![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Jul 8, 2019:
- 5:45 PM Ticket #1982 (bond selection not shown as selection in Sequence Viewer) closed by
- fixed: Fixed. Not pushing until after workshop.
- 4:58 PM Ticket #1901 (RFE: add "running tools" section to Tools menu) closed by
- fixed: Implemented "running tools" section of Tools menu, though I won't push …
- 4:16 PM Ticket #2181 (Choose box face: shapes not aligned) closed by
- duplicate: Duplicate of #2163. Reported by Adam Frost.
- 4:15 PM Ticket #2163 (Choosing box face: shapes not aligned) closed by
- fixed: Fixed. Using mouse in move planes mode raised this error when in VR …
- 3:10 PM Ticket #2182 (Session restore for maps: KeyError: 'map ids') closed by
- fixed: Fixed. ChimeraX session restore of multichannel image series was …
- 2:37 PM Ticket #2182 (Session restore for maps: KeyError: 'map ids') created by
- […]
- 11:23 AM Ticket #2181 (Choose box face: shapes not aligned) created by
- […]
- 10:43 AM Ticket #2180 (QTimer not in QThread (offscreen rendering not working)) created by
- hello, just tested with 0.91 version of Chimera-X. There is still a …
- 8:26 AM Ticket #2179 (Non-graphics windows blank after structure load) created by
- […] chimeraX error WindowsX.png
Jul 5, 2019:
- 10:44 PM Ticket #2177 (Make VR meeting show Oculus or Vive controller layout) created by
- VR meeting currently always shows other participant's hand controllers …
- 5:28 PM Ticket #2085 (Crash in Qt in Mac graphics driver) closed by
- fixed: Tentatively closing this since we have had no further reports of this …
- 4:25 PM Ticket #2175 (Added hydrogen names) closed by
- fixed
- 1:12 PM Ticket #1682 (Expose mmcif template functions to Python) closed by
- fixed: The chief/link atom properties weren't being wrapped correctly in that …
- 12:08 PM Ticket #2097 (Undo aggregate and block context managers) closed by
- fixed
- 12:07 PM Ticket #2124 (Bundle's initialize() method doesn't get called on first installation) closed by
- fixed
- 11:35 AM Ticket #1682 (Expose mmcif template functions to Python) reopened by
- getattr(xxx, 'atoms') works, so it a bug that's tickled by the Shell …
- 8:01 AM Ticket #2176 (Session restore: "named views" is None) created by
- […]
- 4:30 AM Ticket #2175 (Added hydrogen names) created by
- […]
Jul 4, 2019:
Jul 3, 2019:
- 5:19 PM Ticket #2173 (Optimize morph command for near identical sequences) created by
- […]
- 4:27 PM ChangeLog edited by
- (diff)
- 4:21 PM Ticket #2172 (reverse palettes not working correctly for color-by-value without ...) created by
- open 2gbp color by bfactor pal rainbow ... OK, you can see whole range …
- 2:38 PM Ticket #2168 (Graphics context menu: spurious drag select; also delete hydrogens) closed by
- fixed: Spurious drag selection also fixed.
- 11:18 AM Ticket #2171 (Segment Map and Fit to Segments in-tool menus sometimes become transparent) created by
- Screenshot attached. Reassign/change component as needed. This is …
- 11:01 AM Ticket #2170 (Better VR button assignments for Oculus hand controllers) created by
- Make better VR default button assignments for Oculus hand controllers. …
- 10:25 AM Ticket #2169 (Side View: self.view is None) closed by
- duplicate: Duplicate of #2162
- 10:23 AM Ticket #2117 (map stopped updating) closed by
- can't reproduce: Likely a previous error stopped graphics rendering.
- 8:24 AM Ticket #2169 (Side View: self.view is None) created by
- […]
- 6:18 AM Ticket #2168 (Graphics context menu: spurious drag select; also delete hydrogens) created by
- […]
- 4:20 AM Ticket #2167 (ChimeraX installer for Chocolatey package manager) created by
- According to the documentation on Travis-CI …
Jul 2, 2019:
- 4:57 PM Ticket #2165 (Mac OpenGL crash opening session with segmented map) closed by
- nonchimerax: This session opens fine on my iMac (macOS 10.14, Mojave) machine and …
- 4:50 PM Ticket #2166 (Don't cap clipped volume meshes) created by
- Want volume mesh surfaces not to show caps when clipped.
- 4:46 PM Ticket #2165 (Mac OpenGL crash opening session with segmented map) created by
- […]
- 4:15 PM Ticket #2157 (want list of available bundles to actually be installable) closed by
- fixed: Fixed in acc84bf99. Uninstallable bundles (ones whose …
- 4:09 PM Ticket #2164 (Fit to Segments only works when Segment Map tool is also shown?) closed by
- fixed: Fixed. This was because closing the segment map tool actually closed …
- 2:57 PM Ticket #2164 (Fit to Segments only works when Segment Map tool is also shown?) created by
- As far as I can tell, with the same map and atomic models open and the …
- 2:32 PM Ticket #2163 (Choosing box face: shapes not aligned) created by
- […]
- 1:57 PM Ticket #2162 (Side View: self.view.render is None) created by
- […]
- 12:46 PM Ticket #2161 (Residue::find_atom missing from _ISOLDES_ libmolc.so?!?) closed by
- duplicate: It's ticket #1673. I'll add a comment to it and close this.
- 12:27 PM Ticket #2159 (self._positions is None) closed by
- fixed: Tristan says he fixed this.
