![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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
- […]
Jun 7, 2019:
- 7:50 PM Ticket #2021 ("cofr centerofview" not honoring clip changes) closed by
- fixed: Fixed. Made center of view rotation method use depth halfway between …
- 4:15 PM Ticket #1906 (H-bonds from mmCIF more dashes than H-bond display default) closed by
- fixed
- 3:24 PM Ticket #2014 (closing any undocked window crashes ChimeraX) closed by
- fixed: Fixed by calling deleteLater() instead of destroy()
- 2:01 PM Ticket #2029 ("No such file or directory" when recording with roundtrip) created by
- […]
- 1:36 PM Ticket #2020 (Clipping relative to center of rotation) closed by
- fixed: I forgot clip had a "position" argument. I added support so "position …
- 1:08 PM Ticket #2028 ("color modify" not consistently reversible) created by
- […]
- 12:41 PM Ticket #2025 ("Particle coordinate is NaN" error in ISOLDE 1.0b2) closed by
- fixed: Great! I'll go ahead and close this then. Keep an eye out for the new …
- 11:30 AM Ticket #2023 (Unexpected None in data given to BasicActions.restore_snapshot()) closed by
- duplicate: Hi Nicholas, Unfortunately there was an error when this session was …
- 11:16 AM Ticket #1977 (Crash restoring session) closed by
- fixed: Hi Nicholas, Your session restores fine in both the new 0.9 …
- 10:52 AM Ticket #2022 (closing any undocked window crashes ChimeraX) closed by
- duplicate: stack trace and usage scenario essentially identical to #2014
- 10:28 AM Ticket #2027 (MTZ error message logged twice) created by
- […]
- 9:59 AM Ticket #2026 (Allow setting label color and background defaults) created by
- * The default label style used when using the “label” mouse mode vs …
- 8:14 AM Ticket #2025 ("Particle coordinate is NaN" error in ISOLDE 1.0b2) created by
- […]
- 7:15 AM Ticket #2024 (Doc strings / optional arguments for aliases) created by
- […]
- 2:24 AM Ticket #2023 (Unexpected None in data given to BasicActions.restore_snapshot()) created by
- […]
Jun 6, 2019:
- 6:45 PM Ticket #2022 (closing any undocked window crashes ChimeraX) created by
- […]
- 5:53 PM Ticket #2004 ("zone around atoms" loses original state) closed by
- fixed: Fixed. I made the second click on the background show the residues as …
- 5:51 PM Ticket #1999 (Label scaling erratic) closed by
- fixed: This label scaling bug happened because the zone mouse mode did not …
- 4:59 PM ChangeLog edited by
- (diff)
- 3:03 PM Ticket #2021 ("cofr centerofview" not honoring clip changes) created by
- […]
- 2:59 PM Milestone 0.9 completed
- == Features * Tabbed toolbar * Old toolbars will be removed * …
- 2:44 PM 2019-06-06 created by
- 2:14 PM Ticket #2020 (Clipping relative to center of rotation) created by
- […]
- 2:04 PM DeveloperMeetings edited by
- (diff)
- 1:16 PM Ticket #2019 (Higher graphics quality when saving image) created by
- […]
- 1:08 PM Ticket #2018 (Maintain aspect ratio option for image-save UI) created by
- […]
- 12:57 PM Ticket #2017 (Reversing color palettes) created by
- […]
- 11:45 AM Ticket #2016 (session window size not restored even though preference is on) created by
- Attached an image of how the window looked right before I saved the …
- 11:01 AM Ticket #2010 (Selection suggestions) closed by
- wontfix
- 11:01 AM Ticket #2015 ("mc" accelerator equivalent) created by
- […]
- 10:22 AM Ticket #939 (Need command to report various file locations) closed by
- fixed: Elaine is correct in the "info path" now serves this purpose, though …
- 10:15 AM Ticket #2000 (<Library>atomstruct</Library> sufficient to build for Linux and Mac, ...) closed by
- wontfix: Unfortunately, that's a Microsoft compiler idiosyncrasy. On Linux and …
- 10:00 AM Ticket #2014 (closing any undocked window crashes ChimeraX) created by
- In the 6/6 daily build (tested 3x) but not 6/5 release candidate …
- 8:19 AM Ticket #2006 (Initial map thresholds too low for 3kf2 with structure factors) closed by
- fixed: Loaded standard (i.e. 2FO-FC) maps will now auto-contour to reasonable …
- 6:30 AM Ticket #2005 (Error loading structure factors, 1a0m, cannot determine FreeR) closed by
- fixed: If an MTZ or cif reflections file does not designate a free set, one …
- 1:16 AM Ticket #2013 (Trouble pip-installing Pyyaml prereq for bundle) created by
- […] bundle_info.xml
Jun 5, 2019:
- 11:38 PM Ticket #1757 (Need access to password protected web sites) closed by
