Scipion-em

users:
fix create user subsets with classes2D

developers:
pwem.convert.headers.fixVolume: fixes the header of a volume defined as stack, so we can avoid :mrc suffix in paths the paths.
images imported by ProtImportImage and ProtImportMask remove problematic characters -> PROBLEMATIC_SHELL_CHARS = ;<>?"()|*\'&

users:
mrc, pdb, vol files can be open with Chimera from the file browser
rec file can be imported (not yet displayed by xmipp)
fix import of particles stack with one image

developers:
EmSet has a create copy method to properly copy a Set
useful for generic set handling (subset, join set, user subset)
tilt series subsets bug fixed
MaskVolumeWizard - Creates a mask for a volume interactively. Masks currently implemented: Spherical mask

users:
"set filter" protocol and wizard
protocol tree (left panel) collapsed at loading
developers:
protocols.conf created taken from scipion-app defining its own protocols.
Add getTransformMatrix function, finds transformation matrix between to PDB files
Add partial support for eer files, just reading dimensions (part 1)