![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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 …
May 10, 2019:
- 10:59 AM Ticket #1926 (Some kind of QDockWidget event-handling crash) closed by
- can't reproduce
- 10:50 AM DeveloperMeetings edited by
- (diff)
- 9:46 AM Ticket #1928 (RFE cartoon coil smoothing) created by
- Would be nice to have smoothing cartoon path for coil as an option. I …
- 9:43 AM Ticket #1927 (coil not same as protein nonhelix nonstrand?) created by
- If I open some protein (say 2gbp) and use these commands cartoon …
- 2:19 AM Ticket #1926 (Some kind of QDockWidget event-handling crash) created by
- […]
May 9, 2019:
- 6:20 PM Ticket #1925 (silhouettes not shown when first opening session with silhouettes) closed by
- fixed: Fixed. Happened only when "Resize graphics window on session restore" …
- 5:19 PM Ticket #1814 (missing cartoon tethers to nucleotides) closed by
- duplicate: Keep track in #1486.
- 5:17 PM Ticket #1486 (Ribbon slowing graphics enormously for large models) reopened by
- This change broke tethers to nucleotides.
- 4:34 PM Ticket #1445 ("Usage" needs to be more bulletproof) closed by
-
fixed:
usageandusage allskip commands that can't be … - 3:29 PM 2019-05-09 created by
- 2:48 PM DeveloperMeetings edited by
- (diff)
- 11:54 AM Ticket #1074 (selection highlighting nearly invisible for non-terminal stick atoms) closed by
- fixed: I made the selection outline 2 pixels wide on retina displays and 1 …
- 11:08 AM Ticket #1923 (Noisy misplaced selection outline on iMac retina display) closed by
- fixed: Fixed. Code was not using depth test equal when drawing the …
- 10:42 AM Ticket #1924 (cannot import name 'user_error_format') closed by
- fixed
- 9:28 AM Ticket #1925 (silhouettes not shown when first opening session with silhouettes) created by
- Often when I open a session with silhouettes and silhouettes were not …
- 5:54 AM Ticket #1924 (cannot import name 'user_error_format') created by
- […]
May 8, 2019:
- 6:32 PM Ticket #1923 (Noisy misplaced selection outline on iMac retina display) created by
- […] badseloutline.png
- 5:32 PM Ticket #1296 (vseries measure: No module named 'chimerax.core.measure') closed by
- fixed: Fixed. Added measure inertia code.
- 5:25 PM Ticket #1922 (Non-ASCII PDB file should not raise bug-reportable error) created by
- […]
- 3:12 PM Ticket #1920 (Sequence icon using probably-not-ready-for-primetime 'sequence' command) closed by
- fixed: After talking to Eric I made the sequence shortcut icon show a …
- 2:33 PM ChangeLog edited by
- (diff)
- 1:20 PM Ticket #1919 (Vseries not handling two-channel rendering correctly) closed by
- fixed: Fixed I think in tonight's builds. The volume code has changed after …
- 11:15 AM Ticket #1921 (chimera.core.logger.user_error_format missing) closed by
- fixed: Name changed to error_text_format and although I changed all *uses* of …
- 11:06 AM Ticket #1921 (chimera.core.logger.user_error_format missing) created by
- […]
- 10:48 AM Ticket #1920 (Sequence icon using probably-not-ready-for-primetime 'sequence' command) created by
- […]
May 7, 2019:
- 4:16 PM Ticket #659 (Clip mode shift modifier doesn't work) closed by
- fixed: I removed the default mouse binding of shift+right = set pivot. Mouse …
- 2:30 PM Ticket #1919 (Vseries not handling two-channel rendering correctly) created by
- […]
- 12:53 PM Ticket #1884 (O1P/O2P disconnected) closed by
- fixed: An "efficiency" change made awhile back also changed the logic incorrectly.
- 12:28 PM Ticket #1918 (Documentation warnings) created by
- […]
- 12:18 PM Ticket #545 (Volume API for setting surface colors is not intuitive) closed by
- fixed: Currently volume colors can be set using the …
- 12:11 PM Ticket #1071 (vseries failure: list index out of range) closed by
- fixed: Made ChimeraX give a user-friendly error message "No volume series …
- 12:05 PM Ticket #995 (Mouse modes roll over shows no icons) closed by
- fixed: Mouse modes are now part of the tabbed toolbar which does not exhibit …
- 10:59 AM Ticket #1917 (Crash reading ChimeraX-generated mmCIF file) created by
- […] test.cif
- 1:37 AM Ticket #1916 (KeyError saving mmCIF) created by
- […]
May 6, 2019:
- 7:03 PM Ticket #1553 (MeetingServer: Must call either listen, or connect, not both) closed by
- fixed: Gave user friendly error message that current meeting must be closed …
- 6:44 PM Ticket #1584 (multi-file open incorrectly logged) closed by
- fixed
- 5:12 PM Ticket #1915 (Log underscore keywords as camel-case) created by
- Pretty much per summary. Mostly for extensions that use command.run …
- 3:12 PM Ticket #1914 (User errors not logged) closed by
- fixed: User errors should now log again.
