[Chimera-users] How can one create a sculpted view of a cellular assembly?

Kenward Vaughan kay_jay at earthlink.net
Tue Jan 20 23:32:27 PST 2015

As I slowly approach the operational realization of my 
computational/visualization lab, I received your lovely holiday card. 
This seriously elevated my dreams of larger scale possibilities for 
chemistry and biology students through the cellPack resources.

In playing with it, I found myself wanting a more robust version of a 
clipping plane which would have several characteristics:

3 dimensional - take a cell and hack out 1 or 2 adjoining octants 
relative to its center to give a sliced view similar to what is found in 
some texts (also often used in geology books to depict the earth's 
internal structure--see 
http://www.the-science-site.com/earths-interior.html for an example).

Being able to leave the nucleus alone while the surface strips away the 
cytoplasm would be cool, much like the referenced image above showing 
the core of the earth.  Likely a difficult one to actually implement?

Have the clipped surface not be flat, but rather allow a component to 
stay visible as the surface is moved past it until some determined 
relationship at which point it vanishes (perhaps when it has passed 
entirely through the clipping surface?). The clipped surface would thus 
show structure of a sort.

Have the choice of the clipping surface being static with the assembly 
(it could rotate with the assembly, keeping the same internal view), or 
separately static (how a clipping plane behaves now--as I know it--where 
rotating the structure causes things to move through the unmoving plane.

One approach I can imagine would be the use of a spherical or 
ellipsoidal (?) surface of specific size at a specific distance from the 
center of the cellular assembly.

Is this already implemented in a way that can be manipulated to achieve 
at least the major aspects of this effect (e.g. logical ANDing of 
clipping by 3 intersecting planes)?

Sorry for the long question... ;-/

In a completely rational society, the best of us would aspire to be
_teachers_ and the rest of us would have to settle for something less,
because passing civilization along from one generation to the next
ought to be the highest honor and the highest responsibility anyone
could have.     - Lee Iacocca

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