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Series 2.2.3

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 2.2.2.397

  • Filter type of the save-object-as dialog box is now saved to preference. github
  • Different compounds with the same residue name in different files now can be loaded correctly. (Auto-generated topology is now registered as object-local and not system global topology.) github
  • Fixed the problem in PDBFileReader when loading hydrogen atoms (such as HB11 and HB12) misassigned as boron. github
  • Improve edge generation method for spheres. github
  • The secondary structure assignment for beta-bulges is now configurable. github
  • Bonds in the non-standard ligands with alternative conformations are displayed correctly. github
  • Fixed the bug related to QSC file in the folder containing non-ASCII characters with externally linked files. github

Version 2.2.2.391

  • FIXED: The materials are correctly applied, when there are more than two definitions for different output devices (e.g., POV-Ray and LuxRender).
  • FIXED: Camera-motion animation (CamMotion) sometimes generates extra rotation.
  • FIXED: All of the style definitions are lost when the scene is saved with "embed-all" option.
  • FIXED: Edge-line shader does not work correctly in graphics boards other than NVIDIA.
  • FIXED: In the edge rendering mode, unnecessary edge lines are drawn between the arrow head and body of the round-style beta sheet.
  • FIXED: Renderer's property of transparency is alyways set to 1.0 after the execution of animation with the "hide/show" operations.
  • FIXED: Cannot read an mtz file with non-standard SG numbers, such as 3018, created by phenix.
  • FIXED: In MacOS X, POV-Ray rendering fails for images larger than 2600px.
  • FIXED: In MacOS X, Mol view disappears after hiding and showing the window (by shortcut cmd+H, etc)

Version 2.2.2.384

  • Negative peak renderer is also displayed for the Fo-Fc map display in Fetch from PDB/EDS server function
  • Fixed bug in Fetch from PDB/EDS server (clash at the end of the downloading)
  • Implementation of the "fade out" display of the end of the segments of tube and ribbon.

Version 2.2.2.382

  • BUGFIX: Fixed problem in fetching PDB from RCSB web site

Version 2.2.2.381

  • Support preview of edge rendering in the molview window using OpenGL shader
  • Support multiple-window mode (see: cuemol2/MultipleWindow)
  • Implemented composite (or preset?) renderer (see: cuemol2/CompositeRenderer)
  • Implemented editor dialog for renderer styles (see: cuemol2/RendStyles)
  • Implemented creation of new renderer styles based on the existing renderers (see: cuemol2/RendStyles)
  • Append of atom's label to the namelabel renderer with empty name ("") is supported (see: cuemol2/NameLabelRenderer)
  • Implemented copy and paste of styles in the scene panel (see: cuemol2/CopyPaste)
  • BUGFIX: Directions of the arrows of the interaction renderer are rendered in reverse direction in the POV-Ray rendering
  • BUGFIX: "Cancel" button in the query dialog shown in the application termination does not work correctly
  • BUGFIX: Limitation of drawing meshes of MolSurfRenderer by the molecular selection is implemented in all modes
  • BUGFIX: Atom hittest now works in the perspective mode of the molview window
  • BUGFIX: The modified flag of the embeded StyleSet objects are not reset after the save operation of the scene

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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Last-modified: Tue, 15 Aug 2017 17:09:51 JST (42d)