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CueMol Changelog

What's new in CueMol 2.2.2.397

Sep 21, 2016
  • 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

New in CueMol 2.2.2.391 (Jun 27, 2016)

  • Implemented color proofing using the ICC profiles (see: cuemol2/ColorManagementSystem)
  • Implemented LuxRender output (see: cuemol2/LuxRenderExport)
  • Implemented Correct silhouette extraction
  • 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)

New in CueMol 2.2.2.384 (Apr 28, 2016)

  • 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.

New in CueMol 2.2.2.382 (Mar 26, 2016)

  • BUG FIX: Fixed problem in fetching PDB from RCSB web site

New in CueMol 2.2.1.349 (Apr 3, 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 24, 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 2.2.0.315 (Jul 7, 2014)

  • If you move the (qsc) scene file, if it is not embedded in the file the molecules, etc., and some correct the problem to be cut links to external files.
  • Add style Simple, of a Trace (thickening)
  • Add darkgray, the lightgray as a simple set of CPKColoring
  • so as not to Dasa the style menu on the edge renderer the Edge line is not attached

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
  • Fixed a bug that can not drop the renderer to group on Mac

New in CueMol 2.2.0.310 (Jun 12, 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 10, 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 (Apr 11, 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
  • In MacOSX Retina GUI also (hidpi) corresponding
  • Button of MacOSX for full screen mode

New in CueMol 2.1.0.279 Alpha (Oct 21, 2013)

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

New in CueMol 2.1.0.276 Alpha (Sep 3, 2013)

  • 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
  • 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 Alpha (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 Alpha (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.

New in CueMol 2.1.0.261 Alpha (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
  • I have to build a 64bit version of MacOS X

New in CueMol 2.0.1.249 Alpha (Oct 8, 2012)

  • I've implemented the options you do not want to force the use of 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 2.0.1.243 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 2.0.1.241 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 28, 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 2.0.1.188 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)
  • 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 povray output
  • Fixed bug qsc file is not saved to the center of 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 (Sep 17, 2011)

  • Fixed a bug successfully read mtz files generated since PHENIX 1.7.
  • Implementation of the Bond edit dialog. (Such as sugar chain binding and N SS, can now be added or deleted from the GUI for non-standard bond)
  • Fixed bug history is not added to the selection made in Mol struct panel
  • To appear in the command panel on priority Selection panel.
  • The Selection panel, so you can easily see the history of ever using selection

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 Alpha (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.