![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Feb 6, 2020:
- 3:59 PM Ticket #2821 (sym to generate mmCIF assembly loses bfactor info) created by
- For example, open 6oyy sym #1 assembly 1 copies t close #1 color …
- 3:26 PM Ticket #2820 (SideVIew self.view.render is None) created by
- […]
- 3:26 PM Ticket #2819 (SideVIew self.view.render is None) created by
- […]
- 11:57 AM Ticket #2816 (SideVIew self.view.render is None) closed by
- duplicate: dup of #2813
- 11:40 AM Ticket #2814 (SideVIew self.view.render is None) closed by
- duplicate: dup of #2813
- 11:16 AM Ticket #2818 (Improve sample bundle code) created by
- The sample bundle found at …
- 9:39 AM Ticket #2817 (SideVIew self.view.render is None) created by
- […]
Feb 5, 2020:
- 7:00 PM Ticket #2816 (SideVIew self.view.render is None) created by
- […]
- 5:45 PM Ticket #2815 (VR buttons cause shadow recomputation) closed by
- fixed: Fixed.
- 5:41 PM Ticket #2815 (VR buttons cause shadow recomputation) created by
- […]
- 5:27 PM Ticket #2814 (SideVIew self.view.render is None) created by
- […]
- 4:46 PM Ticket #2813 (SideVIew self.view.render is None) created by
- […]
- 3:20 PM Ticket #2812 (Better handling of missing background depth in augmented reality videos) created by
- I need a mechanism to assure complete depth information for the …
- 3:08 PM Ticket #2811 (Volume image black backing face for augmented reality videos) created by
- Add mode where back of volume image display can be made opaque black …
- 3:03 PM Ticket #2810 (Make device realsense enable vr room camera) created by
- For making augmented reality videos it would simplify setup if the …
- 1:58 PM Ticket #2800 (Add "Undock tool" menu entry) closed by
- fixed: Menu item added for tools with no title bars
- 11:36 AM Ticket #2808 (Crash in glDrawArrays_ACC_Exec) closed by
- can't reproduce: Can't reproduce
- 11:33 AM Ticket #2807 ('NoneType' object has no attribute 'needs_update' after 2D labels closed) closed by
- fixed: Hi Shiran, This bug was fixed just yesterday, so if you get the …
- 11:21 AM Ticket #2809 (make ChimeraX website documentation URL point to vdocs) created by
- If possible, it would be great if we could make the URLs …
- 2:51 AM Ticket #2808 (Crash in glDrawArrays_ACC_Exec) created by
- […]
- 2:12 AM Ticket #2807 ('NoneType' object has no attribute 'needs_update' after 2D labels closed) created by
- […]
Feb 4, 2020:
- 6:06 PM Ticket #2806 (Refactor bundleinfo.xml) created by
- 6:00 PM Ticket #2805 (Update toolshed to Python3 and more recent django) created by
- 5:57 PM Ticket #2804 (Update ChimeraX dependencies) created by
- Dependency updates Python 3.8 QT 5.14 MSVC Linux …
- 5:29 PM Ticket #2803 (Dead 2D label being updated) closed by
- fixed
- 4:48 PM Ticket #2802 (saving session w/ 2D arrows gives RuntimeError: Unable to restore ...) closed by
- fixed
- 4:15 PM Ticket #2799 (Normals parellel to Z axis inverted) closed by
- fixed: Fixed. Same bug as #2793. Cylinders pointing along -z were not …
- 4:01 PM Ticket #2793 (Stick bond not circular) closed by
- fixed: Fixed. Bond drawing rotates a cylinder and when the bond points …
- 2:33 PM Ticket #2803 (Dead 2D label being updated) created by
- […]
- 1:38 PM Ticket #2802 (saving session w/ 2D arrows gives RuntimeError: Unable to restore ...) created by
- […]
- 12:46 PM Ticket #2795 (Problem with intra-mol excluded H-bond detection) closed by
- fixed: Has mistyped 'if' as 'is'
- 11:37 AM Ticket #2801 (Model Panel width too narrow) created by
- […]
- 11:35 AM Ticket #2800 (Add "Undock tool" menu entry) created by
- […]
- 8:37 AM Ticket #2799 (Normals parellel to Z axis inverted) created by
- […]
- 5:52 AM Ticket #2798 (Arcane version-conflict reporting) created by
- […]
- 4:42 AM Ticket #2797 (Missing clip caps for models with non-rotation position matrices ...) created by
- […]
Feb 3, 2020:
- 5:03 PM Ticket #2796 (Crash opening structure in conjunction with ISOLDE) created by
- […]
- 12:59 PM ChangeLog edited by
- (diff)
- 12:50 PM Ticket #2795 (Problem with intra-mol excluded H-bond detection) created by
- […]
- 10:29 AM Ticket #2792 (Attempt to save dead Residue in session) closed by
- can't reproduce: Bug from version before code to provide more extensive error …
- 10:17 AM Ticket #2794 (SideVIew self.view.render is None) created by
- […]
- 8:35 AM Ticket #2793 (Stick bond not circular) created by
- […] acetone.zip
Feb 2, 2020:
Jan 31, 2020:
- 4:55 PM Ticket #2471 (Actions menu suggested text & organization) closed by
- fixed: Okay, implemented.
