I have put a lot of work into translucent atoms ... had I realized that it was going to be so much work I probably would not have started :-)
I now have uncovered a usability problem and I need your feedback.
By default, objects inherit the color from the underlying atom. This applies to bonds, cartoons, almost everything.
In a simple case, bonds have no color but will inherit the color of the atom to which they are attached.
So, if the user executes a command to make the atoms translucent, do the objects (in this case the bonds) also become translucent?
Certainly, if the bonds are defined to be a different color then they would have independent translucent/opaque behavior.
But I am interested in people's opinions in the (normal) case where the color is inherited.
I am sure everyone has an opinion on this... so here's mine.
My main motivation for translucency is to see what's behind the atom, not what's inside it. So anything inside it should be translucent. In the same way we need translucency to see behind bonds, though they are normally smaller. We do not normally need translucent atoms to see inside them unless there is something interesting in there. That is only likely to happen if the translucent object is not atom-related but molecule-related (e.g. electrostatic surface.
HTH
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076
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