Changes between Version 4 and Version 5 of Architecture

Timestamp:

Sep 29, 2009, 10:54:54 PM (17 years ago)

Author:

goddard

Comment:

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Architecture

@@ -10 +10 @@
  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
+ 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.