Hello, Kay is absolutely right. Just to make this clear: We all know that in many cases, you start out with poor phases (i.e. a weak SIR/MIR/MAD or a borderline replacement model) and your density is "modest". The prudent thing to do at this stage is, to build only things you trust and have a look at the improved density. Well, we all know also, that an improved density means in most cases a density with improved phases. The term "disorder" means, a region of higher uncertainty. Logically, the more information you have (more actual data points - i.e. reflections == resolution/completeness; more reliable Fs; etc.; _better phases_) the better you can pinpoint these areas. The phase is a magnitude we cannot measure, but that affects the density the most. We determine it through "refinement" (which encompasses density interpretation and computational optimization of atomic parameters with regards to the reflection data). Gedankenexperiment: If you collect data on a crystal, let's say on a sealed tube from 1950 with a photon counter, and you collect the same data from the same crystal on a modern synchrotron with a PAD, you might find certain areas of your molecule "disordered" that you might be able to interpret with (more) data collected from the "better collected data". Probably more so - if you have the same amount of data and poorer or better phases, you have a similar problem. My point being: the term "disorder" is related to the amount of data you have (be it collected (I's) or deduced (phi's)). With very few exceptions (see for example the paper for 1M1N), it's not the method (diffraction) that tricks us, it's just the amount of information that we have, that prevents us from building "complete" models. Most importantly, the term "disordered" - as used in macromolecular terminology - depends on resolution /and/ quality of the phases. (As a side note: What we call "alternative conformations" in macromolecular crystallography is called "disorder" in small molecule crystallography. I don't know what the SM word for the MM "disorder" is...)
Cheers, Jens On Wed, 2012-04-11 at 06:44 +0100, Kay Diederichs wrote: > Hi Dale, > > my experience is that high-B regions may become "visible" in maps only late > in refinement. So my answer to the original poster would be - "both global > reciprocal-space (phase quality) and local real-space (high mobility) > features contribute to a region not appearing ordered in the map". This would > be supported by your experience if those residues that you could not model in > 3BCL had high (or at least higher) B-factors compared to the rest of the > model. Is that so? > > best, > > Kay
