Initial attempt at fix to add chain id removal.
Bugfixes.
Fixed some bugs due to surprising behavior of structure in which same chain ids can appear in multiple distinct chains.
Fixed bug in nosetest for removechains.
Fixed another bug in nosetest.
Merge pull request #52 from jchodera/fix-mutate

Add support for specifying chain ids in chains to remove [ready to merge]
PDBFixer writes a remark containing the original source
Merge pull request #58 from leeping/master

PDBFixer writes a remark containing the original source
Initial positions of added residues are more intelligently chosen
Merge pull request #60 from peastman/master

Initial positions of added residues are more intelligently chosen
Do another energy minimization after annealing
Merge pull request #61 from peastman/master

Do another energy minimization after annealing
Renamed one argument
Merge pull request #63 from peastman/pdbfile

Renamed one argument
Updated version number to 1.1
Merge pull request #64 from peastman/master

Updated version number to 1.1