- 2:32 PM Ticket #2790 (Long atom spec → grako recursion error) created by
- […]
Jan 30, 2020:
- 4:05 PM Ticket #1815 (style selAtom gives keyword error) closed by
- not a bug
- 2:57 PM Ticket #2789 (Attempted instantiation of HeaderSequence during session save) created by
- […]
- 1:40 PM Ticket #2788 (KeyError removing tool from _tool_instances dict) closed by
- can't reproduce
- 11:48 AM Ticket #2788 (KeyError removing tool from _tool_instances dict) created by
- […]
Jan 29, 2020:
- 12:47 PM Ticket #2786 (Multiple "vr false" → 'SteamVRCamera' object has no attribute ...) closed by
- fixed: Fixed SteamVR camera was being created when "vr false" issued, but …
- 12:17 PM Ticket #2787 (Saved images appear faded compared to graphics window, need color profiles) created by
- […]
- 10:00 AM Ticket #2786 (Multiple "vr false" → 'SteamVRCamera' object has no attribute ...) created by
- […]
Jan 28, 2020:
- 11:16 PM Ticket #2785 (Nucleotides saving deleted Residue) created by
- […]
- 6:54 PM Ticket #2779 (Problem saving session after segmentation regions deleted) closed by
- fixed: Fixed. Made Segger realize when region surfaces are closed. This …
- 1:19 PM Ticket #2781 (Crash running "volume flip" command) closed by
- fixed: Fixed. The trouble was that flipping caused negative array strides …
- 11:15 AM Ticket #2784 (Volume morph slider) created by
- […]
- 11:14 AM Ticket #2783 (Disconnecting already-disconnected tooltip slot when click outside ...) created by
- […]
- 8:57 AM Ticket #2782 (Some help files crash ChimeraX) created by
- […]
- 2:27 AM Ticket #2781 (Crash running "volume flip" command) created by
- […]
Jan 27, 2020:
- 7:33 PM Ticket #2778 (Picking segmented clusters: not enough values to unpack) closed by
- fixed: Fixed. Code that was logging what was picked in a drag select was …
- 7:31 PM ChangeLog edited by
- (diff)
- 4:05 PM Ticket #2780 (Error closing Help Viewer when page has 'page closed' URLs) closed by
- fixed: Appears to be a race condition in Qt WebEngine implementation where a …
- 4:03 PM Ticket #2776 (would like Settings.revert()) closed by
- fixed: Added 'reset' and 'restore' methods to settings, that fire the …
- 3:42 PM Ticket #2767 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce: I ran through a "trajectory" (NMR ensemble) with surface on for an …
- 2:07 PM Ticket #2780 (Error closing Help Viewer when page has 'page closed' URLs) created by
- […]
- 12:22 PM Ticket #2775 (Loading volume data: ModuleNotFoundError: No module named 'chimera') closed by
- fixed: Fixed. Fixed memory error reporting, and also issue user error if …
Jan 25, 2020:
- 5:34 AM Ticket #2779 (Problem saving session after segmentation regions deleted) created by
- […]
- 5:04 AM Ticket #2778 (Picking segmented clusters: not enough values to unpack) created by
- […]
- 1:55 AM Ticket #2777 (Tools can be placed offscreen) created by
- […]
Jan 24, 2020:
- 3:43 PM Ticket #2776 (would like Settings.revert()) created by
- Would like a core.Settings revert method that would revert the …
- 2:33 PM Ticket #2772 (Crash in mark_plane_edge_cuts) closed by
- fixed: Fixed. I introduced a bug a few days ago in the volume contour …
- 2:08 PM Ticket #2775 (Loading volume data: ModuleNotFoundError: No module named 'chimera') created by
- […]
- 1:57 PM Ticket #2770 (Return from Model Panel executes command three times(!)) closed by
- fixed: The main UI and tools were forwarding the same keystrokes to the …
