Changes between Version 6 and Version 7 of Architecture

Timestamp:

Sep 29, 2009, 11:39:03 PM (17 years ago)

Author:

goddard

Comment:

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Architecture

@@ -11 +11 @@
  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
  1. Aligning new models to the model with lowest id number is extremely confusing when it produces the wrong alignment.  This confusion could be avoided by distinguishing global rotations/translations where all models are moved together from relative motions where some models are fixed.  The implementation would keep a camera view transform that would include all global motions, while individual model transforms would only be used for relative motions.  The global frame would then be defined by the camera view transform.  The user will find it easier to grasp that moving some models with others fixed moves those in the global coordinate frame, while the fixed ones keep their original positions in the global frame. TG
+ 1. The Chimera developers depend on outside users to guide improvements in usability and utility.  This is very inefficient compared to having the developers directly use the program themselves on real applications.  A combination of outside and internal feedback is needed, but there is inadequate internal feedback.  Demonstrations and actual use by Elaine Meng within the lab generates roughly as much feedback as all outside users combined.  Likewise my use of volume / molecular assembly capabilities accounts for about half of the feedback driving those developments.  We would benefit significantly by arranging that all developers are real users of the program. TG
+ 1. The selectable object system is based on a 3-level hierarchy (graphs, subgraphs, vertices/edges) that maps to molecules, residues, atoms/bonds.  This system struggles to handle 2-level hierarchies of surfaces and surface pieces, and fails to handle >3 level hierarchies needed to handle for example quaternary structure and chains. TG
+ 1. The command language for naming data objects is limited to molecules, residues, and atoms.  Referencing surfaces or defined pieces of surfaces is problematic or not possible. TG