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CueMol Changelog

What's new in CueMol 2.2.3.437

Sep 28, 2018
  • 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.

New in CueMol 2.2.3.434 (Jun 8, 2018)

  • 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.

New in CueMol 2.2.3.430 (Jun 8, 2018)

  • 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.
  • 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.
  • 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.

New in CueMol 2.2.3.422 (Oct 15, 2017)

  • BUGFIX:
  • Crashes when creating symmetry-related molecule

New in CueMol 2.2.3.421 (Aug 16, 2017)

  • "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)

New in CueMol 2.2.3.412 (Apr 25, 2017)

  • Back-face display of molsurf and dsurface renderers are turned on by default (when edge/silhouette line is disabled)
  • Back-face display option for dsurface renderer were implemented
  • The electrostatic potential coloring mode for the dsurface renderer was implemented.
  • The property to change the ramp-above value for electrostatic coloring was implemented.
  • Electrostatic potential coloring option for dsurface renderer were implemented
  • The option for the protein secondary structure assignment was implemented to eliminate a small segment of coils between helices (cylinders) in the cartoon renderer (TO DO: document)
  • 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

New in CueMol 2.2.3.403 (Feb 18, 2017)

  • 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)
  • FIXED: Electrostatic potential coloring of the surface renderes does not correctly work if there are more than two potential objects and surface objects.
  • FIXED: Changing the coloring of the trace renderers from the coloring panel GUI does not work correctly.
  • FIXED: The context menu of dark/light-CPK coloring in the scene panel do not use styles.
  • FIXED: Hydrogen atom of hydroxyl groups (HO3', etc) recognized as Ho (holmium) atom
  • FIXED: Atom data corupts when large mol was saved into the qsc (ver1) file.

New in CueMol 2.2.2.397 (Sep 21, 2016)

  • Type Of The Filter Save-Object-As Dialog Box Is Now Saved To Preference. Github
  • Compounds With The Different 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
  • The Problem In Fixed PDBFileReader When Loading Hydrogen Atoms (Such As HB11 And HB12) Misassigned As Boron. Github
  • Edge Generation Method Improve For Spheres. Github
  • Secondary Structure Assignment The For Beta-Bulges Is Now Configurable. Github
  • In The Non Bonds-Standard Ligands With Alternative Conformations Are Displayed Correctly. Github
  • The Bug Related Fixed To QSC File In The Folder Containing Non-ASCII Characters With Externally Linked Files. Github

New in CueMol 2.2.2.391 (Jun 27, 2016)

  • Color Proofing Using Implemented The ICC Profiles (See: Cuemol2 / ColorManagementSystem )
  • LuxRender Output Implemented (See: Cuemol2 / LuxRenderExport )
  • Implemented Correct silhouette extraction
  • FIXED: The materials are correctly applied, when there are more than two definitions for different output devices (eg, 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: Can not 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)

New in CueMol 2.2.2.382 (Mar 26, 2016)

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

New in CueMol 2.2.2.381 (Mar 19, 2016)

  • Support preview of edge rendering in the molview window using OpenGL shader
  • Multiple-Window Support Mode (See: Cuemol2 / MultipleWindow )
  • (? Or Preset) Implemented Composite Renderer (See: Cuemol2 / CompositeRenderer )
  • Dialog Editor For Implemented Renderer Styles (See: Cuemol2 / RendStyles )
  • Creation Of New Implemented Renderer Styles Based On The Existing Renderers (See: Cuemol2 / RendStyles )
  • Of Atom'S Append Label To The Namelabel Renderer With Empty Name ( "") Is Supported (See: Cuemol2 / NameLabelRenderer )
  • Copy And Paste Implemented 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

New in CueMol 2.2.2.366 (Nov 5, 2015)

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

New in CueMol 2.2.2.365 (Nov 5, 2015)

  • 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.

