Timeline



Jun 7, 2019:

7:50 PM Ticket #2021 ("cofr centerofview" not honoring clip changes) closed by Tom Goddard
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 pett
fixed
3:24 PM Ticket #2014 (closing any undocked window crashes ChimeraX) closed by pett
fixed: Fixed by calling deleteLater() instead of destroy()
2:01 PM Ticket #2029 ("No such file or directory" when recording with roundtrip) created by olibclarke@…
[…]
1:36 PM Ticket #2020 (Clipping relative to center of rotation) closed by Tom Goddard
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 olibclarke@…
[…]
12:41 PM Ticket #2025 ("Particle coordinate is NaN" error in ISOLDE 1.0b2) closed by Tristan Croll
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 pett
duplicate: Hi Nicholas, Unfortunately there was an error when this session was …
11:16 AM Ticket #1977 (Crash restoring session) closed by pett
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 pett
duplicate: stack trace and usage scenario essentially identical to #2014
10:28 AM Ticket #2027 (MTZ error message logged twice) created by goddard@…
[…]
9:59 AM Ticket #2026 (Allow setting label color and background defaults) created by olibclarke@…
* 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 dkreitle@…
[…]
7:15 AM Ticket #2024 (Doc strings / optional arguments for aliases) created by olibclarke@…
[…]
2:24 AM Ticket #2023 (Unexpected None in data given to BasicActions.restore_snapshot()) created by nicholas.sofos@…
[…]

Jun 6, 2019:

6:45 PM Ticket #2022 (closing any undocked window crashes ChimeraX) created by goddard@…
[…]
5:53 PM Ticket #2004 ("zone around atoms" loses original state) closed by Tom Goddard
fixed: Fixed. I made the second click on the background show the residues as …
5:51 PM Ticket #1999 (Label scaling erratic) closed by Tom Goddard
fixed: This label scaling bug happened because the zone mouse mode did not …
4:59 PM ChangeLog edited by Greg Couch
(diff)
3:03 PM Ticket #2021 ("cofr centerofview" not honoring clip changes) created by olibclarke@…
[…]
2:59 PM Milestone 0.9 completed
== Features * Tabbed toolbar * Old toolbars will be removed * …
2:44 PM 2019-06-06 created by Conrad Huang
2:14 PM Ticket #2020 (Clipping relative to center of rotation) created by olibclarke@…
[…]
2:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:16 PM Ticket #2019 (Higher graphics quality when saving image) created by olibclarke@…
[…]
1:08 PM Ticket #2018 (Maintain aspect ratio option for image-save UI) created by olibclarke@…
[…]
12:57 PM Ticket #2017 (Reversing color palettes) created by olibclarke@…
[…]
11:45 AM Ticket #2016 (session window size not restored even though preference is on) created by Elaine Meng
Attached an image of how the window looked right before I saved the …
11:01 AM Ticket #2010 (Selection suggestions) closed by pett
wontfix
11:01 AM Ticket #2015 ("mc" accelerator equivalent) created by olibclarke@…
[…]
10:22 AM Ticket #939 (Need command to report various file locations) closed by pett
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 Conrad Huang
wontfix: Unfortunately, that's a Microsoft compiler idiosyncrasy. On Linux and …
10:00 AM Ticket #2014 (closing any undocked window crashes ChimeraX) created by Elaine Meng
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 Tristan Croll
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 Tristan Croll
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 andresgineranton@…
[…] bundle_info.xml

Jun 5, 2019:

11:38 PM Ticket #1757 (Need access to password protected web sites) closed by Greg Couch
fixed
5:09 PM ChangeLog edited by pett
(diff)
5:09 PM ChangeLog edited by pett
(diff)
5:08 PM ChangeLog edited by pett
(diff)
3:53 PM ChangeLog edited by Elaine Meng
(diff)
3:46 PM Ticket #2012 (Have status bar forward keystrokes) created by olibclarke@…
[…]
3:38 PM Ticket #2011 (Specialized undos + undo move) created by olibclarke@…
[…]
3:27 PM Ticket #2010 (Selection suggestions) created by olibclarke@…
[…]
2:37 PM Ticket #2009 (Notes on images) created by olibclarke@…
[…]
1:58 PM Ticket #2008 (unknown residues numbered like gaps) created by olibclarke@…
[…]
1:48 PM Ticket #2007 (Can't zoom after opening structure factors, scroll is changed to ...) created by goddard@…
[…]
1:39 PM Ticket #2006 (Initial map thresholds too low for 3kf2 with structure factors) created by goddard@…
[…]
1:33 PM Ticket #2002 (No spacegroup of name i 4) closed by Tom Goddard
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 goddard@…
[…]
12:26 PM Ticket #2004 ("zone around atoms" loses original state) created by olibclarke@…
[…]
11:51 AM Ticket #2003 (fetched model scores not remembered in sessions) created by Elaine Meng
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 pett
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 goddard@…
[…]
10:47 AM Ticket #1995 (Crash in Pseudobond destructor) closed by pett
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 Elaine Meng
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 Tristan Croll
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 Greg Couch
fixed: Done!
7:08 AM Ticket #1999 (Label scaling erratic) created by olibclarke@…
[…]
6:59 AM Ticket #1998 (Clip mouse mode control of scene, screen and per-model clip planes) created by olibclarke@…
[…]
6:49 AM Ticket #1997 (Radio-button right-mouse icons) created by olibclarke@…
[…]
5:47 AM Ticket #1996 (Help Viewer html widget link clicked: local variable 'path' referenced ...) created by papai@…
[…]
5:45 AM Ticket #1995 (Crash in Pseudobond destructor) created by papai@…
[…]

Jun 4, 2019:

8:12 PM Ticket #1993 (weird usage in Log if wrong subcommand entered) closed by Greg Couch
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 Conrad Huang
fixed: Fixed in 093343349. ChimeraX should still have tried to …
4:39 PM ChangeLog edited by pett
(diff)
3:47 PM ChangeLog edited by Elaine Meng
(diff)
3:00 PM Ticket #1991 (Help Viewer html widget link clicked: local variable 'path' referenced ...) closed by Conrad Huang
fixed: Fixed in 7010af0f3. Was too aggressive deleting code when …
2:46 PM Ticket #1994 (Volume cropping: index out of range) created by brandon.scott@…
[…]
2:37 PM Ticket #1993 (weird usage in Log if wrong subcommand entered) created by Elaine Meng
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 Tom Goddard
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 Elaine Meng
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 Greg Couch
[…]
6:36 PM Ticket #1990 (model-list widgets need to respond to name changes) created by goddard@…
[…]
5:06 PM Ticket #1989 (vseries play: model.single_color: 'NoneType' object is not subscriptable) closed by Tom Goddard
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 Greg Couch
fixed: Change to treat pseudobonds like bonds for deciding if backbone atoms …
4:13 PM Ticket #1981 (nucleotide tubes disconnected from ribbon) closed by Greg Couch
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 brandon.scott@…
[…]
2:18 PM Ticket #1987 (New per-atom pseudo-bond vector code crashes in destructor) closed by Greg Couch
fixed: Reverted pseubobond tracking change.
2:08 PM Ticket #1986 (Problem reading CCD template: Connection reset by peer) closed by Greg Couch
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 Elaine Meng
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 goddard@…
[…]
10:29 AM Ticket #1962 (ViewDockX: Mol2 reader makes duplicate bonds) closed by Conrad Huang
fixed: Fix worked!

