Changes between Version 7 and Version 8 of Architecture

Timestamp:

Oct 28, 2009, 3:11:45 PM (17 years ago)

Author:

goddard

Comment:

--

Architecture

@@ -13 +13 @@
  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
+ 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. Even molecules may have identical names and id numbers so there is no unique identifier to distinguish them in commands. Also weird assumptions are made about the meaning of "sub-id" numbers. For instance the "findclash" command things of these as members of an nmr ensemble and does not detect clashes with those by default. The sym command uses sub-id numbers for symmetry copies where detecting clashes is of interest. Unique names for data objects are needed. TG