Opening 1jj2 pdb format is slow

[Tom Goddard]

Opening 1jj2 in pdb format takes 6 seconds, while a 3 week old (July 15) Chimera 2 it opens and displays in 2 seconds. Also opening mmCIF 1jj2 in the current Chimera 2 takes only about 1 second.

Timing statements show that the atoms.radii call in structure.py is taking 3.5 seconds for pdb format 1jj2 and only 0.15 seconds for mmCIF. So part of the slow open seems to be atom radius computation.

[Eric Pettersen]

When residue names were switched over to fixed strings, PDBio was no longer canonicalizing them correctly (because a reference wasn't being passed), so two-letter or shorter residue names (nucleic acids) were not matching their templates and many more rings/atom types were being computed.