Jun 2, 2019:

5:10 AM Ticket #1986 (Problem reading CCD template: Connection reset by peer) created by chimerax-bug-report@…
[…]

May 31, 2019:

4:37 PM Ticket #1973 (Ignore iffy CONECT records) reopened by pett
Given that the automatically connectivity generation is pretty good, …
4:20 PM Ticket #1978 (Top command ribbon can tear away) closed by pett
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 Greg Couch
fixed: Fix in 5783dc0da76c58f7f752d3373839ca202dd0d1c6.
11:41 AM Ticket #1095 (alias can cause duplicates in "usage" output) closed by Greg Couch
fixed: Fixed in [58b14027f/git]
10:48 AM Ticket #1985 (Toolshed Clipper install does not install) created by goddard@…
[…] toolshed_clipper.png
9:18 AM 2019-05-30 edited by Conrad Huang
(diff)
9:18 AM Ticket #1984 (Extend mmCIF output to preserve tables that we do not read) created by Conrad Huang
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 tic20@…
[…]

May 30, 2019:

5:18 PM Ticket #1969 (mmCIF write/restore transforms pseudobonds into bonds) closed by Greg Couch
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 pett
fixed: Okay, this patch has been applied to both the develop and release …
2:37 PM 2019-05-30 created by Conrad Huang
2:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:40 PM Ticket #1982 (bond selection not shown as selection in Sequence Viewer) created by Elaine Meng
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 Elaine Meng
In the current release candidate UCSF ChimeraX version: 0.9 …
11:09 AM Ticket #1980 ("align nothing" documentation wrong) closed by pett
duplicate: Hi James, Indeed, that documentation was wrong. The documentation …
11:03 AM ChangeLog edited by Elaine Meng
(diff)
8:08 AM Ticket #1980 ("align nothing" documentation wrong) created by jamesjimitchell@…
[…]

May 29, 2019:

10:32 PM Ticket #1642 (Bundles from other builds being used) closed by Greg Couch
fixed: Got line profiler working with current version of Python. Need to …
5:15 PM Ticket #1973 (Ignore iffy CONECT records) closed by pett
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 Greg Couch
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 Greg Couch
fixed: Like the current solution.
4:54 PM Ticket #1908 (nuc atoms only shows half-ribose after session saved as tube display) closed by Greg Couch
fixed: This appears to be fixed. Not sure when it happened.
12:42 PM Ticket #1979 (sym command logging) created by pett
Currently the sym command logs nothing when it executes. At a …
12:36 PM Ticket #1957 (RFE: optimize surface zone calculations) closed by Tom Goddard
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 Tristan Croll
It turns out that the lovely new tabbed ribbon at the top of the …
7:13 AM Ticket #1977 (Crash restoring session) created by nicholas.sofos@…
[…]
4:21 AM Ticket #1976 ("is_default" does nothing in Open and Save ChimeraXClassifier) created by Tristan Croll
In toolshed/installed.py the value is parsed (lines 490 and 513 for …

May 28, 2019:

4:41 PM Ticket #1974 (writeable metadata) created by Tristan Croll
'metadata' attribute returns a deceptively writable Python dictionary, …
4:36 PM Ticket #1973 (Ignore iffy CONECT records) created by Tristan Croll
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 Tom Goddard
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 pett
duplicate: Duplicate of #1970
8:58 AM Ticket #1972 (Structure factor .cif files: open command extension/disambiguation) created by Tristan Croll
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 lizkellogg@…
[…]
11:07 AM Ticket #1970 (C++ component of Ring gone) created by lizkellogg@…
[…]

May 24, 2019:

1:54 AM Ticket #1969 (mmCIF write/restore transforms pseudobonds into bonds) created by Tristan Croll
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 Greg Couch
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 Elaine Meng
sel ##modeller_zDOPE>1 reports 1 model selected, although it’s …
5:11 PM Ticket #1966 (CA-CB bond not shown) created by pett
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 Elaine Meng
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 Greg Couch
fixed: Excellent!
2:58 PM 2019-05-23 created by Conrad Huang
2:02 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:33 PM ChangeLog edited by Elaine Meng
(diff)
12:32 PM ChangeLog edited by Elaine Meng
(diff)
11:40 AM Ticket #1964 (Make stacked icons more compact or allow unstacking) created by pett
Due to spacing issues, with all text labels removed stacked icons make …
10:44 AM Ticket #1963 (Preset manager needed by session) closed by pett
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 hyl5126@…
[…]
12:38 AM Ticket #1962 (ViewDockX: Mol2 reader makes duplicate bonds) created by i.ihnatenko@…
[…]

