> One topic was tools for displaying isosurfaces (3D contours) or (say) > charge density, etc. overlaid on atoms. Is Jmol able to (a) produce (b) > display isosurfaces?
The short answer is ... No, not yet.
The longer answer is ...
isosurfaces has been one of the 'untouchable' areas for me because it was specifically listed on an NSF grant that I applied for.
However, given that I learned last week that the grant was turned down, I am now free to work on these things.
My condolences. It happens to all of us :-(
This week I have been working on ribbons. The ribbons are curved surfaces that require shading/lighting calculations. So, in some sense, they provide foundation work for iso-surfaces.
Absolutely
Regarding 'production' of iso-surfaces ...
Jmol can properly calculate a solvent-accessible-surface using vdw radii a probe sphere. This can be seen today using the 'dots' display. The protein folks would like to see this rendered as a real surface with charge coloring.
And the small molecule folks as well!
But this is not really an isosurface that is defined by a mathematical model.
Q: Is this the kind of surface that you want, or do you have a 'field' that is defined by a mathematical equation?
(A)
1. A grid of scalars (normally isometric or at least rectangular) is computed and the isosurfaces determined. The steps are then:
- calculation of the grid. This is probably outside Jmol. It could be a probe binding to a protein (cf. Peter Goodford's GRID program), or summation of functions such as atomic orbitals or observed electron density in crystals...
2. The grid is contoured. This could be a single method independent of the nature of the grid. I think Numerical Recipes or Graphics Gems give general routines
3. The contours are rendered.
I am not aware of any standard formal for transferring contours so Jmol would probably have to do steps 2 and 3
(B) An algorithm exists for creating the surface directly. The Connolly surface (dots) you already have is one such. Others include atomic orbitals (spherical harmonics) or atomic displacement "thermal" ellipsoids for crystals. I do not know if there is a general method for triangulating these.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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