Changes between Version 3 and Version 4 of Architecture

Timestamp:

Jul 14, 2009, 11:58:32 AM (17 years ago)

Author:

goddard

Comment:

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Architecture

@@ -9 +9 @@
  1. Molecular surface use is limited.  Each atom can only have one molecular surface associated with it.  For instance, making a surface for chain A, one for chain B and one for the atoms of chain A and B to examine buried surface area is not possible.  Each atom can belong to just one "surface category" and each molecular surface is created from a category.  It is also cumbersome to redefine the surface categories from the default ones (main, ligand, solvent).  The constrained possibilities for molecular surfaces complicate simple problems like looking at electrostatic potential on the interface between two chains.  Allowing multiple molecular surfaces would seem to be conceptually simple and more useful.  Current implementation with surface color, opacity, and display attributes attached to atoms instead of the surface would need to be changed.  Also current practice of using the same model id number for molecules and their surfaces would make referring to different surfaces in commands problematic. TG
  1. Many operations impose arbitrary requirements on how atoms are grouped. For example a sequence based structure alignment can be done on two separate "molecules", but not on two separate "chains" without first partitioning the chains into separate molecules objects.  Fitting two molecules into a density map with distinct rigid motions can be done but two chains of a single molecule cannot be moved independently by the fit-in-map tool.  In other cases two chains would be needed instead of two molecules.  For instance, a single molecular surface can be computed bounding two chains, but not two molecules.  These use restrictions are caused by implementation details such as molecules being positioned by transformation matrices while chains are positioned by individual atom coordinates, and also by graphical user interface design such as a menu that only allows choosing chains. TG
+ 1. Molecule data structures only know when chains are polymers or non-polymers by looking at bond connectivity.  So an alpha carbon only structure has to have bonds between the alpha carbons so that it is recognized as a polymer, so a ribbon could be drawn.  Would be better if the data structures knew which chains were linear polymers without relying on bonds. TG