- 12:21 PM Ticket #2153 (traceback from Fit to Segments "Fit... Close placed copies") closed by
- fixed: Fixed. Using Close Placed Copies twice gave this error because the …
- 12:14 PM Ticket #2152 (Fit to Segments menu File... Save[..] problems) closed by
- fixed: Fixed. I have renamed the Fit to Segments menu entry "Save fit map …
- 11:34 AM Ticket #2161 (Residue::find_atom missing from _ISOLDES_ libmolc.so?!?) created by
- […]
- 11:13 AM Ticket #2151 ('FitSegmentsDialog' object has no attribute 'Close') closed by
- fixed: Fixed. Fit button was trying to close the previous fit dialog and …
- 10:54 AM Ticket #2150 (Segment Map menu "regions...color density map" makes density map disappear) closed by
- fixed: Fixed. Segger uses RGBA colors in range 0-1 which often need to be …
- 8:43 AM Ticket #2160 (QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window) created by
- […]
Jul 1, 2019:
- 5:48 PM Ticket #2158 (usage for unknown commands should not be silent) closed by
- fixed
- 4:42 PM Ticket #2145 (Clearing Atom's aniso_u doesn't register as change) closed by
- fixed: Okay, clearing anise_u now notifies the change tracker as appropriate.
- 4:11 PM Ticket #2159 (self._positions is None) created by
- While trying to reproduce the maybe-double-model-delete error, instead …
- 3:19 PM Ticket #2148 (Fit in Map error when models closed) closed by
- fixed: Fixed. Auto-selection of "special" items caused self.value to be …
- 2:05 PM Ticket #2155 (Markers GUI no longer needs to remove itself from registered state managers) closed by
- fixed: Fixed. Session code no longer registers attributes starting with …
- 2:04 PM Ticket #2158 (usage for unknown commands should not be silent) created by
- And if the command is available, but uninstalled, that should be noted too.
- 2:02 PM Ticket #2139 ("Uninstalled bundle" should occur regardless of command arguments) closed by
- fixed: Fixed. Consumes the rest of the line, including semicolons.
- 1:54 PM Ticket #2157 (want list of available bundles to actually be installable) created by
- Would like Toolshed._get_available_bundles() to return the bundles …
- 1:12 PM Ticket #2156 (Qt initialization) created by
- When I run "debug test", output from one of the tests is: […] I …
- 1:08 PM Ticket #2155 (Markers GUI no longer needs to remove itself from registered state managers) created by
- […]
- 12:36 PM Ticket #2140 (Atom balloon on mouse hover vanishes immediately) closed by
- fixed: Made a separate ticket #2154 for the problem described in comment 3 …
- 12:34 PM Ticket #2154 (No balloon help if continuous redraw) created by
- […]
- 12:03 PM Ticket #2153 (traceback from Fit to Segments "Fit... Close placed copies") created by
- I *think* I added symmetry copies (1gc1 fit into EMDB 5020) with the …
- 11:28 AM Ticket #2152 (Fit to Segments menu File... Save[..] problems) created by
- In File to Segments,trying to use File menu to save things. Choosing …
- 11:22 AM Ticket #2146 (self._positions is None) closed by
- duplicate: Fixed weeks ago. Happened if a volume that was going to be displayed …
- 11:18 AM Ticket #2151 ('FitSegmentsDialog' object has no attribute 'Close') created by
- […]
- 10:58 AM Ticket #2147 (self._positions is None) closed by
- duplicate: duplicate of #2146
- 10:54 AM Ticket #2150 (Segment Map menu "regions...color density map" makes density map disappear) created by
- Open map and use Segment Map to make segmentation model, and then …
- 10:45 AM Ticket #2142 (Atom name > 4 characters) closed by
- duplicate: Duplicate of #2141
- 10:34 AM Ticket #2149 (Command "clip list" reports wrong sign for far plane) closed by
- fixed: Fixed. Also back plane in scene clip planes had wrong sign. Problem …
- 10:31 AM Ticket #2149 (Command "clip list" reports wrong sign for far plane) created by
- […]
- 10:29 AM Ticket #2148 (Fit in Map error when models closed) created by
- […]
- 10:10 AM ChangeLog edited by
- (diff)
- 7:46 AM Ticket #2147 (self._positions is None) created by
- […]
- 7:42 AM Ticket #2146 (self._positions is None) created by
- […]
- 6:23 AM Ticket #2145 (Clearing Atom's aniso_u doesn't register as change) created by
- Pretty much what the summary says. :) Would be ideal if `Atom.aniso_u6 …
- 5:38 AM Ticket #2144 (Model.delete() called twice?) created by
- […]
Jun 29, 2019:
- 12:44 PM Ticket #2143 (Mouse mode that centers and pivots) created by
- […]
- 11:12 AM Ticket #2142 (Atom name > 4 characters) created by
- […]
- 11:10 AM Ticket #2141 (Atom name > 4 characters) created by
- […]
Jun 28, 2019:
- 8:23 PM Ticket #2140 (Atom balloon on mouse hover vanishes immediately) created by
- […]
- 3:47 PM Ticket #2139 ("Uninstalled bundle" should occur regardless of command arguments) created by
- […]
- 3:33 PM Ticket #2134 ('main_view' needs to register itself as a state manager) closed by
- fixed: Reverted to previous code, with slight tweak to avoid adding …
- 11:01 AM Ticket #2137 (Volume set_parameters(cap_faces=False) no longer effective) closed by