- 1:35 PM Ticket #2774 (Showing title in log for model: not enough arguments for format string) closed by
- fixed
- 8:57 AM Ticket #2774 (Showing title in log for model: not enough arguments for format string) created by
- […]
- 8:42 AM Ticket #2773 (Crash installing ISOLDE(?)) created by
- […]
- 7:47 AM Ticket #2772 (Crash in mark_plane_edge_cuts) created by
- […]
- 1:13 AM Ticket #2771 (_openmm fails to load) created by
- […]
Jan 23, 2020:
- 8:03 PM Ticket #2770 (Return from Model Panel executes command three times(!)) created by
- […]
- 4:47 PM Ticket #2769 (mmCIF NMR reading bad for 'coordsets true') closed by
- fixed: Wans't finding existing residues to add coordinates to.
- 2:53 PM Ticket #2769 (mmCIF NMR reading bad for 'coordsets true') created by
- If I "open 2efi coord t", playing through the resulting trajectory …
- 1:14 PM Ticket #1872 (RFE: visual indicator on mouse-mode icons for which mode is active) closed by
- fixed: In the toolbar interface, the active mouse mode is "highlighted" with …
- 1:10 PM Ticket #2745 (closing tab in Help Viewer makes execution links in other tab no ...) closed by
- fixed: Fixed. Reorganized code so Help Viewer uses a single …
- 11:32 AM Ticket #2768 (Crash in free_keys_object/subtype_dealloc) closed by
- duplicate: Duplicate of #2767
- 9:58 AM Ticket #2768 (Crash in free_keys_object/subtype_dealloc) created by
- […]
Jan 22, 2020:
- 8:00 PM Ticket #2767 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 3:21 PM ChangeLog edited by
- (diff)
- 12:05 PM ChangeLog edited by
- (diff)
- 11:28 AM ChangeLog edited by
- (diff)
- 11:22 AM Ticket #2766 ("cartoon smooth" has no effect) closed by
- not a bug: Hi Paul, Smoothing is only applied to beta-strands, and 2HHB does not …
Jan 21, 2020:
- 7:08 PM Ticket #2766 ("cartoon smooth" has no effect) created by
- […]
- 4:53 PM Ticket #2758 (Place.rotation_axis_and_angle not robust) closed by
- fixed: Fixed. I put in special case code to handle the 180 degree rotation …
- 4:09 PM Ticket #2755 (Crash drawing Qt interface) closed by
- nonchimerax: This ChimeraX crash was in the Apple OpenGL graphics driver while Qt …
- 4:02 PM Ticket #2763 (Setting clip_cap property: 'Drawing' object has no attribute 'session') closed by
- fixed: Fixed. Clip caps used to work on a Drawing that is not a Model, but …
- 4:00 PM ChangeLog edited by
- (diff)
- 3:31 PM Ticket #2762 (Clip cap error with zero-length bond) closed by
- wontfix: BondDrawing is unusual in that its position instance matrices can be …
- 2:09 PM Ticket #2761 (mmCIF fetch: Compressed file ended before the end-of-stream marker was ...) closed by
- fixed: Made EOFError during fetch issue an error with explanation but not …
- 11:40 AM Ticket #2765 (Don't want silhouettes on volume meshes) created by
- […] image1.png
- 3:12 AM Ticket #2764 (ISOLDE not longer compatible with 0.9) created by
- […]
Jan 20, 2020:
- 6:29 AM Ticket #2763 (Setting clip_cap property: 'Drawing' object has no attribute 'session') created by
- […]
- 5:56 AM Ticket #2762 (Clip cap error with zero-length bond) created by
- […]
Jan 17, 2020:
- 10:37 PM Ticket #2761 (mmCIF fetch: Compressed file ended before the end-of-stream marker was ...) created by
- […]
- 11:02 AM Ticket #2759 ((corrupted stack?) crash) closed by
- can't reproduce
- 10:59 AM Ticket #2757 (Crash drawing Qt interface) closed by
- duplicate: Duplicate of #2755
- 10:58 AM Ticket #2756 (Crash drawing Qt interface) closed by
- duplicate: Duplicate of #2755
