Fix a syntax error in MDAnalysis.__init__

[jbarnoud]

The PR #1375 introduced a syntax error in MDAnalysis.init. This
commit fixes the defective line.

See comment #1418 (comment) and bellow.

[utkbansal]

The test testsuite.MDAnalysisTests.utils.test_deprecated.test_collections_NotImplementedError fails because it cannot reference collections which was removed in the same commit here.

[jbarnoud]

I still have an error that I do not understand:

ERROR: Setting the resids of atoms changes their residue membership.
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Traceback (most recent call last):
  File "/home/jon/Envs/mda2/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/jon/dev/mdanalysis/testsuite/MDAnalysisTests/plugins/knownfailure.py", line 58, in inner
    raise KnownFailureException(msg)
KnownFailureException: Test skipped due to expected failure

Cleanup: deleting offset files in /home/jon/dev/mdanalysis/testsuite/MDAnalysisTests/data
----------------------------------------------------------------------

The error happens in core.test_topologyattrs.TestResids.test_set_atoms.

By the way, this PR is a duplicate of @kain88-de's #1431. Max shot first.

[kain88-de]

Max shot first.

But seems like I missed.

[kain88-de]

@jbarnoud thanks