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Timeline
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- wontfix: 5tna has been superseded by 6tna, and 6tna works.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 …
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
- […]
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