New in CueMol 2.2.1.354 (Jun 26, 2015)

  • Fixed a phenomenon in which the sheet of Cartoon renderer is twisted by circumstances
  • Ribbon renderer of sheet, Fixed phenomenon twisted funny in some cases is helix
  • Fixed slab setting is ignored trouble only to edge lines and the like in the Edge rendering
  • Fixed NAMD coor file had become unreadable in the Windows version
  • When you regenerate the Mol surface that was created only for the part of the molecule by Selection, Fixed a bug that selection is ignored
  • If you want to specify a selection in the property of the Renderer, Fixed a bug that was not available the macro (definition) created by the user
  • In Scene panel, if you select more than one object / renderer, it was to allow the show / hide from the context menu in one fell swoop against them
  • Fixed a bug that pixmap has not been effectively re-use of the characters in Namelabel such as character-based Dell renderer
  • Fixed points and was a non-efficiency are created and destroyed a rendering of Pixmap label In practice it even if you have off inside
  • Modified as it is (in synchronization with the content) correctly display the eye icon that represents the that contains the visibility settings in the Camera
  • Selection grammar, was to be able to specify the number of floating-point to the part you want to specify a numerical value, such as distance specified around
  • To implement the configuration GUI of Isosurf renderer

New in CueMol 2.2.1.349 (Mar 25, 2015)

  • I was to be able to read even PDB file, including the chain name in lowercase.
  • In PDB format basis, such as including a duplicate atom name I was to read even illegal files.
  • Fixed a bug that crashes when you copy the MolSurfObj in scene panel on MacOS
  • If you have colored using the $ molcol the MolSurfRenderer, not reflected immediately in the changed coloring of MolSurfRenderer even if the coloring of MolCoord to be a parent to correct the problem
  • If you fail to Qsc file read, Fixed a bug that scene that were open at the time from being initialized
  • Fixed a bug that Save file as operation does not work correctly
  • In expression of molecular selectivity, Fixed a bug that mol name specified with around operator does not work correctly
  • CPK, I was to limit automatically detail when it becomes too large number of polygons ballstick renderer.
  • The Camera setting, it was to be able to save the show / hide state of each object / renderer and ( Cuemol2 / CameraVisFlags )
  • In Mol surface cutter, were able to generate both of the cut surface and the cutting shell simultaneously ( Cuemol2 / MolSurfCut )
  • Add the implementation · GUI setting the Tube renderer of putty (changes of thickness depending on the B factor, etc.) ( Cuemol2 / TubeRenderer )
  • Such as the character label even POV-Ray rendering I was to be able to display
  • In POV-Ray rendering dialog was to be able to set the lighting and radiosity ( Cuemol2 / POVRayRenderLighting it, Cuemol2 / Radiosity )
  • Were to be specified in the relative time setting the time specified animation object of animation settings for other animation object and ( Cuemol2 / Anim_Cmb ).
  • Read PyMOL session (PSE) file (but incomplete) ( Cuemol2 / PSEImporter )

New in CueMol 2.2.1.330 (Dec 22, 2014)

  • The POV-Ray 3.7 to ship
  • And available to the multi-cpu rendering in POV-Ray rendering
  • Rendering to be used due to the radiosity you use the POV-Ray
  • Added option to clear the Background color
  • Implemented; (surface display version of contour isosurf) MapSurfRenderer
  • MapSurfRenderer implement the line display of (isosurf) (to become the display close to the electron density display of coot compared to countour)
  • If you on the recenter when reading the density map such like MTZ, perspective instead of moving, the current viewpoint will have to move the display center of the density map to the viewpoint as it
  • If you have used the ability to limit the molecular the display range of MapMeshRenderer (contour), Fixed a bug where setting property page did not work properly
  • Multiple choice and multiple items of copy & paste in the Scene panel, I made it possible to drag & drop
  • The renderer group I was to copy & paste available in Scene panel
  • I was to enable the creation of renderer-group in the create-renderer dialog that is displayed in such Scene panel of + (Add) button
  • Modify because style set of cartoon renderer that is displayed in the context menu of the renderer of Scene panel had became a thing of the ribbon renderer
  • Style and camera modified to file is also embedded in Embed-all option that can be specified at the time of scene Save
  • MolSurfObj me was to be able to easily (by changing the point density, etc.) regenerated from MolCoord.
  • I was to be able to rendering results preview in Animation rendering tool dialog.