- fixed
- 5:09 PM ChangeLog edited by
- (diff)
- 5:09 PM ChangeLog edited by
- (diff)
- 5:08 PM ChangeLog edited by
- (diff)
- 3:53 PM ChangeLog edited by
- (diff)
- 3:46 PM Ticket #2012 (Have status bar forward keystrokes) created by
- […]
- 3:38 PM Ticket #2011 (Specialized undos + undo move) created by
- […]
- 3:27 PM Ticket #2010 (Selection suggestions) created by
- […]
- 2:37 PM Ticket #2009 (Notes on images) created by
- […]
- 1:58 PM Ticket #2008 (unknown residues numbered like gaps) created by
- […]
- 1:48 PM Ticket #2007 (Can't zoom after opening structure factors, scroll is changed to ...) created by
- […]
- 1:39 PM Ticket #2006 (Initial map thresholds too low for 3kf2 with structure factors) created by
- […]
- 1:33 PM Ticket #2002 (No spacegroup of name i 4) closed by
- invalid: This error was with an old copy of 1a0m.cif from 2011. Probably this …
- 1:25 PM Ticket #2005 (Error loading structure factors, 1a0m, cannot determine FreeR) created by
- […]
- 12:26 PM Ticket #2004 ("zone around atoms" loses original state) created by
- […]
- 11:51 AM Ticket #2003 (fetched model scores not remembered in sessions) created by
- maybe this is a known issue... attached session restores with …
- 11:01 AM Ticket #1996 (Help Viewer html widget link clicked: local variable 'path' referenced ...) closed by
- duplicate: Hi Gabor, Thanks for reporting this. Like the other error you …
- 10:51 AM Ticket #2002 (No spacegroup of name i 4) created by
- […]
- 10:47 AM Ticket #1995 (Crash in Pseudobond destructor) closed by
- duplicate: Hi Gabor, Unfortunately there was one day this week when this bug was …
- 10:15 AM Ticket #2001 (poor superposition after modeller comparative) created by
- The attached session shows the result of these commands for modeling a …
- 9:51 AM Ticket #2000 (<Library>atomstruct</Library> sufficient to build for Linux and Mac, ...) created by
- Minor in the grand scheme of things, but annoyingly fiddly to work out …
- 8:19 AM Ticket #1965 (missing tethers, mysterious floating sidechains look like ligands) closed by
- fixed: Done!
- 7:08 AM Ticket #1999 (Label scaling erratic) created by
- […]
- 6:59 AM Ticket #1998 (Clip mouse mode control of scene, screen and per-model clip planes) created by
- […]
- 6:49 AM Ticket #1997 (Radio-button right-mouse icons) created by
- […]
- 5:47 AM Ticket #1996 (Help Viewer html widget link clicked: local variable 'path' referenced ...) created by
- […]
- 5:45 AM Ticket #1995 (Crash in Pseudobond destructor) created by
- […]
Jun 4, 2019:
- 8:12 PM Ticket #1993 (weird usage in Log if wrong subcommand entered) closed by
- fixed: The bug is for only for commands that only have subcommands. Fix in …
- 5:27 PM Ticket #1985 (Toolshed Clipper install does not install) closed by
- fixed: Fixed in 093343349. ChimeraX should still have tried to …
- 4:39 PM ChangeLog edited by
- (diff)
- 3:47 PM ChangeLog edited by
- (diff)
- 3:00 PM Ticket #1991 (Help Viewer html widget link clicked: local variable 'path' referenced ...) closed by
- fixed: Fixed in 7010af0f3. Was too aggressive deleting code when …
- 2:46 PM Ticket #1994 (Volume cropping: index out of range) created by
- […]
- 2:37 PM Ticket #1993 (weird usage in Log if wrong subcommand entered) created by
- This is partly user error but reporting just in case it is easy to …
- 12:41 PM Ticket #1992 (using "pick blobs" on non-cap area of clipped blob raises error) closed by
- fixed: Fixed. Measure command issued by pick blob mouse mode needed to …
- 12:32 PM Ticket #1992 (using "pick blobs" on non-cap area of clipped blob raises error) created by
- I was testing in the current daily build whether Measure and Color …
Jun 3, 2019:
- 10:44 PM Ticket #1991 (Help Viewer html widget link clicked: local variable 'path' referenced ...) created by
- […]
- 6:36 PM Ticket #1990 (model-list widgets need to respond to name changes) created by
- […]
- 5:06 PM Ticket #1989 (vseries play: model.single_color: 'NoneType' object is not subscriptable) closed by
- duplicate: You reported this same vseries error 4 weeks ago, bug #1919, and I …
- 4:15 PM Ticket #1983 (Structure continuously redrawn because atom hide bits change every frame) closed by
- fixed: Change to treat pseudobonds like bonds for deciding if backbone atoms …
- 4:13 PM Ticket #1981 (nucleotide tubes disconnected from ribbon) closed by
- fixed: This was fixed as part of #1965.