- 12:48 PM Ticket #1914 (User errors not logged) created by
- […]
- 12:47 PM Ticket #1905 (ringfill not saved in session) closed by
- fixed
- 12:25 PM Ticket #1810 (Morph: ValueError: models have different number of chains) closed by
- fixed: Made morph with different numbers of chains generate a UserError and …
- 12:01 PM Ticket #1894 (AttributeError: 'was_deleted' in PseudobondGroup) closed by
- can't reproduce: Not enough info to debug this without a session file.
- 9:20 AM Ticket #1913 (Clipper: name '_f_sigf_chooser' is not defined) created by
- […]
May 4, 2019:
- 11:53 PM Ticket #1840 (Session restore with BILD objects: Unable to restore objects of ...) closed by
- fixed: Make AtomicShapeDrawings saveable in sessions.
- 12:56 AM Ticket #1660 (Unexpected None data given to StructureSeq.restore_snapshot()) closed by
- fixed: Revised code to not (over)write session file when there is an error. …
May 3, 2019:
- 6:55 PM Ticket #1912 (Toolbar icons logs dozens of sRGB profile warnings on startup) closed by
- fixed: Used "pngcrush -ow -rem allb -reduce file.png" to remove erroneous …
- 4:32 PM Ticket #1728 (AddH adds spurious hydrogens when called twice) closed by
- fixed: Fixed the atom.is_missing_heavy_template_neighbors() problem.
- 8:15 AM ChangeLog edited by
- (diff)
May 2, 2019:
- 6:06 PM Ticket #1912 (Toolbar icons logs dozens of sRGB profile warnings on startup) created by
- […]
- 5:26 PM Ticket #1911 (Error saving image in VR mode) closed by
- fixed: Fixed. OpenVR compositor submit() changed OpenGL read framebuffer.
- 5:24 PM Ticket #1911 (Error saving image in VR mode) created by
- […]
- 3:08 PM Ticket #1731 (Crash due to registration error when starting from icon) closed by
- can't reproduce
- 3:04 PM Ticket #1404 (Bad bonds in mmCIF 1lpv) closed by
- duplicate: Same as #1195.
- 3:00 PM 2019-05-02 created by
- 1:58 PM DeveloperMeetings edited by
- (diff)
- 12:47 PM Ticket #1907 (OpenGL buffer problem) closed by
- can't reproduce: Could not find the cause of this error. Could not reproduce it. The …
- 11:34 AM Ticket #1910 (Crash with symmetry expansion) closed by
- nonchimerax: This is a problem with macOS that I have seen before. If you ask the …
- 11:22 AM Ticket #1909 (Crash doing *something* with a DockWidget) closed by
- can't reproduce
- 6:04 AM Ticket #1910 (Crash with symmetry expansion) created by
- […]
May 1, 2019:
- 6:16 PM Ticket #1909 (Crash doing *something* with a DockWidget) created by
- […]
- 2:52 PM Ticket #1782 (Crash finding 6-member planar NR2 ring in 5vpx) closed by
- duplicate: duplicate of #1781
- 2:51 PM Ticket #1781 (Crash finding 6-member planar NR2 ring in 5vrj) closed by
- fixed: Wasn't guaranteeing that the neighbors of the first ring atom were …
- 2:06 PM Ticket #1716 (Missing bond) closed by
- fixed: LINK/SSBOND now not treated as specifying all the connectivity of the …
- 12:35 PM Ticket #1908 (nuc atoms only shows half-ribose after session saved as tube display) created by
- After I show all atoms of a nucleotide, then change to tube/slab, and …
- 11:54 AM Ticket #1907 (OpenGL buffer problem) created by
- […]
Apr 30, 2019:
- 6:52 PM Ticket #1906 (H-bonds from mmCIF more dashes than H-bond display default) created by
- (e.g. 1bna and show it as atoms the H-bonds have more dashes than the …
- 6:43 PM Ticket #1905 (ringfill not saved in session) created by
- If I save a session with filled rings and restore it the rings are not …
- 3:48 PM Ticket #1892 (Provide documentation for managers/providers) closed by
- fixed: Fixed by replacing old tag documentation with link to current …
- 3:16 PM Ticket #1890 (Blast protein results columns for ligand all shown as {{ctx.content}}) closed by
- fixed: Fixed in e476b93f6. The problematic columns were all …
- 2:33 PM WikiStart edited by
- (diff)
- 7:44 AM Ticket #1904 (Background-dependent distance color) created by
- […]
- 7:41 AM Ticket #1903 (Tabbed toolbar customization) created by
- […]
Apr 29, 2019:
- 4:21 PM ChangeLog edited by
- (diff)
- 4:20 PM ChangeLog edited by
- (diff)
- 4:18 PM ChangeLog edited by
- (diff)