- can't reproduce: I opened a map (emd 1080) set a low contour level and used …
- 10:52 AM Ticket #2138 (Keep directory history in Save File dialog) created by
- From: Alexis Rohou Subject: [chimerax-users] suggestion for ChimeraX …
- 9:54 AM Ticket #2135 (Structure in a bad state can crash ChimeraX) closed by
- wontfix: I am open to suggestions, but I have no inclination to guard every use …
- 9:08 AM Ticket #2137 (Volume set_parameters(cap_faces=False) no longer effective) created by
- I think this is meant to be superseded by `VolumeSurface.clip_cap = …
- 8:26 AM Ticket #2136 (add "basic primer" for ChimeraX python scripting) created by
- Similar to the Chimera one …
- 8:08 AM Ticket #2135 (Structure in a bad state can crash ChimeraX) created by
- […]
- 5:26 AM Ticket #2134 ('main_view' needs to register itself as a state manager) created by
- […]
Jun 27, 2019:
- 6:20 PM Ticket #1054 (command "open" doesn't work on URLs without suffix) closed by
- fixed: The last example works when given as: open …
- 5:36 PM Ticket #2050 (Crash drawing Side View after close) closed by
- fixed: Fixed in changeset:ee83b922765b17928d4054cc20e967cc39ba565d. Called …
- 2:53 PM Ticket #1682 (Expose mmcif template functions to Python) closed by
- fixed: Extended the mmCIF module with two additional functions: […] …
- 2:29 PM Ticket #2105 (mmCIF save: local variable '_1to3' referenced before assignment) closed by
- fixed: Fixed.
- 1:57 PM Ticket #2131 ('view' command: 'Objects' object is not iterable) closed by
- duplicate
- 1:39 PM Ticket #2132 (Crash in Qt handling event) closed by
- fixed: Hi Diogo, We _think_ this problem is fixed for daily builds dated …
- 1:30 PM Ticket #2132 (Crash in Qt handling event) created by
- […]
- 12:29 PM Ticket #2123 (self._child_drawings.remove(d): not in list (after earlier KeyError)) closed by
- duplicate: The last tracebacks appear to result from using "volume zone" with the …
- 12:29 PM Ticket #2131 ('view' command: 'Objects' object is not iterable) created by
- […]
- 12:23 PM Ticket #2119 (Surface capping not working) closed by
- fixed: Duplicate of #2130. Problem was "surface dust" caused caps not to …
- 12:19 PM Ticket #2130 (Surface caps not working consistently) closed by
- fixed: Fixed. Surface capping was not making caps if a surface had triangles …
- 11:45 AM Ticket #2125 (Qt::AA_ShareOpenGLContexts) closed by
- duplicate: Duplicate of #2121. This warning is a Qt bug from QWebEngine.
- 11:44 AM Ticket #2120 ('view' command: 'Objects' object is not iterable) closed by
- fixed: Fixed in bf9fe95e2. Undo code got too clever and tried to …
- 11:34 AM Ticket #2127 (Silhouettes on transparent drawings) closed by
- duplicate: Making silhouettes transparent is requested in ticket #607. …
- 11:29 AM Ticket #2113 (User installed tools should take precedence over app-included tools) closed by
- fixed
- 11:28 AM Ticket #2130 (Surface caps not working consistently) created by
- […] image1.png
- 11:27 AM ChangeLog edited by
- (diff)
- 11:20 AM Ticket #2129 (Surface caps not working) closed by
- not a bug: As your "surface cap" command says, you have surface caps turned off. …
- 11:16 AM Ticket #2128 ('view' command: model is None) closed by
- duplicate: Bug in 0.8 fixed long ago.
- 11:13 AM Ticket #2129 (Surface caps not working) created by
- […]
- 6:19 AM Ticket #2128 ('view' command: model is None) created by
- […]
- 6:00 AM Ticket #2127 (Silhouettes on transparent drawings) created by
- […]
- 5:50 AM Ticket #2126 (Glitchy dual-screen behavior) created by
- […]
- 3:23 AM Ticket #2125 (Qt::AA_ShareOpenGLContexts) created by
- […]
- 1:28 AM Ticket #2124 (Bundle's initialize() method doesn't get called on first installation) created by
- In order to correctly load its libraries for OpenCL and CUDA, OpenMM …
Jun 26, 2019:
- 4:45 PM Ticket #2123 (self._child_drawings.remove(d): not in list (after earlier KeyError)) created by
- […]
- 4:44 PM Ticket #2114 (self._positions is None) closed by
- can't reproduce: I tried this in the same ChimeraX daily build (6/25/2019) on Windows …
- 4:32 PM Ticket #2116 (Adjust surface geometry: not enough values to unpack) closed by
- fixed: The subdivideSurface unpack error is fixed and the Cut fraction error …
- 4:30 PM Ticket #2077 (wrong result from specifying palette with value,color pairs) closed by
- fixed: Fixed. Palette values were being ignored because the way default …
- 4:09 PM Ticket #2122 ("volume zone" can create duplicate model IDs) closed by
- fixed: Fixed. Now issues an error message "Tried to create model #6 which …
- 1:52 PM Ticket #2122 ("volume zone" can create duplicate model IDs) created by
- […]
- 12:13 PM Ticket #2121 (Startup warning about Qt::AA_ShareOpenGLContexts) created by
- ChimeraX on Mac is giving a startup warning Attribute …
- 11:02 AM Ticket #649 (bundle specification of open/save arg UI) closed by
- duplicate: Now a duplicate of #2079
- 11:00 AM Ticket #183 (Make pseudobonds end on cartoons) closed by
- fixed: No complaints yet.
