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Series 2.2.3

Version 2.2.3.443

• Implemented SDF format molecule file reader
• Implemented MOL2 format molecule file reader
• FIXED: Composite renderers are not shown in the renderer-selection dialog opened from PDB-fetch menu.
• FIXED: Atoms becomes unclickable after doing ssm-superpose

Version 2.2.3.437

• Edge lines now become (semi)transparent according to the color of the belonging triangle edges. This enables "segment end fadeout" display of the ribbon and cartoons with edge lines.
• Error in the "Mol Superpose" dialog of auto-recenter checkbox is fixed.

Version 2.2.3.434

• APBS and PDB2PQR are now also bundled in the MacOSX release.
• Multi-gradient coloring for isosurf and molsurf renderers was implemented.
• GUI for editing the multi-gradient coloring was implemented.(cuemol2/MultiGrad)
• GUI for changing the grid spacing of FFT to arbitrary number was implemented in the MTZ file reader dialog.
• Mol surface cutter was improved to allow cutting by multiple intersecting planes.
• MolSurf object generator of the isosurf renderer was improved to create the meshes with closed boundaries.
• Maxop prop of symm renderer was implemented to limit the maximum number of symmetry operators to be rendered.
• Zoom-in action for scalar-field objects was implemented.
• GUI for changing the PBC option of map renderers was implemented.
• Contour level setting by absolute value was implemented for mesh and isosurf renderes.
• The default behaviour of the mol selection widget was improved.
• Bug fixes:
• FIXED: The rendering settings (especially, projection type) are not saved after closing the dialog in the pov-ray rendering dialog.
• FIXED: Renderers using opengl shader function are not displayed after deleting one of the views in the multi-view mode.
• FIXED: Child processes spawned from CueMol does not inherit env vars, such as LD_LIBRARY_PATH.

Version 2.2.3.430

• Several molecule editor functions were implemented. (cuemol2/MolEdit)
• Changing the chain name operation was implemented.
• Changing the residue index operation was implemented.
• Delete operation of the selected atoms was implemented.
• Merge operation from one to another molecule objects was implemented.
• You can now select the download site for PDB and density map in the fetch PDB GUI. cuemol2/FetchPDB
• The max extent of the isosurf renderer works correctly. In the property dialog of the isosurf renderer, GUI for changing the max extent for the isosurf renderer was implemented.
• Bug fixes:
  • FIXED: Cannot copy multiple renderers in the workspace panel.
  • FIXED: Cannot load PSE file generated pymol version 1.7.6 and later.
  • FIXED: The max extent value in the density map panel is not updated, when the bufsize prop of the mapmesh renderer is changed.
  • FIXED: Points noise are displayed in the pov-ray rendering of the MapSurfRenderer.
  • FIXED: Preview OpenGL edge rendering of the MapSurfRenderer is not displayed correctly.
  • FIXED: xformMat property of MolCoord object does not work correctly for the embeded molecule in the qsc file.
  • FIXED: Change of the xformMat property of MolCoord object is ignored by the ribbon, cartoon, and namelabel renderers
  • FIXED: Sequence panel's contents are not displayed after loading the PDB file.
  • FIXED: Default duration of the new anim objs becomes zero.
  • FIXED: Animation slider does not work correctly.

Version 2.2.3.422

• BUGFIX: Crashes when creating symmetry-related molecule

Version 2.2.3.421

• "show unit-cell" button was added in the density panel.
• Now coordinates files are fetched from RCSB web site in the mmCIF format that supports large molecules.
• Internal representation unit of the time value was changed from milli-second to nano-second to increase the animation precision.
• You can now specify start/end cap properties separately in the atomintr renderer settings. (documents??)
• You can now copy the amino-acid seqences in the sequence panel in text format (cuemol2/SequenceDisplayPanel).
• Pre-view of the edge rendering for cylinder of ballstick was implemented.
• You can mix the opaque edge lines and semitransparent surfaces (document??)
• xform_mat property of objects was implemented (document?)
• BUGFIX: Load of OpenDX format file generated other than APBS fails by "Invalid map format" exception.
• BUGFIX: Animation rendering (and CueMol app itself) crashes when rendering applications (ffmpeg, povray) cannot be launched in MacOS X.
• BUGFIX: The chains containing residues with non-descendent order are not displayed correctly in the sequence panel.
• BUGFIX: Sequence and name are misaligned when a large number of molecules and chains are loaded in the sequence panel.
• BUGFIX: Drag&drop of multiple files does not work correctly.
• BUGFIX: CPK renderer is not displayed in GDI-generic implementation of windows OpenGL.
• BUGFIX: Atoms outside the slab planes are clickable.
• BUGFIX: CPK renderer does not support color proofing
• BUGFIX: Alpha (transparency) notation of color syntax does not function correctly (cuemol2/ColorSyntax)

