Hi Ed, On Thu, Oct 21, 2010 at 12:18:31PM -0400, Ed Pozharski wrote: > Let's say I have a ligand on symmetry axes and so it appears in two > conformations. If I reduce symmetry, there are two possible scenarios. > > a. In lower symmetry, ligand still appears in two conformations. Shall > use higher symmetry. > b. In lower symmetry, ligand appears to be in single conformation (this > is what Mohinder says, if I am not mistaken). In this case, the true > symmetry is lower, and it is simply overwhelmed by the fact that most of > the structure (but not all) obeys higher symmetry.
I think I understand what you're getting at: you have a lower symmetry with a NCS axis that is basically perfectly aligned with the corresponding crystallographic axis in the higher symmetry spacegroup. And the only part of the model not obeying this NCS is the ligand. But then what about a water on a special position (2-fold with occ=0.5)? If I remove that 2-fold from my spacegroup symmetry and refine I get ... a single water with occupancy 1.0 ... or 2 waters with occupancy 0.5? Hmmm, diffcult to decide on the true spacegroup here ;-) So it all depends * how clear the difference between high-symmetry/double conformation and low-symmetry/single-conformation is * how symmetrical the ligand is * how the refinement in the lower-symmetry spacegroup is done - since there is a real danger (in case it is the high-symmetry spacegroup after all) that because of model bias and poorer (independent observations)/parameter ratio what seems like a clear single conformation is difficult to confirm. > I recall Bruce Foxman describing a b) case (I am sure there is more than > one example) for a small molecule crystal, where a single heavy atom had > higher symmetry than the rest of the molecule. There is a recent nice example of a very interesting symmetry/disorder siuation by Yves Muller: 2xgc. It took some time for me to get my head around what it is in the PDB file and what it means ... but it's very neat! 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) ***************************************************************