New in CueMol 2.2.0.320 (Jul 30, 2014)

  • Fixed a bug that can not be copy & paste the Object
  • I have to be able to morphing forced even if the atom number do not match MorphMol
  • and implement additional UI of MorphMol / MolAnim to anim_panel
  • I have to choose the conversion to MorphMol from MolCoord implementation and start-up menu to convert to MorphMol from MolCoord (only add) implement morphanim-tool
  • I have to be able to set the name of the frame mounting · MorphMol insertAt, is delete MorphMol editing tool
  • There is a bug in time widget of Animation-related, the bug is fixed is ignored time of 1 second or less
  • Implement the property setting of MolAnim
  • To help identify the problems of the Animation rendering at the time, was able to save the (ffmpeg and all povray) log.
  • Fixed a bug that gets confused if you zero the time span of Animation
  • Change in solid ($ molcol) the default coloring of Nucl renderer, was to put the nucl => yellow coloring in the direction of mol
  • I was made to auto-detect input whether byte swapped in NAMDCoorReader.
  • Fixed a bug that is not recognized in Mol superposition and Interaction tool, if you specify a user-defined selection in the specified selection
  • Was to be able to on / off the readonly of Style. Style you load was set to be in read-only by default.

New in CueMol 2.2.0.313 (Jun 20, 2014)

  • I was to lead to smooth the connection point of the Edge line. edge line is no longer become jagged also the value small detail
  • After you run the Save scene as, was to put the MRU list the file name
  • Fixed a bug that did not can be set properly in the frame rate for Movie rendering, option of ffmpeg is not appropriate. Since there are cases where it was doubling the frame of the first frame and the last good movie make loop, made a Loop option

New in CueMol 2.2.0.310 (Jun 11, 2014)

  • P1, a = b = c = 1 to Cryst1 record when reading PDB, I have to ignore determines that the NMR data ....
  • Fixed a bug in the density map display by mtz file read. (Make sure to match the results of the FFT of CCP4)

New in CueMol 2.2.0.309 (Jun 9, 2014)

  • I tried not to issue a QDF format from the choice of file format in the File open dialog
  • (Executable from the menu) you have to be able to erase the information UndoRedo
  • In RenderPov dialog, to be specified in mm, such as the image size cm
  • In the File open option dialog, etc., I have to be the same as the previous state, the initial value of the checkbox (of recenter, etc.).
  • Improvement of interaction extraction GUI. Output to register & log in → atomintr generate a list of atoms at a given distance from (extraction only interaction between the specified → the object 2 and object 1) a specified portion
  • In order to be able to run in the UI bysidech mol selection of which depends on the UI
  • Improved behavior when there is more than one alpha in the Post-render alpha blending. (→ alpha value is as impossible only jump 0.1) processed together the objects of near alpha value
  • has enabled me to keep copy of the image in pov render dialog
  • To implement the prop setting UI of Disorder renderer
  • To allow a drag & drop the tab of Molview
  • (The abolition of ⇒ up and down buttons) to allow a drag & drop the object / renderer in the Scene panel
  • So as to make the (only one level) folder to the implementation object in the Renderer Group, it has become possible to put a renderer in it.
  • Previous state actions were to remain in the Reassign secondary str dialog
  • Fixed a bug in the code of the serialization of AtomIntrRenderer
  • I have to be able to change the designation of Stereo eye separation value Pov renderer dialog.
  • I have modified (renderer is OK) from the movement of the (item) selection after the deletion is a funny object in the Scene panel
  • Lock column is deprecated in Scene panel
  • (Tab) is to leave the state before operation in the Property edit dialog
  • The bug is fixed display position of Molview becomes funny in Windows in the Display configuration changes when I was (expanding) the DPI

New in CueMol 2.2.0.298 (Jun 9, 2014)

  • I have to be able to draw a line in the edge Pov rendering
  • I have to be able to draw the silhouette in Pov rendering
  • setting UI of nucl renderer
  • Implemented (in combination with ballstick) new type of nucl renderer.
  • I have to be able to on / off the drawing of the base pair connection in nucl renderer
  • Implement the auto-detect function of Basepair. PDBFileReader was to call on load automatically.
  • Made a renderer for displaying the dotted line of Disorder
  • Implemented putty equivalent of pymol to TubeRenderer
  • implement (fancy equivalent of pymol) molscript wind cross-section tube, the ribbon renderer
  • I have to be specified separately from the back of the Helix, the color of the side of the Sheet in the ribbon renderer
  • Add the style of Fancy1 to become a molscript style in ribbon renderer.
  • aspect of color ribbon renderer, like ring of color ballstick renderer, qualifier was made to work if you have specified a $ molcol
  • I was in the $ molcol the default color of the ring ballstick renderer. (Specified by default_styles.xml)
  • I have to pick from the list, the Material settings Renderer common page.
  • (From the context menu of the workspace panel) implement the change type of Renderer
  • The GUI of the Tube renderer, modified to specify the tube shape width1/width2 instead of tuber
  • I tried to put around byres and around to the right-click menu of the Scene panel / molview (Experimental)
  • Drag & Drop in the File, fixed a bug that occurs when reading PDB
  • Fixed a bug that scene of the old version that loaded the MSMSFile can not read
  • transition to xulrunner 23

New in CueMol 2.2.0.294 (Jan 16, 2014)

  • Bug fix version.