- 2:55 PM Ticket #1989 (vseries play: model.single_color: 'NoneType' object is not subscriptable) created by
- […]
- 2:18 PM Ticket #1987 (New per-atom pseudo-bond vector code crashes in destructor) closed by
- fixed: Reverted pseubobond tracking change.
- 2:08 PM Ticket #1986 (Problem reading CCD template: Connection reset by peer) closed by
- fixed: Just report the failure now without a traceback.
- 11:32 AM Ticket #1988 (chain trace pbond shown when displaying sequence-adjacent sidechains) created by
- This may not be avoidable (how can you distinguish it from cases where …
- 11:07 AM Ticket #1987 (New per-atom pseudo-bond vector code crashes in destructor) created by
- […]
- 10:29 AM Ticket #1962 (ViewDockX: Mol2 reader makes duplicate bonds) closed by
- fixed: Fix worked!
Jun 2, 2019:
May 31, 2019:
- 4:37 PM Ticket #1973 (Ignore iffy CONECT records) reopened by
- Given that the automatically connectivity generation is pretty good, …
- 4:20 PM Ticket #1978 (Top command ribbon can tear away) closed by
- fixed: Added explicit option to allow tool windows to suppress their title …
- 12:29 PM Ticket #1324 (RFE: include aliases in session files) closed by
- fixed: Fix in 5783dc0da76c58f7f752d3373839ca202dd0d1c6.
- 11:41 AM Ticket #1095 (alias can cause duplicates in "usage" output) closed by
- fixed: Fixed in [58b14027f/git]
- 10:48 AM Ticket #1985 (Toolshed Clipper install does not install) created by
- […] toolshed_clipper.png
- 9:18 AM 2019-05-30 edited by
- (diff)
- 9:18 AM Ticket #1984 (Extend mmCIF output to preserve tables that we do not read) created by
- Current mmCIF output include tables that (a) ChimeraX reads but does …
- 4:54 AM Ticket #1983 (Structure continuously redrawn because atom hide bits change every frame) created by
- […]
May 30, 2019:
- 5:18 PM Ticket #1969 (mmCIF write/restore transforms pseudobonds into bonds) closed by
- fixed: Closing for now since there is a workaround. Long term we may want a …
- 3:50 PM Ticket #1933 (RFE: "intelligent" atom transform) closed by
- fixed: Okay, this patch has been applied to both the develop and release …
- 2:37 PM 2019-05-30 created by
- 2:04 PM DeveloperMeetings edited by
- (diff)
- 1:40 PM Ticket #1982 (bond selection not shown as selection in Sequence Viewer) created by
- Took me forever to figure out why when I selected a residue it wasn't …
- 12:08 PM Ticket #1981 (nucleotide tubes disconnected from ribbon) created by
- In the current release candidate UCSF ChimeraX version: 0.9 …
- 11:09 AM Ticket #1980 ("align nothing" documentation wrong) closed by
- duplicate: Hi James, Indeed, that documentation was wrong. The documentation …
- 11:03 AM ChangeLog edited by
- (diff)
- 8:08 AM Ticket #1980 ("align nothing" documentation wrong) created by
- […]
May 29, 2019:
- 10:32 PM Ticket #1642 (Bundles from other builds being used) closed by
- fixed: Got line profiler working with current version of Python. Need to …
- 5:15 PM Ticket #1973 (Ignore iffy CONECT records) closed by
- fixed: SSBOND/LINK records are now generated that correspond to the …
- 5:04 PM Ticket #1783 (mmCIF: non-standard nucleotides disconnected in 5tna) closed by
- wontfix: 5tna has been superseded by 6tna, and 6tna works. And in 5tna, all of …
- 4:56 PM Ticket #1156 (RFE nucleotide color follows residue (cartoon) color instead of atom color) closed by
- fixed: Like the current solution.
