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



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On Fri, 11 Oct 2002, Frank Vondelft wrote:

> 
> > 
> > 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*

I agree - from a representation standpoint, the algorithm used is
irrelevant.  However, it is also the basis by which decisions are made
about the model, and the defining evidence used to back those decisions!  
As such, perhaps the more correct representation is appropriate.  Caveat
emptor.

> 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.  

Mind-boggling problem???  Volumetric renderings of three dimensional 
scalar fields are simple - you just need a raytracer.  POVRay handles them 
just fine, and POVScript+ is set up to use the DF3 feature in order to 
generate them (see http://www.brandeis.edu/~fenn/povscript/df3.html).

> 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.
> 

I agree - fewer lines and smoother corners are great - but they should
reflect a consistent and correct topology (which is a direct result of the
computation/gradient used to achieve that end).

	-Tim F

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        Tim Fenn
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