- 8:25 AM Ticket #2120 ('view' command: 'Objects' object is not iterable) created by
- […]
- 6:01 AM Ticket #2119 (Surface capping not working) created by
- […]
- 5:36 AM Ticket #2118 (Color zone sharp: Cut fraction is out of range) created by
- […] colorzone.tar.gz
- 5:11 AM Ticket #2117 (map stopped updating) created by
- […]
- 5:04 AM Ticket #2116 (Adjust surface geometry: not enough values to unpack) created by
- […]
- 3:18 AM Ticket #2115 (Erratic shell tab completion) created by
- […]
Jun 25, 2019:
- 5:28 PM Ticket #2114 (self._positions is None) created by
- […]
- 5:12 PM Ticket #2113 (User installed tools should take precedence over app-included tools) created by
- […]
- 11:45 AM Ticket #2091 (mmCIF not writing "exptl"/"exptl data" headers) closed by
- fixed: exptl table is now in mmCIF output if it was in the input.
- 6:20 AM Ticket #2112 (ClipPlanes.set_clip_position argument change) closed by
-
fixed: Never mind - I see the last argument to
set_clip_position()has … - 6:16 AM Ticket #2112 (ClipPlanes.set_clip_position argument change) created by
- […]
- 5:58 AM Ticket #2111 (SetupTools version number "normalisation" breaks bundle_builder) created by
- PEP 440 does some (annoying, IMO) second-guessing of version numbering …
Jun 24, 2019:
- 7:19 PM Ticket #2110 (ToolInstance id problem restoring session) created by
- […]
- 6:02 PM Ticket #2109 (error logging for inconsistent command option shows underscore version ...) closed by
- fixed: A little tricky, but fixed.
- 5:47 PM Ticket #1157 (need to change initial display of nucleotides) closed by
- fixed
- 5:13 PM Ticket #707 (trying to open incorrect http URL creates file history entry) closed by
- fixed: Fixed by fix for #706.
- 5:12 PM Ticket #706 (using File History to open http URL echoes command with "http" as database) closed by
- fixed: Made it so "files" that are opened in the web browser are not logged …
- 4:13 PM Ticket #2109 (error logging for inconsistent command option shows underscore version ...) created by
- For example, command save nerts.cif models #2,3 relModel #1 format …
- 4:01 PM Ticket #2107 (save mmCIF crashes ChimeraX) closed by
-
fixed: Fix mistakely translated code.
is not '.'should be {{{!= … - 2:21 PM Ticket #2108 (Session adds non-statemanager to list of state managers) created by
- […]
- 10:58 AM Ticket #2107 (save mmCIF crashes ChimeraX) created by
- I was testing the new mmCIF save option "relModel" and both times …
Jun 22, 2019:
- 5:23 PM Ticket #1634 (Inconsistent ToolShed download statistics) closed by
- fixed: The code was indeed only capturing one (random) platform for each …
- 2:41 PM Ticket #2013 (Trouble pip-installing Pyyaml prereq for bundle) closed by
- fixed
Jun 21, 2019:
- 2:23 PM Ticket #1341 (Friendlier alignment API) closed by
- fixed: Seems like that would be consistent behavior. I have made the change. …
- 11:26 AM Ticket #2102 (Crash in Qt in Mac graphics driver) closed by
- duplicate: duplicate of #2085
- 11:21 AM Ticket #2101 (Crash as QFileDialog processes QEvent) closed by
- can't reproduce
- 11:21 AM Ticket #2106 (core.geometry.PlaceState lacks reset_state method) created by
- […] flu_antibody.cxs
- 10:02 AM Ticket #2105 (mmCIF save: local variable '_1to3' referenced before assignment) created by
- On my Linux machine in the RedHat ChimeraX 0.9 release, attempting to …
- 9:59 AM Ticket #2104 (Clipper: 'NXmapHandler' object has no attribute 'set_display_style') created by
- […]
- 8:03 AM Ticket #2103 (Solo blobs) created by
- […]
- 7:21 AM Ticket #2102 (Crash in Qt in Mac graphics driver) created by
- […]
Jun 20, 2019:
- 8:05 PM Ticket #2101 (Crash as QFileDialog processes QEvent) created by
- […]
- 6:42 PM Ticket #2100 (Jittery resize on Mac development build, but not daily build) created by
- […]
- 5:28 PM Ticket #2095 (mmCIF write: support 'relModel' keyword) closed by
- fixed
- 4:35 PM Ticket #2099 (Error saving mmcif with relModel option) closed by
- fixed: Use "if x is not None:" instead of "if x:"
- 3:35 PM Ticket #2099 (Error saving mmcif with relModel option) created by
- […]
- 3:33 PM Ticket #2098 (Ephemeral convexity display) created by
- […]
- 2:55 PM 2019-06-20 created by
- 2:10 PM DeveloperMeetings edited by
- (diff)
- 1:38 PM Ticket #2096 (amino-acid capping residues in polymer not classified as protein) closed by
- fixed: 'protein' selector was easy to fix. 'backbone' selector already worked.