- 4:54 PM Ticket #1908 (nuc atoms only shows half-ribose after session saved as tube display) closed by
- fixed: This appears to be fixed. Not sure when it happened.
- 12:42 PM Ticket #1979 (sym command logging) created by
- Currently the sym command logs nothing when it executes. At a …
- 12:36 PM Ticket #1957 (RFE: optimize surface zone calculations) closed by
- fixed: Ok. I made setting a surface zone before a surface has been computed …
- 9:33 AM Ticket #1978 (Top command ribbon can tear away) created by
- It turns out that the lovely new tabbed ribbon at the top of the …
- 7:13 AM Ticket #1977 (Crash restoring session) created by
- […]
- 4:21 AM Ticket #1976 ("is_default" does nothing in Open and Save ChimeraXClassifier) created by
-
In
toolshed/installed.pythe value is parsed (lines 490 and 513 for …
May 28, 2019:
- 4:41 PM Ticket #1974 (writeable metadata) created by
- 'metadata' attribute returns a deceptively writable Python dictionary, …
- 4:36 PM Ticket #1973 (Ignore iffy CONECT records) created by
- When writing PDB, should generate SSBOND/LINK records based on the …
- 1:08 PM Ticket #1967 ('select' command reports misleading(?) number of models) closed by
- fixed: Fixed in devel, not in 0.9. For some reason the select command …
- 11:30 AM Ticket #1971 (C++ component of Ring gone) closed by
- duplicate: Duplicate of #1970
- 8:58 AM Ticket #1972 (Structure factor .cif files: open command extension/disambiguation) created by
- I've implemented a structure factor .cif reader for the Clipper …
May 27, 2019:
- 12:27 PM Ticket #1971 (C++ component of Ring gone) created by
- […]
- 11:07 AM Ticket #1970 (C++ component of Ring gone) created by
- […]
May 24, 2019:
- 1:54 AM Ticket #1969 (mmCIF write/restore transforms pseudobonds into bonds) created by
- Sorry to do this so close to the 0.9 release, but I spent yesterday …
May 23, 2019:
- 5:46 PM Ticket #1968 (use ajax to update ChimeraX download page) created by
- Would like the downloads page's content to be updated automagically. …
- 5:22 PM Ticket #1967 ('select' command reports misleading(?) number of models) created by
- sel ##modeller_zDOPE>1 reports 1 model selected, although it’s …
- 5:11 PM Ticket #1966 (CA-CB bond not shown) created by
- As per Elaine's example from #1965: open 3bp5 hide delete ~protein …
- 4:17 PM Ticket #1965 (missing tethers, mysterious floating sidechains look like ligands) created by
- It is not acceptable that when somebody is showing ribbons and then …
- 3:22 PM Ticket #1486 (Ribbon slowing graphics enormously for large models) closed by
- fixed: Excellent!