- 10:55 AM Ticket #2754 ((corrupted stack?) crash) closed by
- can't reproduce
- 10:54 AM Ticket #2753 ((stack corrupted?) crash) closed by
- can't reproduce
- 6:48 AM Ticket #2759 ((corrupted stack?) crash) created by
- […]
- 2:45 AM Ticket #2758 (Place.rotation_axis_and_angle not robust) created by
- […]
- 1:59 AM Ticket #2757 (Crash drawing Qt interface) created by
- […]
- 1:27 AM Ticket #2756 (Crash drawing Qt interface) created by
- […]
- 1:25 AM Ticket #2755 (Crash drawing Qt interface) created by
- […]
- 12:03 AM Ticket #2707 (Problem showing Toolbar help: failed to load external entity) closed by
- can't reproduce: Whoops :-). Can't reproduce this bug.
Jan 16, 2020:
- 10:17 PM Ticket #2754 ((corrupted stack?) crash) created by
- […]
- 7:00 PM Ticket #2753 ((stack corrupted?) crash) created by
- […]
- 5:55 PM Ticket #2752 (Save dialog has duplicate formats png and PNG) closed by
- fixed: Fixed. Registering the image settings options gui for the save dialog …
- 4:39 PM Ticket #2752 (Save dialog has duplicate formats png and PNG) created by
- […]
- 4:37 PM Ticket #2751 (Clip cap mistakenly remains visible) closed by
- fixed: Fixed. Clip plane change did not cause cap update because clip plane …
- 3:58 PM Ticket #2747 (Fetched map truncated) closed by
- fixed: The fetch worked fine for me on a Windows machine. I see from the …
- 2:12 PM Ticket #2746 (Graphics driver error/crash after fitting structure to map) closed by
- nonchimerax: This ChimeraX crash was caused by Apple's OpenGL graphics driver …
- 12:38 PM Ticket #2744 (Problem opening tif files with brackets in their name) closed by
- duplicate
- 12:33 PM Ticket #2742 (Problem restoring nucleotides in sessions) closed by
- duplicate: Fixed quite awhile back now.
Jan 15, 2020:
- 6:30 PM Ticket #2751 (Clip cap mistakenly remains visible) created by
- […]
- 6:16 PM Ticket #2750 (Certificate error fetching EDS map on some platforms) created by
- […]
- 5:27 PM PyQt created by
- 4:36 PM Ticket #2749 (ISOLDE installed into incompatible Ubuntu build of ChimeraX) created by
- […]
- 3:14 PM Ticket #2748 (GPU with insufficient OpenCL support leads to traceback in ISOLDE) created by
- […]
- 1:30 PM Ticket #2747 (Fetched map truncated) created by
- […]
- 11:46 AM Ticket #2746 (Graphics driver error/crash after fitting structure to map) created by
- […]
- 11:14 AM Ticket #2745 (closing tab in Help Viewer makes execution links in other tab no ...) created by
- maybe mac-specific... tested in 0.91 and in current daily build …
- 11:04 AM Ticket #2744 (Problem opening tif files with brackets in their name) created by
- […]
- 11:02 AM Ticket #2743 (Problem opening tif files with brackets in their name) created by
- […]
- 9:27 AM Ticket #2742 (Problem restoring nucleotides in sessions) created by
- […]
Jan 14, 2020:
- 12:41 PM Ticket #2741 (nicer form for ligand-table selection command, when possible) closed by
- fixed: Now only uses ::name="123" when needed
- 12:08 PM Ticket #2731 (Error in Basic Actions restoring session: invalid atom specifier) closed by
- fixed: Fixed in 8c604053a. Instead of ordering the name …
- 11:01 AM Ticket #2741 (nicer form for ligand-table selection command, when possible) created by
- […]
Jan 13, 2020:
- 7:10 PM Ticket #2740 (Cap colors don't track surface colors) created by
- […]
- 6:29 PM Ticket #2739 (Poor visibility for side view clip planes) created by
- […] sideview.png
- 5:54 PM Ticket #2709 (No bonds for residue UNL (unknown ligand) in 6dhf) closed by