- 12:14 PM Ticket #2097 (Undo aggregate and block context managers) created by
- Undo manager needs to provide ways of aggregating undo for multiple …
- 12:01 PM Ticket #2096 (amino-acid capping residues in polymer not classified as protein) created by
- If possible, would be nicer if these residues when appearing as part …
Jun 19, 2019:
- 7:19 PM Ticket #2095 (mmCIF write: support 'relModel' keyword) created by
- […]
- 2:32 PM Ticket #2088 (Tiling not handling surfaces) closed by
- fixed: Fixed in c6eba37af. Only atomic structures are tiled now, …
- 10:33 AM Ticket #924 (Clipper plugin not pulling dependency from PyPI) closed by
- can't reproduce: I think pulling from PyPI is working. If not, check #2013 which is …
Jun 18, 2019:
- 10:53 PM Ticket #2086 (Report of problem with ChimeraX) closed by
- nonchimerax: Yes, ChemOffice2002 is the problem. It should either (1) not have a …
- 4:08 PM Ticket #2090 (alignment reader not handling non-ASCII characters) closed by
- can't reproduce: Couldn't reproduce this with an alignment file with non-ASCII …
- 3:21 PM Ticket #2089 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') closed by
- fixed: Updated to opt.value API
- 1:03 PM Ticket #2094 (RFE: frames argument in torsion command for animating bond rotation) created by
- Facilitate scripting multi-frame bond rotations for movies or other …
- 12:19 PM Ticket #2093 (Pivot not restored in sessions) created by
- […]
- 12:15 PM Ticket #2092 (Promiscuous gesture scrolling) closed by
- fixed: Thanks for the additional info. The problem is surely connected to …
- 11:23 AM Ticket #1190 (Mac bundle builds fail when compiling C code) closed by
- fixed
- 11:15 AM Ticket #1421 (Earlier detection of core incompatibilities) closed by
- fixed: In the GUI, users are notified via dialog that the bundle cannot be …
- 11:11 AM Ticket #1966 (CA-CB bond not shown) closed by
- fixed
- 10:46 AM Ticket #945 (RFE: ctypes-friendly plugin build system) closed by
- wontfix
- 7:43 AM Ticket #2092 (Promiscuous gesture scrolling) created by
- […]
- 7:07 AM Ticket #2091 (mmCIF not writing "exptl"/"exptl data" headers) created by
- […]
- 12:37 AM Ticket #2090 (alignment reader not handling non-ASCII characters) created by
- […]
Jun 17, 2019:
- 8:29 PM Ticket #2089 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') created by
- […]
- 6:09 PM Ticket #2052 (Opening .pyc: source code string cannot contain null bytes) closed by
- duplicate: Duplicate of #1723.
- 6:01 PM Ticket #1723 (Drop of .pyc file → source code string cannot contain null bytes) closed by
- fixed: Can properly open .pyc files now.
- 3:48 PM Ticket #1683 (Can't install OpenEye from pip) closed by
- wontfix: No update for 4 months.
- 3:43 PM Ticket #2017 (Reversing color palettes) closed by
- fixed: Implemented in c29223bd.
- 3:31 PM Ticket #1698 (Session save: No bundle information for ...) closed by
- fixed: Fixed upstream.
- 3:27 PM Ticket #1009 (molecular surface not included in command-line specifiers of ...) closed by
- fixed: No complaints for a year.
- 3:24 PM Ticket #1802 (Python shell: tab completion produces "KeyError: 'matches' " after ...) closed by
- fixed: ipykernel 5.1.1 was released and the problem appears fixed. Errors no …
- 3:12 PM Ticket #2028 ("color modify" not consistently reversible) closed by
- not a bug: To see how the color modifiers work, check out https://colorme.io/. …
- 3:05 PM Ticket #1846 (Either: Tempy broken, or Registration internal error -- dealer's choice) closed by
- wontfix
- 12:20 PM Ticket #1557 (Bad bond selection) closed by
- duplicate: Merging with #1011.
- 12:07 PM Ticket #1836 ("toolshed uninstall": JSONDecodeError) closed by
- duplicate: Same as #2043.
- 11:47 AM Ticket #1168 ("safe mode" startup for use with devel command) closed by
- fixed: Added in 7140446.
- 11:45 AM Ticket #1671 (Permission denied installing Clipper) closed by
- fixed: Permission errors are now reported as user errors rather than tracebacks.
- 11:43 AM Ticket #1518 (Clipper: No matching distribution found) closed by
- wontfix: If this error happens, we really really want the error text. And we …
- 11:40 AM Ticket #1506 (Non-existent attribute tests wong) closed by
- fixed: Fixed in 06a907d.
- 11:25 AM Ticket #1142 (after isolde install) closed by
- not a bug: Eric's suggestion is correct.
- 11:19 AM Ticket #1175 (Add define and undefine CModule/CLibrary entries) closed by
- fixed: Added Tristan's patch in 0d03fc7.
- 11:13 AM Ticket #2088 (Tiling not handling surfaces) created by
- […]
- 11:00 AM Ticket #1722 (toolshed uninstall Toolbar → JSONDecodeError) closed by
- duplicate: Fixed in #2043.
