Hi Terry, there are two separate things: 1) grid step for maps calculation (for example, in Xplor/CNS format). Here, smaller the grid step, better the maps appear. The price for this: 1) big map files, 2) slow manipulations in visualization programs (like PyMol, SwissPDB, etc...). 2) grid step used in indirect, FFT based, structure factors and gradients calculation for refinement. There are three main parameters that affect the accuracy of FFT based structure factors and gradients calculation: grid step, atomic radius (the region around atom where the density is considered non-zero) and additional smearing b-factor. The optimization problem here is: given data and model, find such combination of {grid step, atomic radius, smearing b-factor}that produces the structure factors of desired accuracy (compared to direct calculations) for the minimal time. Different programs use different strategies to solve this. The default in phenix.refine is grid_step = highest_resolution / 3, MAIN uses grid_step = highest_resolution / 4. In some programs the atomic radius is preset constant (I believe something like 2.0A in CNS), in phenix.refine it is determined dynamically for each atom. To get feeling about how the grid step affects the runtime and accuracy, you can play with it in phenix.refine : % phenix.refine model.pdb data.mtz structure_factors_and_gradients_accuracy.grid_resolution_factor=XXX where for XXX you can try a few values like 1/2, 1/3, 1/4, 1/5, 1/6, and grid_step = highest_resolution * grid_resolution_factor I would suggest the following reading (of course the list is incomplete): Acta Cryst. (1977). A33, 486-492 Efficient structure-factor calculation for large molecules by the fast Fourier transform L. F. Ten Eyck Acta Cryst. (1978). A34, 791-809 A new least-squares refinement technique based on the fast Fourier transform algorithm R. C. Agarwal Some review and comprehensive set of references: Acta Cryst. (2004). A60, 19-32 On a fast calculation of structure factors at a subatomic resolution P. V. Afonine and A. Urzhumtsev Pavel. On 10/29/2007 6:29 PM, Terry Lang wrote:
Hey Everyone,
I have been told by several crystallographers that the general rule of thumb for grid spacing when generating a map is one third the resolution (eg If your crystal structure has a resolution of 1.2 A, your grid spacing should be 0.4). Is there a mathematical reason why this ratio should be maintained or is this simply a holdover from slower computers with lower memory? More importantly for my application, is there a lower limit on how fine the grid spacing can be? In other words, is there a lower limit at which one is oversampling the data for a particular resolution? Any information and/or references would be greatly appreciated.
Sincerely, Terry