= Simple molecular graphics attributes for Feb 2015 Chimera 2

These are graphical molecular attributes that should be part of the C++ molecule classes or their base classes.

"*" indicates something we may change in Chimera 2.

== Atom ==
{{{
}}}

== !BaseSphere (base class for Atom) ==
{{{
 drawMode (Dot, Sphere, EndCap, Ball)
}}}

== Connectible (base class for !BaseSphere) ==
{{{
 display (true/false)

 color
}}}

== Connection (base class for Bond/!PseudoBond) ==
{{{
 display (true/false)

 drawMode (wire, stick, spring)
 radius

 color
 halfbond (color each half of bond to match near atom)
}}}

== Residue ==
{{{
 ribbonDisplay (true/False)
 ribbonDrawMode (2D, edged, round, custom)
 ribbonColor
 ribbonXSection (for custom cross-sections)
 ribbonStyle (width and thickness scale factors, e.g. for worms)
}}}


== Chain ==
{{{
}}}
  
== Molecule, also inherits from Model ==
{{{
 ballScale (float, scale ball size in ball and stick)
 stickScale (float, scale factor for bond radius)

 ribbonType (bspline, cardinal)
 ribbonStiffness (float, interpolation parameter)
 ribbonSmoothing (strand | coil mask, to smooth specific secondary structures)
 ribbonInsideColor (for inside/outside dual coloring)
 ribbonHidesMainChain (true/false)
 residueLabelPositionMode (centroid, backbone, primary-atom)
}}}

== Model ==
{{{
 display (true/false)

 color
}}}

== !PseudoBondGroup (global bond settings like Molecule) ==
{{{
 stickScale (float, scale factor for bond radius)
}}}

== Changes ==

7. Should color objects be immutable?  Chimera 1 allows redefining a color and having all graphics objects using that color automatically update.  Complex code.

8. How to handle different materials in addition to colors?

9. Keep color hierarchy (model->atom, model->ribbon)?  What about surface colors?