- 10:56 AM Ticket #1627 (Startup error: KeyError: 'ChimeraX_ISOLDE') closed by
- fixed: Probably fixed by 97393c7. Ignore bad or incomplete …
- 10:52 AM Ticket #1844 (Toolshed cache KeyError crashes startup from app icon) closed by
- fixed: Toolshed now catches KeyErrors when loading available bundles from …
- 10:38 AM Ticket #998 (Toolshed tool install gives long traceback when no permission to ...) closed by
- fixed: Toolshed._pip_install catches PermissionError and converts it to a …
- 10:35 AM Ticket #2043 (Uninstall Clipper: JSONDecodeError) closed by
- fixed: Hacked fix in 5c6c03148. distlib, since 0.2.8, does not …
- 9:05 AM Ticket #2038 (Install Clipper: 'utf-8' codec can't decode byte) closed by
- fixed
- 9:03 AM Ticket #1292 (Registration code not handling some date formats) closed by
- fixed: Fixed in 0062071d.
- 8:56 AM Ticket #1860 (Blast Protein results widget flaky? (sometimes no horizontal scroll)) closed by
- fixed: Fixed in 3a7f70280. Made table layout use bootgrid …
- 2:03 AM Ticket #2087 (Problem with distutils-generated loader flags) created by
- […]
Jun 15, 2019:
- 11:09 AM Ticket #986 (impressions of chimeraX) closed by
- fixed: Nucleotides code has been updated to provide many more display …
- 11:05 AM Ticket #1855 (Can't set 'vertices' attribute on Drawing) closed by
- fixed: All the old versions of ISOLDE/Clipper have been removed and the …
- 9:46 AM Ticket #2086 (Report of problem with ChimeraX) created by
- […]
Jun 14, 2019:
- 5:05 PM Ticket #2085 (Crash in Qt in Mac graphics driver) created by
- […]
- 12:40 PM Ticket #2084 (Surface clip cap settings not saved in sessions) closed by
- fixed: Fixed. Surface cap settings (on/of and offset) are now always saved …
- 12:39 PM Ticket #2084 (Surface clip cap settings not saved in sessions) created by
- Hi Tom, the mesh settings are now restored correctly, however the …
- 12:14 PM Ticket #528 (Atom specifier wildcard characters * and ? in chain name) closed by
- fixed: This was apparently implemented at some point.
- 12:09 PM Ticket #1147 (make failing when bundle has a pip dependency) closed by
- fixed: I think this ticket was fixed but never closed.
- 12:05 PM Ticket #297 (RFE: add cartoon (ribbon) presets) closed by
- fixed: Eric implemented presets, including cartoon style presets.
- 12:03 PM Ticket #550 (Toolshed install of Clipper bundle does nothing) closed by
- fixed: ChimeraX now warns that the bundle could not be installed and logs the …
- 11:50 AM Ticket #1141 (Unable to install clipper) closed by
- can't reproduce: ISOLDE/Clipper installation has evolved quite a bit since this ticket …
- 11:40 AM Ticket #1131 (ISOLDE not compatible with v 0.7?) closed by
- fixed: ISOLDE works with 0.8 and 0.9 now.
- 10:51 AM Ticket #2083 (cxcmd:save saves to documentation directory, not working directory) closed by
- not a bug: Yes, this is a feature. Use ~/Desktop/filename for saving.
- 8:29 AM Ticket #2083 (cxcmd:save saves to documentation directory, not working directory) created by
- Just noticed this when running the ISOLDE tutorial. The commands …
- 7:14 AM Ticket #2082 (Poor visibility for the selection outline) created by
- […]
Jun 13, 2019:
- 7:01 PM Ticket #2081 (Empty (2D) label throws exception) closed by
- fixed: Fixed. Code that converts text to an image for rendering did not like …
- 5:28 PM Ticket #2081 (Empty (2D) label throws exception) created by
- […]
- 4:26 PM Ticket #2080 (Awkward text copy from Help Viewer (HTML widgets?)) created by
- […]
- 3:41 PM Ticket #2078 (label colors not set/updated correctly) closed by
- fixed: Fixed. 2D labels were not listening for graphics background color …
- 3:15 PM Ticket #2079 (Manager/provider for open/save dialog format options) created by
- per summary
- 2:08 PM DeveloperMeetings edited by
- (diff)
- 2:03 PM Ticket #2078 (label colors not set/updated correctly) created by
- For both 2D and 3D labels, if the label color is not set then it is …
- 12:25 PM Ticket #2070 (Side View: molecule disappears on second monitor) closed by
- nonchimerax: (FYI, no need to cc Tom and me on your replies to ChimeraX-bugs, we're …
- 12:24 PM Ticket #2072 (Mesh map setting not restored by session) closed by
- fixed: Fixed. Unfortunately some volume code changes made mesh style not get …
- 11:16 AM Ticket #2068 (Transparency retained when coloring) closed by
- not a bug: This is the intended behavior -- allowing you to change colors while …
- 11:11 AM Ticket #2066 (Save dialog: name 'fn' is not defined) closed by
- fixed: Fixed. Rearranging save dialog options panel last few days broke this.
