Scipion-em

users:
- New viewer: ChimeraAttributeViewer: analyze scalar attributes of the residues or atoms in a structure
- Local resolution viewers use now native ChimeraX key
- Adding the protocol "Manual check point" that kept running for a time determined by a parameter or until
the user determines it is convenient.
- Calculating the FSC resolution value and displaying it in the viewer.

users:
- New protocol: numeric classes extractor: Extracts items from a SetOfClasses based on number of items assigned to the classes
- Filter ser protocol can filter by ranking: ascending or descending getting N items or a percentage.
- Outputs predefined for:
import masks
import mics
import movies
movie alignments
ctf estimators
pickings
extraction
- Filebrowser preview for images limited to 500MB (default). MAX_PREVIEW_FILE_SIZE (in MB) can be used to change this value.

users:
JAVA_MAX_MEMORY defaults to 4GB for a better user experience with large datasets
Take CHIMERA_HOME from chimera plugin if available. Otherwise will go for chimerax-1.2.5 as default
Clean problematic characters in filenames: ;<>?"()|*\'&
"filter set" protocols extended to filter by coordinate distance.
"edit set" protocol extended to allow editing angular information.
.gain files are treated as tiff files when getting its dimensions.

developers:
Transform class provides a "create" (factory method) to create common transformations.
pwem.convert.headers.fixVolume: to fix mrc headers of volumes.

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)