New in CueMol 2.1.0.279 (Oct 22, 2013)

  • Fixed a bug that comes to be click many times in single click of the mouse.

New in CueMol 2.1.0.276 (Sep 2, 2013)

  • I have to be able to release the one you selected on the residue level in the double click of the Mouse.
  • Label is displayed Click once on the atom, but made it clear the label when you click again.
  • Enhanced error handling when the execution failed in PDB2PQR/APBS dialog
  • In Mol superposition dialog, you have to not close dialog if it fails to superposition
  • If the Style file is an external link, style was set to write the external file when you export a qsc.
  • Of embedded or external links of the Style file is to be able to undo / redo
  • I have implemented the Undo / Redo (create, destroy, modify) of the Camera-related operations. I have implemented the Undo / Redo of file-linked of the Camera.
  • The Retina display for the Mac, was HiDPI display corresponding molecular view (GUI remains low res).
  • Fixed the problem that in MacOS X, do not show molecular view has got hidden they are being taken out of the dock.

New in CueMol 2.1.0.270 (Mar 15, 2013)

  • Instead of recalculating the secondary str in Create symm object, I have to have copied from the original. In addition, mol coloring was set to be the default.
  • Fixed a problem that can not be the correct rendering POVRay use the Material Setup
  • In Cartoon renderer, I made it possible to provide a prop constant at a value that specifies the thickness helix width mode ?
  • Fixed a bug that was not reflected at the law be changed to show label at (view distance) AtomIntrRenderer
  • Label was to disappear when you click the label atom that has already left
  • Even Animation mode, I was able to use the atom click / ctxt menu
  • At DoubleClick, I was made to toggle the residue selection
  • Fixed in POV rendering, how to calculate the line width scale was so funny

New in CueMol 2.1.0.262 (Feb 11, 2013)

  • Made it possible to set the destination alpha value other than 1 in the fade in / out of Animation
  • In Animation rendering dialog, I added a rawvideo encoding the encoding of ffmpeg. Also, I have to be able to specify any option that you can edit the textbox of the command line option.
  • Consider creating videos for playback cycle, I tried not to be rendering (which will be the same as the first frame =) the last frame.

New in CueMol 2.1.0.261 (Jan 12, 2013)

  • Fixed a bug that will crash if the position of the atoms and subtle, is that altconf in Mol surface generation. (Altconf be changed to make the surface only to A)
  • Paint correction menu panel is the scene did not work properly
  • it did not improve the qsc only supports files (such as in the PDB file open double click on the ⇒ CueMol Win) shell open. to use the same code as the drag & drap, etc. can be opened pdb (basic, by extension). Similarly, if you start from the command line, I was able to open as well, such as pdb.
  • I've implemented the property dialog of Cartoon renderer.
  • In the scene panel, allows you to change the display order of the object by the up / down buttons.
  • On other occasions as well, as much as possible to use the $ molcol coloring, coloring of the molecular objects has to be used when creating or actively Renderer.
  • Implementing the UI part of the style definition. (Definition of colors, the definition of molecular selectivity, and import / export of Style)

New in CueMol 2.1.0.250 Alpha (Nov 24, 2012)

  • Fixed crash bug in setting the boundaries of the electron density map

New in CueMol 2.1.0.249 Alpha (Oct 8, 2012)

  • Implemented the option that doesn't force the use of the OpenGL shader.
  • LOG fix is ​​coming out in large numbers to each set Material
  • Implemented the option to generate a cross-section only at (CutByPlane2) MolSurfCutter
  • Fixed a bug that may crash when you switch between display and non-display, such as Object

New in CueMol 2.1.0.243 Alpha (Aug 13, 2012)