May 22, 2019:

6:19 PM Ticket #1960 (Updating VR UI images: division by zero) closed by Tom Goddard
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 pett
The toolshed US geographic download map for a bundle doesn't get …
2:49 PM ChangeLog edited by Greg Couch
(diff)
2:48 PM ChangeLog edited by Greg Couch
(diff)
10:33 AM Ticket #1960 (Updating VR UI images: division by zero) created by chimerax-bug-report@…
[…]

May 21, 2019:

6:43 PM Ticket #1958 (problems with "resfit" in 2017 movie-making tutorial) closed by Tom Goddard
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 Elaine Meng
[…] resfit.mp4
10:04 AM Ticket #1957 (RFE: optimize surface zone calculations) created by Tristan Croll
(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 pett
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 Tom Goddard
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 Tom Goddard
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 Tom Goddard
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 Tom Goddard
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 Tom Goddard
fixed
1:45 PM Ticket #1956 (Interface plot, ValueError: Axis limits cannot be NaN or Inf) created by goddard@…
[…]
1:35 PM Ticket #1952 (select-drag: glDrawBuffer: invalid operation) closed by Tom Goddard
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 pett
can't reproduce
11:04 AM Ticket #1955 (Association GUI immediately makes new association) created by pett
[…]

May 19, 2019:

11:05 PM Ticket #1946 (Nucleotides: 'N' not in standard_bases) closed by Greg Couch
fixed: Fixed it.

May 18, 2019:

6:57 AM Ticket #1952 (select-drag: glDrawBuffer: invalid operation) created by chimerax-bug-report@…
[…]

May 17, 2019:

4:20 PM Ticket #1951 (Crash doing *something* with a DockWidget) created by chimerax-bug-report@…
[…]
2:58 PM Ticket #1949 (Problem reading TIFF planes: index out of range) closed by Tom Goddard
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 Tom Goddard
duplicate: Duplicate of #1774. Fixed.
2:10 PM Ticket #1948 (OpenGL buffer problem) closed by Tom Goddard
duplicate: Duplicate of #1615. Fixed long ago.
2:07 PM Ticket #1943 (Error using named selection holding deleted model) closed by Tom Goddard
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 pett
duplicate: Duplicate of #1660
1:29 PM Ticket #1950 (OpenGL buffer was not deleted before core.graphics.Buffer destroyed) created by chimerax-bug-report@…
[…]
1:27 PM Ticket #1945 (An RGBA channel for a marker is negative) closed by Tom Goddard
fixed: Fixed. This ChimeraX error was from reading a marker file …
1:18 PM Ticket #1944 (volumecommand.volume transparency argument broken) closed by Tom Goddard
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 chimerax-bug-report@…
[…]
1:12 AM Ticket #1948 (OpenGL buffer problem) created by chimerax-bug-report@…
[…]

May 16, 2019:

1:48 PM Ticket #1947 (Unexpected None data given to NamedView.restore_snapshot()) created by shiwei.zhu@…
[…]
10:32 AM Ticket #1946 (Nucleotides: 'N' not in standard_bases) created by dborgesrmit@…
[…]
7:56 AM Ticket #1945 (An RGBA channel for a marker is negative) created by victoria.ruiz.serra@…
[…]

May 15, 2019:

11:47 PM Ticket #1944 (volumecommand.volume transparency argument broken) created by tic20@…
[…]
11:39 PM Ticket #1915 (Log underscore keywords as camel-case) closed by Greg Couch
fixed
7:23 PM Ticket #484 (Make contact graph mouse button behavior match graphics window (select ...) closed by Tom Goddard
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 Elaine Meng
[…]
3:55 PM Ticket #482 (Contact graph hide/show chains ignores ribbons) closed by Tom Goddard
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 Tom Goddard
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 Tom Goddard
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 Elaine Meng
[…]
11:31 AM Ticket #1940 (self._positions is None) closed by Tom Goddard
fixed: Fixed. Deleting volume image submodel caused this error because …
11:10 AM Ticket #1941 (Test report) closed by Tom Goddard
not a bug
11:09 AM Ticket #1941 (Test report) created by goddard@…
[…]
10:17 AM Ticket #1939 (Unexpected None data given to NamedView.restore_snapshot()) closed by pett
duplicate: duplicate of #1660
9:48 AM Ticket #1940 (self._positions is None) created by chimerax-bug-report@…
[…]
7:14 AM Ticket #1939 (Unexpected None data given to NamedView.restore_snapshot()) created by chimerax-bug-report@…
[…]

