (probably it would be crystal clear if I studied some photonics:).
EDIT
OK, I found this http://en.wikipedia.org/wiki/Phase_problem and kind of understood that it's not rotation around the direction axis ( http://www.helpsavetheclimate.com/lightwave1.gif ) but it's translation along that axis, right? Is the difference that big? I mean the x-rays have wavelength of about nanometers or smaller, so it should not matter that much, should it?
Waves have maxima and minima and waves can be summed up to form a new wave. In order to calculate an electron density distribution in 3D (i.e. the structure of a molecule), we use a formula for adding waves (information derived from a diffraction experiment using X-rays and crystals). To sum up the waves (with individual wavelenght and amplitude) you require one more information, namely "phase information" because the "superposition" of one wave with respect to another wave matters if you need to sum them up. So, the phase problem is an important issue in crystallography.
Read the publication by Garry Taylor, Acta Cryst. D59, 1881-1890 (2003).
The PDF is open access: http://journals.iucr.org/d/issues/.../ba5050/ba5050.pdf
- J. -
So it's not like phase in relation to detector but in relation to each other?
Thank for the article, I'll try to read it :)
Phases are even more important than structure factors amplitudes in crystallography !
The problem is that when you measure diffraction data the only information that you get is spot intensities, and the phase information is lost...
To find those phases, different strategies are used :
- molecular replacement : use of the phases calculated from a known structure with high sequence identity compared to your protein.
- heavy-atom methods (SIR, MIR, SAD, MAD...) : can give you the phases but needs you to incorporate heavy-atoms in your crystals (Se-Met or crystal soaking).
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