  • Fix a bug that I had not come back to the original renderer after the move in the Slide in / out animation
  • Fix a bug in the alpha blending using Shader
  • Fix (enable / disable the widget according to the radio button) GUI of Secondary str tool
  • When you run the create symm object, so as to perform calculations of secondary structure re-
  • Fixed a bug when you view the Unit cell renderer fall

New in CueMol 2.1.0.241 Alpha (Aug 4, 2012)

  • That implement the · UI-related features Animation
  • Was added to the UI of the start / stop / pause the animation also ActiveX version
  • implementing the ad-hoc animation (spin one lap in 10 seconds)
  • That implements the UI to create an animation movie using POV-Ray + FFmpeg
  • DOS window that comes up when not to, such as POV-Ray rendering subprocess is running in Windows.
  • Can not be put up for shade when the Orthographic projection in the POR-Ray rendering
  • Gave the option to display the shadow either case projection Orthographic / Perspective in POR-Ray rendering
  • Was also to be able to image rendering non-square in the POR-Ray rendering
  • default value of rendering dialog has to be the same as the size of the current view.
  • That lets you specify the DPI of POR-Ray rendering output in PNG
  • There are multiple semi-transparent object after improvement of alpha blending POV-Ray rendering, improving the way they blend in situations that overlap
  • Was able to UNDO / REDO of Interaction tool
  • That implements the Map mesh renderer that uses the GPU geometry shader
  • That implements the Map volume renderer using GPU shader
  • Change to make using the fragment shader, the alpha blending in OpenGL
  • When reading PDB, if you do not automatic secondary strucutre assignment was to read the HELIX / SHEET record of the PDB.
  • That created the UI to do automatic recalculation of the secondary structure assignment.
  • That created the UI manually perform the secondary structure assignment.
  • That you learn to use the alpha test) improve the transparency and semi-transparent handling of the character label
  • wearing a button to apply renderer property dialog. Was able to see the impact of changes to the display of property without closing the dialog with OK.

New in CueMol 2.0.1.212 Alpha (May 10, 2012)

  • Fixed a bug of paint coloring configuration changes could not undo

New in CueMol 2.0.1.211 Alpha (Apr 23, 2012)

  • In the property dialog, was to be able to edit the value vector
  • Fixed a bug that does not reflect changes even if you change the property of the camera
  • In the SSM superpose, Fixed crash bug in generating sequence alignment after superposition
  • Fixed a bug if you can shadow orthographic projection in the POV-Ray rendering
  • Fixed a bug that crashes when you cut the ribbon by selecting parts that are adjacent in the Ribbon renderer is Helix-end/Helix-start

New in CueMol 2.0.1.208 Alpha (Mar 30, 2012)

  • Fixed a crash in the MacOS X version Interaction tool
  • Modified so that it can undo / redo the interaction representation can be created in the Interaction tool

New in CueMol 2.0.1.207 Alpha (Mar 20, 2012)

  • Modification
  • Correction because it did not come to be made is the electrostatic potential map only part that is specified in the selected APBS/PDB2PQR tool.
  • and, when you read the MapMeshRenderer from qsc, if that failed to load Fixed bug that crashed shortly after
  • was fixed, etc. If you fail with invalid povray rendering mesh is generated by the cartoon renderer
  • (C drive would have access to the forward and reverse) would fix the problem is out of dialog to access the f drive in the Windows version is povray.exe
  • Modified to work correctly even if the synthesis of three or more images (blendpng) semi-transparent synthetic
  • Fixed a bug in the UI molecule selection, if you select the text, the characters in the editing disappears
  • If you (can not read the link, etc.) when qsc file read failed, was to read to the end without giving up any abnormalities.
  • Because there was a crash due to lack of memory property of the Map renderer, if you specify a larger buffer size, more than 200 were not to be set.
  • Bug fix: wrong position when switching to a molecular view of (hardware stereo) OpenGL quadbuffer
  • The new implementation
  • The qsc file to be embedded in an electron density map
  • For implementing the coloring (MolCoord) molecule, rather than Renderer. (Documentation required future)
  • Automatic Extraction of creating a UI interaction. (Documentation required future)
  • external file and save it as not only an embedded camera, you can be shared by more than one scene. (Documentation required future)
  • Read the initial implementation of NAMD psf / coor
  • Add (for hardware stereo) a flag to swap the stereo eye to View
  • Cuemol icon with the icon was to come out when you mount the dmg in the MacOS X. made it easy to install put a shortcut to the Application folder in the dmg file.