- fixed: Changed code to connect atoms by distance when template (CCD entry) …
- 2:03 PM Ticket #2738 (Make volume mesh_lighting = False keep depth cueing) created by
- Currently mesh lighting false turns off all lighting including depth …
- 1:28 PM Ticket #2733 (Changing lighting in VR: CompositorError_TextureUsesUnsupportedFormat) closed by
- can't reproduce: Looks like a graphics drive problem. The VR created textures where it …
- 1:14 PM Ticket #2737 (Normals reversed for negative contours) closed by
- not a bug: There are Volume options that control these behaviors and there are …
- 12:51 PM Ticket #2734 (Closing tools before session restore: 'MainWindow' object has no ...) closed by
- duplicate
- 6:38 AM Ticket #2737 (Normals reversed for negative contours) created by
- […] wireframe_lighting.jpg
- 6:04 AM Ticket #2736 (all-same-value attribute coloring yields black instead of 'mid' color) created by
- […]
Jan 12, 2020:
- 6:42 AM Ticket #2735 (OpenMM crash running simulation) created by
- […]
- 3:22 AM Ticket #2734 (Closing tools before session restore: 'MainWindow' object has no ...) created by
- […]
Jan 11, 2020:
Jan 10, 2020:
- 2:20 PM Ticket #2732 (BILD arrow shaft juts through arrowhead) closed by
- fixed: That is correct. The cone_geometry() returns a cone centered at the …
- 11:04 AM Ticket #2732 (BILD arrow shaft juts through arrowhead) created by
- […]
- 6:51 AM Ticket #2731 (Error in Basic Actions restoring session: invalid atom specifier) created by
- […]
Jan 9, 2020:
- 3:57 PM Ticket #1390 (Need merged view of help documentation) closed by
- fixed: Make it so vdocs can built using the chimerax-daily build to generate …
- 3:52 PM Ticket #2599 ("select pyrimidine" doesn't select anything) closed by
- not a bug: There are no actual pyrimidines in 1bna (or regular nucleic acids for …
- 2:19 PM Ticket #2730 (Surface recomputation: cannot convert float NaN to integer) closed by
- can't reproduce: This error occurred due to NaN atom coordinates when recomputing a …
Jan 8, 2020:
- 5:25 PM Ticket #2730 (Surface recomputation: cannot convert float NaN to integer) created by
- […]
- 1:25 PM Ticket #2729 (Graphics error after switching users) created by
- […]
- 9:53 AM Ticket #2728 (Clipper: math domain error) created by
- […]
- 1:43 AM Ticket #2727 (Cannot launch on Windows) created by
- […]
Jan 7, 2020:
- 3:55 PM Ticket #2721 (Index out of bounds showing interface contact residues) closed by
- fixed: Fixed. The error resulted from making an interfaces plot and then …
- 2:25 PM Ticket #2726 (Have selection remember ordering) created by
- Selecting 4 atoms with the mouse and then using 'sel' as the atom spec …
- 2:23 PM Ticket #2719 (Graphics problem drawing silhouettes) closed by
- duplicate: Duplicate. Believed fixed about 4 months ago.
- 1:50 PM Ticket #2713 (Clashes: "Include intramolecule" option throws error) closed by
- fixed: Fix available in next build.
- 1:28 PM Ticket #2725 (Problem starting ISOLDE) closed by
- duplicate: Duplicate of #2215.
- 10:49 AM Ticket #2717 (AddH: can't form new hydrogen name) closed by
- nonchimerax: Hi Michael, Glad you were able to resolve the issue yourself. This …
- 10:43 AM Ticket #2716 (User confused about how to show trajectories) closed by
- not a bug
- 7:33 AM Ticket #2725 (Problem starting ISOLDE) created by
- […]
- 1:06 AM Ticket #2722 (Wrong version of ChimeraX for ISOLDE) closed by
- not a bug
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