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



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> > 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.  

Maybe not, but "looking better" does seem more germane to the issue of
*representation*, which is all these contours are, after all:  a
somewhat desperate attempt to get go grips with the mind-boggling
problem of electron density volumes.  Clarity and simplicity are what
matter most in representations, and by this criterion, fewer lines and
smoother corners probably can be considered "better".  Computations,
gradients etc. are of course quite a different matter.

(Just this user's 0.4993c worth, since the point was opened to the
floor, and with the caveat that I have neither a bobscript/O nor a
povscript+ figure in front of me.)

phx.



>  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.  ;)


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