- 2:58 PM 2019-05-23 created by
- 2:02 PM DeveloperMeetings edited by
- (diff)
- 12:33 PM ChangeLog edited by
- (diff)
- 12:32 PM ChangeLog edited by
- (diff)
- 11:40 AM Ticket #1964 (Make stacked icons more compact or allow unstacking) created by
- Due to spacing issues, with all text labels removed stacked icons make …
- 10:44 AM Ticket #1963 (Preset manager needed by session) closed by
- duplicate: Hi Hyunwook, We will work to address this issue. Your session file …
- 9:42 AM Ticket #1963 (Preset manager needed by session) created by
- […]
- 12:38 AM Ticket #1962 (ViewDockX: Mol2 reader makes duplicate bonds) created by
- […]
May 22, 2019:
- 6:19 PM Ticket #1960 (Updating VR UI images: division by zero) closed by
- fixed: Fixed. This error happened when there were no right-column tool …
- 4:42 PM Ticket #1961 (Toolshed US download map not colored) created by
- The toolshed US geographic download map for a bundle doesn't get …
- 2:49 PM ChangeLog edited by
- (diff)
- 2:48 PM ChangeLog edited by
- (diff)
- 10:33 AM Ticket #1960 (Updating VR UI images: division by zero) created by
- […]
May 21, 2019:
- 6:43 PM Ticket #1958 (problems with "resfit" in 2017 movie-making tutorial) closed by
- fixed: Fixed resfit movie recording. It was trying to do interpolated motion …
- 12:11 PM Ticket #1958 (problems with "resfit" in 2017 movie-making tutorial) created by
- […] resfit.mp4
- 10:04 AM Ticket #1957 (RFE: optimize surface zone calculations) created by
- (Not urgent, but it would be nice in many ways) I've been spending …
May 20, 2019:
- 5:56 PM Ticket #1955 (Association GUI immediately makes new association) closed by
- fixed: generic menu-button chooser was auto-selecting the "single" menu item …
- 5:53 PM Ticket #1577 (Make volume crop mouse mode issue a command) closed by
- fixed: Mouse and vr now issue volume region command on crop button release.
- 5:51 PM Ticket #1574 (Make swapaa mouse mode issue command) closed by
- fixed: Made vr and mouse mode issue swapaa command on button release.
- 5:50 PM Ticket #1578 (Make bond rotation mouse mode issue command) closed by
- fixed: Made VR and mouse bond rotation issue torsion command on button release.
- 5:50 PM Ticket #1579 (Make selection mouse mode issue command) closed by
- fixed: Made VR select of atoms, residues, volumes and promotion issue commands.
- 1:48 PM Ticket #1956 (Interface plot, ValueError: Axis limits cannot be NaN or Inf) closed by
- fixed
- 1:45 PM Ticket #1956 (Interface plot, ValueError: Axis limits cannot be NaN or Inf) created by
- […]
- 1:35 PM Ticket #1952 (select-drag: glDrawBuffer: invalid operation) closed by
- duplicate: Duplicate. Bug in Dec 2018 ChimeraX 0.8 fixed a few months ago.
- 11:05 AM Ticket #1951 (Crash doing *something* with a DockWidget) closed by
- can't reproduce
- 11:04 AM Ticket #1955 (Association GUI immediately makes new association) created by
- […]
May 19, 2019:
May 18, 2019:
May 17, 2019:
- 4:20 PM Ticket #1951 (Crash doing *something* with a DockWidget) created by
- […]
- 2:58 PM Ticket #1949 (Problem reading TIFF planes: index out of range) closed by
- fixed: User was opening an ImageJ TIFF hyperstack > 4 Gbytes in size where …
- 2:12 PM Ticket #1950 (OpenGL buffer was not deleted before core.graphics.Buffer destroyed) closed by
- duplicate: Duplicate of #1774. Fixed.
- 2:10 PM Ticket #1948 (OpenGL buffer problem) closed by
- duplicate: Duplicate of #1615. Fixed long ago.
