[Imgcif-l] Electron density map parameters
Joe Krahn krahn at niehs.nih.govTue Feb 27 04:09:59 GMT 2007
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A few comments on the work-in-progress for density (etc.) maps. The current spec says: "The map sampling is being done in the middle of each grid division" This conflicts with Fourier maps, where values are on grid vertices, rather than the pixel/voxel centers. The reason is that Fourier maps represent point samples, rather than the integration of a pixel/voxel, as it is in the case of most images. Rather than making density maps special, maybe there should be a property that distinguishes between point samples and integrated divisions. This sort of problem is common in graphics rasterization, and imaging/graphics APIs often have alternate origin choices. For grid divisions, maps have one of the following two representations, from the examples: loop_ _array_structure_list_axis.axis_id _array_structure_list_axis.fract_displacement _array_structure_list_axis.fract_displacement_increment CELL_A_AXIS 0.01 0.02 CELL_B_AXIS 0.01 0.02 CELL_C_AXIS 0.01 0.02 loop_ _array_structure_list_axis.axis_id _array_structure_list_axis.displacement _array_structure_list_axis.displacement_increment X 7.5e-8 1.5e-7 Y 7.5e-8 1.5e-7 Z 7.5e-8 1.5e-7 Both of these have the problem that the displacement increment can produce cumulative rounding errors. It would be better to have a system that better allows for an integer number of grid divisions per unit cell. Detector images could benefit from this sometimes as well. One possibility is to specify a displacement-maximum, instead of an increment. Another possibility is to specify the inverse of the fract_displacement parameters. In the case of fract_displacement, is it intended that _axis.vector[*] be the unit-cell, rather than a dimensionless unit vector? Another thing important to electron density maps is symmetry operations, which are already defined for structures in category _symmetry_equiv. It might be useful to define symmetry with simply matrices/vectors instead. Are there any ideas already being considered in this area? Joe Krahn
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