Subject: RE: Summary: Visualization of molecules and arbitrary geometric o bjects

From: "Smith JA (Jack)" <[email-masked]>
Date: Wed, 8 Jul 1998 09:55:58 -0500

> 3. Import and display multiple geometric objects, such as
triangulated
	> meshes, iso-surfaces of a field, spheres of arbitrary radius,
lines.
	> These should be arbitrary data specified by the user, not
something
	> computed from the molecule by the tool itself.

I find this deficiency (mainly lack of user-defined objects) in almost
all modeling packages somewhat strange.  It seems like such a relatively
minor, yet useful, enhancement to such otherwise complex applications.
We're just talking about basic geometry stuff - not chemistry, physics
or quantum mechanics.

This reminds me of a related feature I've always wanted to see in
modeling packages.  I'd like to be able to select a subset of atoms in a
structure and have the program (or let the user) determine the principle
axes (mass-weighted or not), construct/display your choice of a variety
of geometric enclosures (sphere, ellipsoid, cone, cylinder, cube, and
other polyhedra, including the 7 crystallographic cell types), with or
without using VdW/covalent/ionic contacts, and report/export the
dimensions, angles, surface area, volume, density, etc.  I'd also like
to see the 'inverse' feature (athough, somewhat more ambiguous) for
characterizing cavities. 

A similar feature would be to fit/display a 2D surface (simple plane,
quadratic surface, plane wave, etc.) through a selected subset of atoms
- again, relative to the principle or user-defined axes.  The fit could
be mass-weighted or plain least-squares.  The coordinate system could be
rectilinear, curvilinear, oblique, etc.  Fitting a 3D surface would be a
bit more challenging, but also potentially useful.

I think that quantifying the shape and size of molecular fragments
(cavities) is an important, useful and often overlooked aspect of most
molecular modeling packages.

- Jack

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 Jack A. Smith             ||
 Union Carbide             || Phone:  (304) 747-5797
 Catalyst Skill Center     || FAX:    (304) 747-4672
 P.O. Box 8361             || 
 S. Charleston, WV  25303  || [email-masked]
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