- 2:07 PM Ticket #1943 (Error using named selection holding deleted model) closed by
- fixed: Fixed. The Objects instance that holds frozen named selectiions was …
- 1:32 PM Ticket #1947 (Unexpected None data given to NamedView.restore_snapshot()) closed by
- duplicate: Duplicate of #1660
- 1:29 PM Ticket #1950 (OpenGL buffer was not deleted before core.graphics.Buffer destroyed) created by
- […]
- 1:27 PM Ticket #1945 (An RGBA channel for a marker is negative) closed by
- fixed: Fixed. This ChimeraX error was from reading a marker file …
- 1:18 PM Ticket #1944 (volumecommand.volume transparency argument broken) closed by
- fixed: Fixed. I eliminated the volume surface transparency_factor and …
- 6:33 AM Ticket #1949 (Problem reading TIFF planes: index out of range) created by
- […]
- 1:12 AM Ticket #1948 (OpenGL buffer problem) created by
- […]
May 16, 2019:
- 1:48 PM Ticket #1947 (Unexpected None data given to NamedView.restore_snapshot()) created by
- […]
- 10:32 AM Ticket #1946 (Nucleotides: 'N' not in standard_bases) created by
- […]
- 7:56 AM Ticket #1945 (An RGBA channel for a marker is negative) created by
- […]
May 15, 2019:
- 11:47 PM Ticket #1944 (volumecommand.volume transparency argument broken) created by
- […]
- 11:39 PM Ticket #1915 (Log underscore keywords as camel-case) closed by
- fixed
- 7:23 PM Ticket #484 (Make contact graph mouse button behavior match graphics window (select ...) closed by
- fixed: I've made zooming the plot work with scroll wheel or two-finger drag …
- 4:01 PM Ticket #1943 (Error using named selection holding deleted model) created by
- […]
- 3:55 PM Ticket #482 (Contact graph hide/show chains ignores ribbons) closed by
- fixed: Fixed. I made interfaces plot remember which atoms and ribbons are …
- 2:41 PM Ticket #1867 (Errors restoring session with TIFF stacks or directly opening them) closed by
- fixed: Fixed. Tested with a compressed TIFF file I created, but don't know …
- 2:39 PM Ticket #1942 (matplotlib traceback drawing interfaces diagram) closed by
- can't reproduce: I am not able to reproduce this error. Will need a reproducible case …
- 12:39 PM Ticket #1942 (matplotlib traceback drawing interfaces diagram) created by
- […]
- 11:31 AM Ticket #1940 (self._positions is None) closed by
- fixed: Fixed. Deleting volume image submodel caused this error because …
- 11:10 AM Ticket #1941 (Test report) closed by
- not a bug
- 11:09 AM Ticket #1941 (Test report) created by
- […]
- 10:17 AM Ticket #1939 (Unexpected None data given to NamedView.restore_snapshot()) closed by
- duplicate: duplicate of #1660
- 9:48 AM Ticket #1940 (self._positions is None) created by
- […]
- 7:14 AM Ticket #1939 (Unexpected None data given to NamedView.restore_snapshot()) created by
- […]
May 14, 2019:
- 5:50 PM Ticket #1938 (nucleotides tube selection not usable by commands) created by
- Maybe selecting the tube should select ribose atoms? Ctrl-click …
- 5:16 PM Ticket #1937 (Cannot find consistent set of bond orders for ring) created by
- […]
- 5:11 PM Ticket #1389 (port Chimera's Select menu) closed by
- fixed: Missing select-by-attribute; that will be added once the …
- 2:31 PM Ticket #1936 ("view sel" with volume isosurf selected causes traceback) closed by
- fixed: Fixed. Code that handled selected objects (Objects class) did not …
- 1:31 PM Ticket #1936 ("view sel" with volume isosurf selected causes traceback) created by
- e.g. open 1pho molmap helix 5 select #2 view sel Traceback (most …
- 11:48 AM Ticket #1922 (Non-ASCII PDB file should not raise bug-reportable error) closed by
- fixed: Because of collation, doesn't produce any dialog, but better than before.
- 11:11 AM Ticket #1934 (smoothlines: 'NoneType' object has no attribute 'shape') closed by
- fixed: Fixed. User tried to apply smoothlines to a molecule. It require a …
- 10:29 AM Ticket #1935 (Crash removing DockWidget) closed by
- can't reproduce
- 8:41 AM Ticket #1935 (Crash removing DockWidget) created by
- […]
- 7:21 AM Ticket #1934 (smoothlines: 'NoneType' object has no attribute 'shape') created by
- […]
- 2:00 AM Ticket #1933 (RFE: "intelligent" atom transform) created by
- Would be great to have a function to apply a rigid-body transformation …
May 13, 2019:
- 5:32 PM Ticket #1932 (mlp should only work on proteins) closed by
- fixed: Fixed. Yes mlp only has tables for proteins. I've changed the mlp …
- 3:04 PM Ticket #1932 (mlp should only work on proteins) created by
- Probably there should be some preliminary filtering to only run mlp …
- 2:37 PM Ticket #1931 (Atom spec parsing consumes torsion command angle argument) created by
- […]
- 11:24 AM Ticket #1930 (RFE: Blast Protein ability to use sequence from Sequence Viewer as query) created by
- At least for the command, we already have ways to specify an …
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