- 11:07 AM Ticket #2077 (wrong result from specifying palette with value,color pairs) created by
- I have no idea when this broke. We must have tested it when it was …
- 10:41 AM Ticket #2059 (Toolshed allows very old ISOLDE/Clipper to install) closed by
- fixed: All versions of ISOLDE 0.9.24 and prior, and Clipper 0.1.9 and prior …
- 8:28 AM Ticket #2076 (Clear instructions for preparing bundle help files) created by
- I may have just missed it, but the instructions on how to make a …
- 7:04 AM Ticket #2075 (resfit record movie every Nth residue) created by
- […]
- 7:01 AM Ticket #2074 (Next steps: building into density) created by
- A lovely example I came across the other day: […] What's there is …
- 6:09 AM Ticket #2073 (Session notes/notebook) created by
- […]
- 5:57 AM Ticket #2072 (Mesh map setting not restored by session) created by
- […]
- 5:44 AM Ticket #2071 (Undockable settings; wider entry fields) created by
- […]
- 5:40 AM Ticket #2070 (Side View: molecule disappears on second monitor) created by
- […]
- 5:26 AM Ticket #2069 (Two-way depth cueing) created by
- […]
- 5:07 AM Ticket #2068 (Transparency retained when coloring) created by
- […]
Jun 12, 2019:
- 9:26 PM Ticket #74 (Atom spec parsing eats following file path.) closed by
- wontfix: I think the conclusion we reached is that a filename is either the …
- 9:17 PM Ticket #1631 (UnicodeDecodeError during ISOLDE install) closed by
- fixed: Fixed in fd27a41. Escape illegal utf-8 characters.
- 7:37 PM Ticket #1522 (ViewDockX: No suitable models found for ViewDockX) closed by
- fixed: Fixed in ea93d0e. Raise UserError instead of ValueError …
- 7:28 PM Ticket #1931 (Atom spec parsing consumes torsion command angle argument) closed by
- fixed: Fixed in ad8ad0bf6. Atom name ranges are no longer allowed.
- 6:57 PM Ticket #1565 (Can't upload bundle to ToolShed) closed by
- fixed: This problem is fixed. Unfortunately, others have popped up.
- 6:37 PM Ticket #2044 (Basic Actions: KeyError: 'selector') closed by
- fixed: Fixed in 1a233ddb2. Selector was missing because the …
- 5:56 PM Ticket #2066 (Save dialog: name 'fn' is not defined) created by
- […]
- 4:45 PM Ticket #2018 (Maintain aspect ratio option for image-save UI) closed by
- fixed: Done.
- 3:56 PM Ticket #2062 (Add include maps option to save file dialog) closed by
- fixed: Done. Added the include maps option to the save file dialog when …
- 3:22 PM Ticket #2065 (No status messages during EMDB fetch) closed by
- fixed: Fixed. Create opengl context when status bar window exposed.
- 3:18 PM Ticket #2065 (No status messages during EMDB fetch) created by
- […]
- 1:47 PM Ticket #2064 (Linux resize crashes on old graphics) closed by
- wontfix
- 1:30 PM Ticket #2063 (Open/Save options in GUI) closed by
- duplicate: Effectively a duplicate of #2062
- 12:45 PM Ticket #2058 (Crash in QTimer activation (redraw timer?)) closed by
- can't reproduce: Crash 15 levels deep in Qt native Mac code ending with …
- 12:39 PM Ticket #2057 (Crash OpenGL on Mac in Qt drawing user interface) closed by
- can't reproduce
- 12:37 PM Ticket #2054 (Surface geometry calculation: cannot convert float NaN to integer) closed by
- can't reproduce: Appears that some atom position was NaN causing an error in surface …
- 12:25 PM Ticket #2060 (Secondary status message not visible if ChimeraX window not maximised) closed by
- fixed: Fixed. Window resize was not updating the status bar size properly. …
- 11:23 AM Ticket #2064 (Linux resize crashes on old graphics) created by
- […]
- 11:05 AM Ticket #2063 (Open/Save options in GUI) created by
- […]
- 11:02 AM Ticket #2061 (Uninstall Clipper: JSONDecodeError) closed by
- duplicate: As Tristan points out, duplicate of #2043; adding Scooter to that
- 11:02 AM Ticket #2062 (Add include maps option to save file dialog) created by
- […]
- 10:48 AM Ticket #2056 (Surface geometry calculation: cannot convert float NaN to integer) closed by
- duplicate: functional duplicate of #2054
- 10:46 AM Ticket #2055 (Surface geometry calculation: cannot convert float NaN to integer) closed by
- duplicate: Functional duplicate of #2054
- 4:56 AM Ticket #2061 (Uninstall Clipper: JSONDecodeError) created by
- […]
- 3:50 AM Ticket #2060 (Secondary status message not visible if ChimeraX window not maximised) created by
- On my Linux machine in the 0.9 release: […] The message is …
- 3:41 AM Ticket #2059 (Toolshed allows very old ISOLDE/Clipper to install) created by
- […]
- 2:49 AM Ticket #2058 (Crash in QTimer activation (redraw timer?)) created by
- […]
- 2:24 AM Ticket #2057 (Crash OpenGL on Mac in Qt drawing user interface) created by
- […]
- 2:00 AM Ticket #2056 (Surface geometry calculation: cannot convert float NaN to integer) created by
- […]
- 1:55 AM Ticket #2055 (Surface geometry calculation: cannot convert float NaN to integer) created by
- […]
- 1:40 AM Ticket #2054 (Surface geometry calculation: cannot convert float NaN to integer) created by
- […]
Jun 11, 2019:
- 8:00 PM Ticket #2053 (Session restore failure: 'chimerax.core.graphics' has no attribute ...) closed by