New in CueMol 2.0.1.192 Alpha (Mar 20, 2012)

  • QSL file type of format came to be registered (win / osx). Icon came to be set.
  • Option dialog is now displayed when exporting QSL. Bulk Configuration of detail, compression settings, options can be set, such as law the qsl open the exported file.
  • Modified if the terminal N, so there was a bug when axialdetail is odd, the end portion of the tube is not displayed correctly and that the ends of the sheet in the Ribbon.
  • Add (dsurface renderer) Renderer molecular surface of the display type you want to attach to MolCoord.
  • Fixed in the secondary structure assignment, there was a bug that start and end of the helix is ??not recognized correctly and a structure such as N-terminal helix that begins with a sudden.
  • Fixed a bug that can not be read properly when entering non-ASCII characters in the path name of the file being referenced from within qsc file
  • (UI changes in radius) implements the property dialog of cpk renderer
  • That implements (to fit in unsigned short) in the export division of VBO QSL. Began to appear at most the number of polygons.
  • (IOS version is not supported yet, however) was to write out a letter to the QSL label

New in CueMol 2.0.1.188 Alpha (Jan 19, 2012)

  • Light weight scene file format, etc. for the Viewer for Mobile device (qsl) export function that implements the ability to read.
  • qsc when writing files, the next time you Save, option with the same last used (such as compression) can not be saved.
  • In the version of MacOS X, which fixes a problem that can not be copied and pasted in the workspace panel of molecular

New in CueMol 2.0.1.183 Alpha (Dec 30, 2011)

  • In the overlapping molecular Fixed crash bug with selection becomes empty
  • To display the log in the overlapping molecular sequence alignments
  • The display area of ​​the electron density mesh was improved by limiting the choice to show how the molecular
  • Implementation of a simple configuration GUI renderer molecular surface properties
  • Implementation of a simple configuration GUI renderer property electron density
  • Implementing the inertial scrolling (by default it is off)
  • Upgraded to 9.0.1 to XULRunner (version including Mac)
  • How to change the text display:
  • Select the statement was modified to specify the decimal minute argument around
  • Fixed a bug in the molecule can not be copied and pasted workspace panel

New in CueMol 2.0.1.172 Alpha (Nov 21, 2011)

  • Cartoon implementing renderers
  • ActiveX control to implement
  • Fixed: the distance is reflected in the povrayutput
  • Fixed bug qsc file is not saved to the centerf the Density map renderer
  • Projection from the View menu and made it possible to change the center mark

New in CueMol 2.0.1.161 Alpha (Oct 24, 2011)

  • implementation of the dialog to edit the information of crystallographic symmetry. (Available from the symmetry panel)
  • undo / redo the editing of crystallographic symmetry information
  • Improved Protein secondary structure assignment. Ribbon view, especially as it had gotten a twisted ribbon is shown as a single helix is ??continuous even if the two helix has improved now appear separately.
  • display ribbon, and they show off in the middle of the helix / sheet by selection, had a strange bug that displayed the cross-section as it appears.
  • When qsc file name and save, and re-saved in a separate folder, and fix a bug in the PDB file was unreadable information from qsc.
  • Made available for things like mini web browser.

New in CueMol 2.0.1.153 Alpha (Oct 24, 2011)

  • Fixed a bug in the mtz file read successfully generated since PHENIX 1.7.
  • Implementing the Bond edit dialog. (Or N-binding sugar chain such as SS, was removed from the GUI can add non-standard bond).
  • Fixed a bug that is not added to the history made in Mol struct panel selection
  • As a priority appear in the command panel Selection panel.
  • The Selection panel, so you can easily see the history of ever using selected

New in CueMol 2.0.1.149 Alpha (Sep 8, 2011)

  • Version of Win, in both the version of MacOSX, crashes when you try to view the display atom labels and distance, and bug fix.