Version 2.2.3.412

• Improvements of dsurface renderer (To do: documentation)
• Back-face display option for dsurface renderer were implemented
• The electrostatic potential coloring mode for the dsurface renderer was implemented.
• Electrostatic potential coloring option for dsurface renderer were implemented
• The property to change the ramp-above value for electrostatic coloring was implemented.
• Back-face display of molsurf and dsurface renderers are turned on by default (when edge/silhouette line is disabled)
• The option for the protein secondary structure assignment was implemented to eliminate a small segment of coils between helices (cylinders) in the cartoon renderer (cuemol2/Prot2ndryStr)
• The selection renderer is now auto-created by changing selection.
• gpu_mapmesh render now supports transparency and line width properties
• The implementation of the atom picking routine was improved
• The donwload source of electron density map was changed from EDS to EBI server
• RectSelection tool now works correctly, when the selection rect spans more than two molecules.
• BUGFIX: POV-Ray Rendering crashes when the scene contains dot surface (molsurf renderer with dot display mode)
• BUGFIX: Hi/Mid/Lo colors in the Elepot color panel don't work
• BUGFIX: LuxRender exporter outputs spheres with smaller than the actual sizes
• BUGFIX: Import of PyMOL session file containing negative number residues fails by exception
• BUGFIX: User-defined color names do not appear in color picker GUI of the solid coloring
• BUGFIX: Double bonds are not correctly displayed when the coordinates contain hydrogen atoms

Version 2.2.3.403

• Supported 64bit version (Windows 7 and later)
• Supported reading molecular coordinates in mmCIF file format
• Implemented new qsc file format (version 2), with LZMA (xz) compression and new molecular structure format (without limitation of atom number, residue number, chain name length, etc).
• Implemented "reset to default style" menu in the coloring panel.
• Implemented GUI for setting cylinder helix properties of Cartoon renderer.
• Separated the detail values of sections to those of helix, sheet, and coil in GUI of cartoon renderer settings.
• Added new LuxRender background types (plane and box)
• BUGFIX: Electrostatic potential coloring of the surface renderes does not correctly work if there are more than two potential objects and surface objects.
• BUGFIX: Changing the coloring of the trace renderers from the coloring panel GUI does not work correctly.
• BUGFIX: The context menu of dark/light-CPK coloring in the scene panel do not use styles.
• BUGFIX: Hydrogen atom of hydroxyl groups (HO3', etc) recognized as Ho (holmium) atom
• BUGFIX: Atom data corupts when large mol was saved into the qsc (ver1) file.

Series 2.2.2

Version 2.2.2.366

• BUGFIX: Support for Windows XP
• BUGFIX: Fixed bug in the Windows version installer
• BUGFIX: Support for MacOS X 10.6 and later

Version 2.2.2.365

• BUGFIX: PDB file reader cannot read SSBOND record without trailing spaces
• BUGFIX: Pov file rendering fails with spheres with nearly-zero radius
• BUGFIX: Animation rendering dialogbox does not remember the output prefix
• XULRunner is updated to version 39.0
  Build environment for Win32 is updated to VS2013
  Build environment for MacOS X is updated to clang-6.1 (Xcode 6.4)
• Implementation of density map loader by PDB ID from EDS server (see: cuemol2/FetchPDB)
• Implementation of chain or secondary-structure based coloring in RainbowColoring class
• Implementation of sequence display panel (see: cuemol2/SequenceDisplayPanel)
• Implementation of ribbon style helix rendering by CartoonRenderer (see: cuemol2/CartoonRenderer)
• Support for MRC-type map file
• Rendering of spheres and cylinders (cpk and ballstick renderers) using GL shader (see: cuemol2/CPKRenderer and cuemol2/BallStickRenderer)
• Dropped the support for the CueMol2 ActiveX control in the Windows version.

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