- 3:37 PM Ticket #1902 (RFE: surface should update during trajectory playback) created by
- ... as it would in Chimera, for example. Currently it is very …
- 2:28 PM Ticket #1899 (option to disable docking) closed by
- wontfix: Hi Oliver, There are two existing features that may help in this …
- 2:28 PM Ticket #1901 (RFE: add "running tools" section to Tools menu) created by
- ...similar to what's in Chimera or currently shown in ChimeraX with …
Apr 28, 2019:
- 11:42 AM Ticket #1900 (File history UI suggestions) created by
- […]
- 11:38 AM Ticket #1899 (option to disable docking) created by
- […]
- 11:31 AM Ticket #1898 (Option to number based on reference sequence) created by
- […]
Apr 27, 2019:
- 9:16 AM Ticket #1897 (OpenMM ToolShed bundle) created by
- As discussed in our meeting in March (if there's already a ticket on …
Apr 26, 2019:
- 1:29 PM Ticket #1895 (Problem deleting from command history) closed by
- duplicate: Fixed awhile ago
- 1:10 PM Ticket #1893 (Unexpected None data given to AtomicStructure.restore_snapshot()) closed by
- duplicate: Hi Alex, Unfortunately the real error occurred when the session was …
- 12:01 PM Ticket #1593 (multi-level "sel back/forward") closed by
- wontfix: Setting a selection is complex and multi-level undo is rarely actually …
- 10:59 AM Ticket #1889 (Incorrect ChimeraX version for ISOLDE) closed by
- can't reproduce: Hi Fabrizio, I'm glad something is working. :-) FYI, using "open -a …
- 9:08 AM Ticket #1896 (RFE: measure rmsd command) created by
- Fairly trivial to implement, but unless I've just failed to find it it …
- 6:41 AM Ticket #1895 (Problem deleting from command history) created by
- […]
- 5:24 AM Ticket #1894 (AttributeError: 'was_deleted' in PseudobondGroup) created by
- […]
- 1:59 AM Ticket #1893 (Unexpected None data given to AtomicStructure.restore_snapshot()) created by
- […]
Apr 25, 2019:
- 2:47 PM 2019-04-25 created by
- 2:09 PM DeveloperMeetings edited by
- (diff)
- 1:23 PM Ticket #1892 (Provide documentation for managers/providers) created by
- No documentation in …
- 1:21 PM Ticket #1891 (RFE: Blast Protein query sequence from text) created by
- I.e. allow searching with sequence input as text, not just sequences …
- 12:42 PM Ticket #1890 (Blast protein results columns for ligand all shown as {{ctx.content}}) created by
- I tried a couple different searches so I don't think it matters what …
- 12:27 PM Ticket #1888 (Silhouettes: glBlitFramebuffer: invalid operation) closed by
- nonchimerax: Showing silhouette edges gives an OpenGL error with this Mesa VMWare …
- 11:17 AM ChangeLog edited by
- (diff)
- 10:30 AM Ticket #1889 (Incorrect ChimeraX version for ISOLDE) reopened by
- 5:46 AM Ticket #1861 (OpenMM crash) closed by
- can't reproduce: Re-ran the same scenario on the same computer without a crash. It's …
- 5:26 AM Ticket #1889 (Incorrect ChimeraX version for ISOLDE) closed by
- not a bug: You'll need to be using the ChimeraX 0.8 release version to install …
- 3:06 AM Ticket #1889 (Incorrect ChimeraX version for ISOLDE) created by
- […]
- 1:20 AM Ticket #1888 (Silhouettes: glBlitFramebuffer: invalid operation) created by
- […]
Apr 24, 2019:
- 2:47 PM Ticket #1842 (Session save: Unable to restore objects of ImageDrawing class in ...) closed by
- fixed: Fixed. Made image rendering submodel restore itself in sessions so …
- 12:08 PM Ticket #1887 (windowsize command not obeyed (after showing Volume Viewer?)) closed by
- not a bug
- 11:33 AM Ticket #1887 (windowsize command not obeyed (after showing Volume Viewer?)) created by
- I'd successfully made windowsize 256 x 256 but after I opened a volume …
- 10:16 AM Ticket #1886 (Attempt to open Chimera 1 session) closed by
- not a bug
- 9:18 AM Ticket #1886 (Attempt to open Chimera 1 session) created by
- […]
Apr 23, 2019:
- 8:58 PM Ticket #1396 (PC requires restart to launch ChimeraX a second time) closed by
- nonchimerax: Hello, My apologies for not following up on this earlier. Do you …
- 8:47 PM Ticket #1684 (BZip2 missing in Linux daily builds) closed by
- fixed: Dropped use of bz2.
