Re: [ccp4bb]: how to draw the electric density map by Molscript?

[Tim F <fenn@brandeis.edu>]

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On Fri, 11 Oct 2002, David R. Cooper wrote:

> 
> Povscript+ is an extension of Molscript that allows you to display electron
> density maps, GRASP surfaces and more.

Thanks for the plug.  ;)

> In my opinion, the maps from Bobscript do look better than those from
> Povscript+.

The problem of "looking better" is not equivalent to *correctness* of the
isosurface.  I'm in the process of publishing the povscript+ stuff, but
the Diamond algorithm that O, bobscript and various other crystallographic
viewing programs employ is consistent but incorrect - the algorithm works
in 2D planes through the scalar field, so any contours lying along 3
dimensional points not sharing a common coordinate (e.g. a diagonal) is
missed.  The body centered marching tetrahedra algorithm povscript+ uses
avoids this problem, as 3 dimensional cells are considered in each pass.  
However, the idea of "too many" polygons from the resulting isosurface is
a well known problem with marching tetrahedra.  I'm working on approaches
like vertex clustering (the treece "regularised marching tetrahedra"  
algorithm), but thats in the works.  I may throw in the old and deprecated
Diamond algorithm, but mathematical ethics has so far prevented me from
doing so.  ;)

	-Tim F

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        Tim Fenn
        fenn@brandeis.edu
        Rosenstiel Basic Medical Sciences Research Center
        Brandeis University, Mail Stop 029
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