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Re: [Imgcif-l] Electron density map parameters

How about

   _array_structure_list_axis.fract_grid_divisions

to specify the number of divisions into which the axis is
intended to be divided?  Computationally this would simply
imply the fract_displacement_increment as the reciprocal
of fract_grid_divisions.

The "spec" does not say that "The map sampling is being done
in the middle of each grid division".  That sentence is
just an explanation of that particular example which has
a value of 0.01 for _array_structure_list_axis.fract_displacement.
You are free to pick any point in the cell to start placing
your samples, but they have to be placed somewhere.  It is
hard to contour a map when you are not sure where it is
relative to the cell.

Fractional coordinates are inherently dimensionless, but
the system is, of course, based unit cell vectors.

The choice of symbolic symmetry ops versus matrices to give
the symmetry of a map is up to the user, but it would seem more natural
to use space group symbols or symbolic operations when working in 
fractional coordinates, and to use matrices and vectors when working
in orthogonal coordinates.


At 11:09 PM -0500 2/26/07, Joe Krahn wrote:
>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
>_______________________________________________
>imgcif-l mailing list
>imgcif-l@iucr.org
>http://scripts.iucr.org/mailman/listinfo/imgcif-l


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