I also updated the Wiki page.
2. There was a small mistake introduced by the last commits. This has been 
   fixed.
3. Code cleaning

Blendphys

according to the "Style Guide for Python Code" 
(http://www.python.org/dev/peps/pep-0008/) and the recent review
(http://codereview.appspot.com/6815052). Some slight changes were done, too. 
Extensive tests have shown that the code is still well working.

Blendphys

Also in the PDB IO: relict from old times, which has been removed

Blendphys.

Some cosmetics ... .

When exporting structures from Blender into a PDB file it happened 
sometimes that the xyz positions of the atoms weren't correctly 
stored. Bug fixed.

Some cosmetics ...

Blendphys.

The Atomic Blender panel is loaded correctly when a blend file is loaded.

Blendphys.

- Option 'smooth' permits now a better 'polishing' of the sticks.

- The default value for the precision of the sticks (unit length)
  has been put from 0.2 onto 0.05. If the sticks are shown, they do not 
  overlapp anymore.

- Code cleaning

- Due to the recent large changes of the code the addon has been tested 
  with even more PDB files.
  
  
Blendphys 

PS: see recent comment here: http://blenderartists.org/forum/showthread.php?235003-Atomic-Blender-for-loading-PDB-files-into-Blender-2.5&p=2079416&viewfull=1#post2079416

1. New: The user can now decide whether the panel is always, once or never shown 
after a PDB file is loaded. Note that the panel is quite essential since it 
helps quickly modifying PDB structures.
2. Some code cleaning
3. Wiki has been updated

Blendphys 

Attention: big changes in __init__.py, almost no changes in import_pdb.py
and export_pdb.py

1. With respect to the propositions made by Campbell and Sebastian
(see http://projects.blender.org/tracker/?func=detail&group_id=153&aid=29226&atid=469)
I changed the code. The PDB IO has now the preset option in the file dialog
of the importer and exporter.

2. Furthermore, I have put all properties into one group, which is located
in bpy.contect.scene. 

3. Some code cleaning

Soon, I will put in a new option (next days): the user can decide whether the 
panel is always, once or never shown after a PDB file is loaded. Note that
the panel is essential for me and also my students. It helps quickly modifying
PDB structures.

Blendphys 

PDB - Importer/Exporter
=======================
- Update of date


Blendphys 

Exporter
- Either active objects with a proper element name or all active objects are
  exported depending on EnumProperty in File dialog: all <-> element 
- Removed a bug in the exporter: 'import_pdb.ATOM_PDB_ELEMENTS_DEFAULT' is
  used instead of 'import_pdb.ATOM_PDB_ELEMENTS' <= is sometimes empty list

Importer
- The name of the representive ball of a dupliverts technique is now shorter:
  from 'Ball (NURBS)_<element>' to  'Ball_<element>'; The name of the element 
  is not cut in the outliner.


Blendphys 

MHX importer: temporary commit for Bmesh. UV coordinates are ignored, but at least the script does not crash.