May 14, 2019:

5:50 PM Ticket #1938 (nucleotides tube selection not usable by commands) created by Elaine Meng
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 goddard@…
[…]
5:11 PM Ticket #1389 (port Chimera's Select menu) closed by pett
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 Tom Goddard
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 Elaine Meng
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 pett
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 Tom Goddard
fixed: Fixed. User tried to apply smoothlines to a molecule. It require a …
10:29 AM Ticket #1935 (Crash removing DockWidget) closed by pett
can't reproduce
8:41 AM Ticket #1935 (Crash removing DockWidget) created by chimerax-bug-report@…
[…]
7:21 AM Ticket #1934 (smoothlines: 'NoneType' object has no attribute 'shape') created by chimerax-bug-report@…
[…]
2:00 AM Ticket #1933 (RFE: "intelligent" atom transform) created by Tristan Croll
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 Tom Goddard
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 Elaine Meng
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 goddard@…
[…]
11:24 AM Ticket #1930 (RFE: Blast Protein ability to use sequence from Sequence Viewer as query) created by Elaine Meng
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 pett
can't reproduce
10:50 AM DeveloperMeetings edited by Conrad Huang
(diff)
9:46 AM Ticket #1928 (RFE cartoon coil smoothing) created by Elaine Meng
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 Elaine Meng
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 chimerax-bug-report@…
[…]

May 9, 2019:

6:20 PM Ticket #1925 (silhouettes not shown when first opening session with silhouettes) closed by Tom Goddard
fixed: Fixed. Happened only when "Resize graphics window on session restore" …
5:19 PM Ticket #1814 (missing cartoon tethers to nucleotides) closed by Greg Couch
duplicate: Keep track in #1486.
5:17 PM Ticket #1486 (Ribbon slowing graphics enormously for large models) reopened by Greg Couch
This change broke tethers to nucleotides.
4:34 PM Ticket #1445 ("Usage" needs to be more bulletproof) closed by Greg Couch
fixed: usage and usage all skip commands that can't be …
3:29 PM 2019-05-09 created by Conrad Huang
2:48 PM DeveloperMeetings edited by Conrad Huang
(diff)
11:54 AM Ticket #1074 (selection highlighting nearly invisible for non-terminal stick atoms) closed by Tom Goddard
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 Tom Goddard
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 pett
fixed
9:28 AM Ticket #1925 (silhouettes not shown when first opening session with silhouettes) created by Elaine Meng
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 tic20@…
[…]

May 8, 2019:

6:32 PM Ticket #1923 (Noisy misplaced selection outline on iMac retina display) created by goddard@…
[…] badseloutline.png
5:32 PM Ticket #1296 (vseries measure: No module named 'chimerax.core.measure') closed by Tom Goddard
fixed: Fixed. Added measure inertia code.
5:25 PM Ticket #1922 (Non-ASCII PDB file should not raise bug-reportable error) created by chimerax-bug-report@…
[…]
3:12 PM Ticket #1920 (Sequence icon using probably-not-ready-for-primetime 'sequence' command) closed by Tom Goddard
fixed: After talking to Eric I made the sequence shortcut icon show a …
2:33 PM ChangeLog edited by pett
(diff)
1:20 PM Ticket #1919 (Vseries not handling two-channel rendering correctly) closed by Tom Goddard
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 pett
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 goddard@…
[…]
10:48 AM Ticket #1920 (Sequence icon using probably-not-ready-for-primetime 'sequence' command) created by Elaine Meng
[…]
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