Dear James, On Tue, May 12, 2009 at 11:26:55AM -0700, James Holton wrote: > However, do not get too excited if this resolution limit is 6 A. > Although 6 A phases are better than no phases at all, have you ever > LOOKED at a 6 A map? It can be very hard to tell if it is protein or > not, even with perfect phases and all the right hand choices, etc. > Programs and crystallographers alike can get confused by this. I know > that there are still many structural biologists out there who "just want > to get the structure",
Completely agree. The big misconception is that the result of the X-ray experiment is anything else than 'just' such an electron density map. What we usually see as 'the structure' is only a model: a PDB file to help us measuring distances, looking at on the display and making nice pictures ... just a useful interpretation of the electron density. So at lower resolution one needs to think more like an EM structural scientist and not an X-Ray one I guess. > The success of phase extension does depend on resolution. Although I do > not have a quantitative argument for it, the success of SAD structure > determination at worse than 4 A does seem to drop precipitously. Not just SAD, but also MAD, MIR, SIR et al (in my experience). Somewhere below 3.5-4A it becomes VERY hard to extend the phases to the full resolution of the dataset. Unless you have NCS (the more the better) - which is just great in those cases. So if one gets crappy crystals at least get them with a huge asymmetric unit ;-) > This could simply be correlated with the crappiness of the crystals, > but it is important to remember that SAD relies heavily on density > modification technology, such as solvent flattening and histogram > matching, etc, and these methods loose a great deal of power as the > resolution of the map decreases (and the protein-solvent contrast > becomes less clear). I always thought it had more to do with the look-and-feel of lower resolution maps (helices are big sausages, sheets blend into flat patches and side-chains are not visible): the methods modifying the density in real-space have probably different assumptions and default parameters (radii for masking, histograms becoming messy, absolute scaling nearly impossible etc). Also: the typical low resolution (20A and below) that is often neglected (beamstop size and masking? Overloads?) becomes more important. In the end 'resolution' comes into play in some way after all I guess - at least when we see 'resolution' as what it is mostly used in that context: a simple concept to describe several actual difficulties (poor crystals which only diffract to low resolution, weak experimental phases, anisotropy, radiation damage etc). Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