- fixed: Fixed. Changed clip plane classes yesterday and older sessions needed …
- 3:51 PM Ticket #2003 (fetched model scores not remembered in sessions) closed by
- fixed: Much like the surface-area attribute, the additional score weren't …
- 3:18 PM Ticket #2053 (Session restore failure: 'chimerax.core.graphics' has no attribute ...) created by
- […] model-pdl-analysis.cxs
- 1:54 PM Ticket #2052 (Opening .pyc: source code string cannot contain null bytes) created by
- […]
- 11:55 AM ChangeLog edited by
- (diff)
- 11:23 AM Ticket #2051 (Movie fails to encode using Chimerax: dyld: Symbol not found: ...) closed by
- invalid: Duplicate of #1379. We have only seen this error on old macOS …
- 10:58 AM Ticket #2049 (Basic Actions: KeyError: 'selector') closed by
- duplicate: duplicate of #2044
- 10:57 AM Ticket #2048 (Basic Actions: KeyError: 'selector') closed by
- duplicate: duplicate of #2044
- 10:57 AM Ticket #2047 (Basic Actions: KeyError: 'selector') closed by
- duplicate: duplicate of #2044
- 10:56 AM Ticket #2046 (Basic Actions: KeyError: 'selector') closed by
- duplicate: duplicate of #2044
- 10:54 AM Ticket #2045 (Basic Actions: KeyError: 'selector') closed by
- duplicate: duplicate of #2044
- 10:36 AM Ticket #2051 (Movie fails to encode using Chimerax: dyld: Symbol not found: ...) created by
- […]
- 7:00 AM Ticket #2050 (Crash drawing Side View after close) created by
- […]
- 5:37 AM Ticket #2049 (Basic Actions: KeyError: 'selector') created by
- […]
- 4:26 AM Ticket #2048 (Basic Actions: KeyError: 'selector') created by
- […]
- 4:25 AM Ticket #2047 (Basic Actions: KeyError: 'selector') created by
- […]
- 1:57 AM Ticket #2046 (Basic Actions: KeyError: 'selector') created by
- […]
- 1:57 AM Ticket #2045 (Basic Actions: KeyError: 'selector') created by
- […]
- 1:55 AM Ticket #2044 (Basic Actions: KeyError: 'selector') created by
- […]
- 1:12 AM Ticket #2043 (Uninstall Clipper: JSONDecodeError) created by
- […]
Jun 10, 2019:
- 8:09 PM Ticket #2042 (Old large icons / color-selection dialog) created by
- […]
- 4:35 PM Ticket #2041 (Replace "auto-clip" text in side view with "Clip") closed by
- fixed: Fixed in 803de04a80ca105e5ba73dd3777469c57332348a
- 3:42 PM Ticket #2041 (Replace "auto-clip" text in side view with "Clip") created by
- The text at the bottom of side-view that says "auto-clip" should be …
- 3:07 PM Ticket #2040 ("cartoon style nucleic" changes protein coil cartoon if model has ...) closed by
- fixed: Fixed in e8f65f3c2. Code testing for coil is "not helix …
- 3:02 PM Ticket #2032 (Pref for auto-adjustment of clip planes) closed by
- fixed: Ok, so the real problem is that center-of-view mode for the rotation …
- 2:22 PM Ticket #2039 (Crash in Qt in Mac graphics driver) closed by
- nonchimerax: ChimeraX crashed in the Mac graphics driver which was being used by …
- 2:11 PM Ticket #2037 ("measure sasa" not setting attribute?) closed by
- fixed: Fixed. Registered area attribute so color byattribute knows about it.
- 1:46 PM Ticket #2029 ("No such file or directory" when recording with roundtrip) closed by
- fixed: Fixed. Looks like movie encoding thought there was one more recorded …
- 1:33 PM Ticket #1988 (chain trace pbond shown when displaying sequence-adjacent sidechains) closed by
- fixed: Chain traces are no longer shown if both residues have ribbon depictions
- 12:27 PM Ticket #2040 ("cartoon style nucleic" changes protein coil cartoon if model has ...) created by
- at least that's my theory of when it happens. open 5mv5 cartoon style …
- 11:57 AM Ticket #2039 (Crash in Qt in Mac graphics driver) created by
- […]
- 11:34 AM Ticket #2038 (Install Clipper: 'utf-8' codec can't decode byte) created by
- […]
- 11:32 AM Ticket #2034 (Immediate OpenGL error (glBlitFramebuffer)) closed by
- duplicate: Duplicate of #2033.
- 11:31 AM Ticket #2033 (Immediate OpenGL error (glDrawBuffer)) closed by
- nonchimerax: This ChimeraX OpenGL error is most likely a bug in your graphics …
- 11:24 AM Ticket #2037 ("measure sasa" not setting attribute?) created by
- After I open any protein and then use measure sasa protein …
- 10:27 AM Ticket #2027 (MTZ error message logged twice) closed by
- can't reproduce: Can't reproduce it on my Mac either. Closing for now.
- 10:04 AM Ticket #2030 (closing any undocked window crashes ChimeraX) closed by
- duplicate: dup of #2022
- 7:49 AM Ticket #2036 (Clip command specifying initial plane position) created by
- […]
- 6:09 AM Ticket #2035 (Nucleotides tethers: Bond drawing: cylinder and endpoint arrays differ ...) created by
- […]
Jun 9, 2019:
- 4:23 AM Ticket #2034 (Immediate OpenGL error (glBlitFramebuffer)) created by
- […]
- 4:18 AM Ticket #2033 (Immediate OpenGL error (glDrawBuffer)) created by
- […]
Jun 8, 2019:
- 1:57 PM Ticket #2032 (Pref for auto-adjustment of clip planes) created by
- […]
- 1:20 PM ChangeLog edited by
- (diff)
- 1:30 AM Ticket #2030 (closing any undocked window crashes ChimeraX) created by
- […]
Note:
See TracTimeline
for information about the timeline view.