- 8:40 PM Ticket #1670 (about.html missing on Linux) closed by
- fixed: Fixed on 23 January 2019.
- 4:20 PM Ticket #1843 (Move selected models uses wrong coordinates if parent model moved in scene) closed by
- fixed: Fixed rotate and translate selected models. Would need a test case to …
- 3:52 PM Ticket #1881 (Clicking Model panel show button on volume does not show it) closed by
- fixed: Fixed.
- 2:54 PM Ticket #1883 (Open command "vseries true" option does not work with Amira files) closed by
- fixed: Fixed. Any map format can now be used with vseries option, although …
- 2:07 PM Ticket #1882 (Show errors that occur before main window started in GUI log) closed by
- fixed: Collations logs don't normally collate bugs (allowing them to …
- 1:44 PM Ticket #1885 (error using BLOSUM100 in blast) created by
- […]
- 11:45 AM Ticket #872 (Add chirality property to atoms) closed by
- fixed: If the corresponding CCD template has been read (which it should if …
- 2:33 AM Ticket #1884 (O1P/O2P disconnected) created by
- […]
Apr 22, 2019:
- 11:57 PM Ticket #1879 (ChimeraX does not start on Windows 10) closed by
- fixed: Disabled use of "-X faulthandler" which makes things work again when …
- 5:57 PM Ticket #1883 (Open command "vseries true" option does not work with Amira files) created by
- The vseries option to the open command is supposed to treat the …
- 5:51 PM Ticket #1882 (Show errors that occur before main window started in GUI log) created by
- When an error occurs before the main window is shown the error goes to …
- 5:46 PM Ticket #1881 (Clicking Model panel show button on volume does not show it) created by
- With AICS_10-136.ome.tif clicking the show button on channel 4 (model …
- 5:43 PM Ticket #1880 (Have macOS installer dmg show arrow to drag ChimeraX to Applications) created by
- At the ChimeraX microscopy tutorial I found another user running …
- 4:06 PM Ticket #1879 (ChimeraX does not start on Windows 10) created by
- […]
- 3:09 PM Ticket #1878 (Smarter handling of ATOM/HETATM column 21) created by
- Column 21 of ATOM/HETATM records is not officially assigned a meaning …
- 2:26 PM ChangeLog edited by
- (diff)
- 11:08 AM Ticket #1877 (measure buriedArea syntax documentation problem) closed by
- fixed
- 8:20 AM Ticket #1877 (measure buriedArea syntax documentation problem) created by
- […]
Apr 21, 2019:
- 5:59 PM Ticket #1865 (rerunning BLAST from same instance of tool puts unformatted data at ...) closed by
-
fixed: Fixed in 3e4701234.
The
bootgridtable was used … - 4:33 PM Ticket #1864 (BLAST results show parameter settings different from blast command ...) closed by
- fixed: Fixed in 7ae130f8. The BLAST search parameters are now …
Apr 19, 2019:
- 11:52 AM Ticket #1876 (Allow writing OME TIFF files containing multichannel optical ...) created by
- Would like to be able to write out optical microscopy data including …
- 11:40 AM Ticket #1875 (Allow creating multiple marker sets) created by
- Currently the marker placement mouse mode always adds markers to the …
- 8:41 AM Ticket #1874 (ISOLDE: isolde/libmolc.so: undefined symbol) created by
- […]
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