New in CueMol 2.0.1.148 Build 20110827230102 (Sep 3, 2011)

  • Copy and paste that can be moved up and down / the entry PaintColoring
  • However, there is something wrong with the operating portion of undo / redo
  • Fix did not work fine because the PNG file and export scene
  • Fixed a bug that is negative Zoom
  • Electron density (Density) panel display range (extent) of the fix did not work properly designated
  • Fixed to work bufsize property of the renderer to specify the electron density
  • Upgraded to 6.0 XULRunner (including version Mac)
  • MacOSX version, the file open dialog now displays the drop-down list box to select the format. However, what is the file listed here may also select the file format is a problem that does not filter (of investigation).
  • Version of Win, in both the version of MacOSX, and you try to view a display atom labels and distance, there is a crash. Install the "User settings, etc." Since the start of normal operation to remove the Application as set in, if it crashes, please try it.

New in CueMol 2.0.1.145 (Sep 3, 2011)

  • Versions up to 5.0 XULRunner (Mac version 2.0)
  • Scene file (qsc file) option when you save (compressed text format) allows you to specify.
  • Improved copy and paste (Object mainly)
  • Copy and paste the Camera
  • The font size when displaying the label off the bottom of the letter Fixed
  • Implementation of the recently used file menu item
  • When you double-click the file qsc were to be loaded in a new tab instead of new windows.
  • transferred to the Preferences → Mouse settings trackpad, so that was also applied to the current View is already open (MacOS X)
  • Scene files even MacOS X (qsc file) that can be opened by double-clicking in the Finder. QSC is displayed as icons.
  • Electrostatic potential map-related bug fixes

New in CueMol 2.0.1.138 (Sep 3, 2011)

  • Upgrade to XULRunner 2.0
  • Molecular surface (solvent excluded surface) add the ability to generate (unwanted MSMS)
  • Improved cleavage of the molecular surface features (polygons no longer funny or cause as before).
  • pdb file compressed gzip (*. pdb.gz) was to be read directly.
  • Now that you have time to drop the compressed version from the download PDB rcsb, should have been faster.
  • Implementing the Dial button in the View panel
  • Add translucent overlay rendering capabilities Pymol-like
  • You can change the mouse binding molecule in the View
  • Copy and paste function of the Renderer
  • Copy and paste function of the Object (some buggy incomplete)

New in CueMol 2.0.0.125 (Sep 3, 2011)

  • Fix to be able to save files correctly qsc changes CPKColoring.
  • Fixed bug with crash! Bysidech in such a select statement.
  • POV-Fixed the behavior of funny when you close the Ray rendering windows.
  • The POV-Ray rendering, fixes a bug that can not render correctly when you set the clipping.

New in CueMol 1.1.0.196 Alpha (Sep 3, 2011)

  • The name of nucleic acid base residues can not be properly recognized because there was residue was added to the alias.
  • Correct implementation is so funny dotted line GeomLineRenderer.

New in CueMol 1.1.0.189 Alpha (Sep 3, 2011)

  • Fixed the strange that the MTZ file and read twice.
  • MTZ files created by Sharp (which partially damaged), so load the fix to be read.

New in CueMol 1.1.0.187 Alpha (Sep 3, 2011)

  • Were to be loaded directly to the MTZ file. Fourier transform with the Column of the MTZ file specified, the map is calculated.
  • Unit cell for the map to cover all or created from the MTZ was also able to view the map out of the unit cell. (Periodic boundary)
  • When you change the screen view, you automatically move to be the center point of rendering the map. (This will be turned off and turned off the auto update option in the renderer map)
  • Some mesh tubes used to render and Ribbon.
  • Be corrected because there was a strange sequence of residues in Mol struct palette.
  • Some other bugfix

New in CueMol 1.1.0.175 Alpha (Sep 3, 2011)

  • Export MQO Format
  • Introduces the concept of mesh.
  • Faster rendering to be performed by molecular surface mesh MolSurf.

New in CueMol 1.1.0.162 Alpha (Sep 3, 2011)

  • Fixed SetScriptColoring not work correctly
  • Fix was not written correctly when writing in the form of anti-aliasing in PNG.

New in CueMol 1.1.0.161 Alpha (Sep 3, 2011)

  • DisplayList not freed properly when Renderer invalidation, fixes a memory leak that was happening.
  • To specify the color that fore / background of TextRenderer.
  • The positioning of PictRenderer, halign, you can specify the valign.
  • In the mouse of View, I had to fix the screen turns freely but does not drag (WM_MOUSEMOVE come Why is sent when the user presses OK in the dialog script execution, particularly around the screen freely was. unknown cause).