Timeline



Nov 6, 2020:

9:45 PM Ticket #3919 (KeyError deleting models during 'close session') created by pett
[…]
9:21 AM Ticket #3676 (Out-of-date mmCIF templates) closed by Greg Couch
fixed: Changed the bundled templates to use the version from components.cif …
7:41 AM Ticket #3918 (Qt crash (main window resize?)) created by chimerax-bug-report@…
[…]
12:11 AM Ticket #3897 (subprocess.run being called with a BundleInfo instance argument) closed by Greg Couch
fixed: Fixed installing particular versions of bundles.

Nov 5, 2020:

4:32 PM Ticket #2016 (session window size not restored even though preference is on) closed by pett
fixed: The sequence initially draws itself by laying out 50 characters per …
4:17 PM NeteSOW edited by Elaine Meng
(diff)
2:57 PM NeteSOW edited by Elaine Meng
(diff)
2:55 PM NeteSOW edited by Elaine Meng
(diff)
2:49 PM NeteSOW edited by Elaine Meng
(diff)
2:45 PM Ticket #3917 (ISOLDE: get_symmetry_handler: structure is None) created by s1960571@…
[…]
1:05 PM NeteSOW edited by Tom Goddard
(diff)
1:01 PM NeteSOW edited by Tom Goddard
(diff)

Nov 4, 2020:

9:13 PM Ticket #3800 (Add bundle builder support for Python 3 Stable ABI) closed by Greg Couch
fixed
9:13 PM Ticket #3799 (Toolshed search is not finding bundles) closed by Greg Couch
fixed
9:12 PM Ticket #3901 (Update Bundles dialog too persistent) closed by Greg Couch
fixed: Fixed. The code for detecting if the chosen toolshed had changed, …
8:19 PM NeteSOW edited by Tom Goddard
(diff)
8:17 PM NeteSOW edited by Tom Goddard
(diff)
8:12 PM NeteSOW edited by Tom Goddard
(diff)
7:26 PM Ticket #3891 (Session size 8x larger ChimeraX 1.0 vs 0.92) closed by Tom Goddard
fixed: Fixed. Made lz4 the default compression when saving a session. …
3:39 PM Ticket #3916 (Saving mmCIF files too slow to work with large structures) created by goddard@…
[…]
2:21 PM Ticket #3907 (Crash in graphics driver) closed by Tom Goddard
nonchimerax: Says ChimeraX was using 14.2 Gbytes, a hefty amount. * CFRetain() …
1:30 PM Ticket #3915 (subprocess.run being called with a BundleInfo instance argument) closed by pett
duplicate: Duplicate of #3897
1:27 PM Ticket #3914 (Traceback when Update Bundles cancelled) closed by pett
duplicate: Duplicate of #3905; adding reporter to cc list for that ticket.
1:26 PM Ticket #3913 (Traceback when Update Bundles cancelled) closed by pett
duplicate: Duplicate of #3905
1:23 PM Ticket #3912 (Traceback when Update Bundles cancelled) closed by pett
duplicate: Duplicate of #3905
1:22 PM Ticket #3911 (Traceback when Update Bundles cancelled) closed by pett
duplicate: Duplicate of #3905
12:01 PM Ticket #3906 (Crash during garbage collection) closed by pett
can't reproduce: I've seen this happen more than once, e.g. #3854; #3804; #3762; #3483
7:10 AM Ticket #3915 (subprocess.run being called with a BundleInfo instance argument) created by chimerax-bug-report@…
[…]
2:41 AM Ticket #3914 (Traceback when Update Bundles cancelled) created by david.abbasi_perez@…
[…]
2:39 AM Ticket #3913 (Traceback when Update Bundles cancelled) created by chimerax-bug-report@…
[…]
1:30 AM Ticket #3912 (Traceback when Update Bundles cancelled) created by chimerax-bug-report@…
[…]
1:30 AM Ticket #3911 (Traceback when Update Bundles cancelled) created by chimerax-bug-report@…
[…]

Nov 3, 2020:

10:11 PM Ticket #3910 (Gaussian surfaces for chains not parallelizing well) closed by Tom Goddard
fixed: Fixed. Sum of gaussians C++ code was not releasing the GIL. Added …
7:50 PM Ticket #3910 (Gaussian surfaces for chains not parallelizing well) created by goddard@…
[…]
7:40 PM Ticket #3909 (Large structure 5y6p opens unexpectedly slowly, 27 seconds) created by goddard@…
[…]
7:33 PM Ticket #3908 (Slow surface calculation, 862 chains, 5y6p) closed by Tom Goddard
fixed: Fixed. Now "surf #1 res 20 grid 7" takes 7.5 seconds instead of 153. …
5:32 PM Ticket #3908 (Slow surface calculation, 862 chains, 5y6p) created by goddard@…
[…]
1:59 PM Ticket #3907 (Crash in graphics driver) created by pett
[…]
10:46 AM Ticket #3902 (struts command needs up-to-date graphics) closed by Tom Goddard
fixed: Fixed. Made struts update structure graphics before computing …
10:44 AM Ticket #3906 (Crash during garbage collection) created by chimerax-bug-report@…
[…]
10:21 AM Ticket #3905 (Traceback when Update Bundles cancelled) created by daniel.palma.i@…
[…]
9:16 AM Ticket #3903 (preset command including trailing space in preset name) closed by pett
fixed: Rest-of-line arg needed to be .strip()ed
6:52 AM Ticket #3904 (Input/output error reading session) created by chimerax-bug-report@…
[…]

Nov 2, 2020:

6:15 PM Ticket #3898 (Toolshed Python 3.8 bundle won't install in Python 3.7) reopened by Tom Goddard
This seems like an error prone solution. It is too easy to forget to …
5:54 PM Ticket #3898 (Toolshed Python 3.8 bundle won't install in Python 3.7) closed by Greg Couch
fixed: Added limitedAPI argument to BundleInfo in bundle_info.xml. So in …
5:26 PM Ticket #3903 (preset command including trailing space in preset name) created by goddard@…
[…]
4:20 PM Ticket #3902 (struts command needs up-to-date graphics) created by pett
In a script, if I change from a non-ribbon depiction to a ribbon …
11:32 AM WikiStart edited by Tom Goddard
(diff)
11:31 AM WikiStart edited by Tom Goddard
(diff)
11:30 AM WikiStart edited by Tom Goddard
(diff)
11:27 AM WikiStart edited by Tom Goddard
(diff)
11:07 AM Ticket #3901 (Update Bundles dialog too persistent) created by pett
[…]
10:52 AM Ticket #3900 (subprocess.run being called with a BundleInfo instance argument) closed by pett
duplicate: Duplicate of #3897
10:50 AM Ticket #3900 (subprocess.run being called with a BundleInfo instance argument) created by goddard@…
[…]
10:27 AM Ticket #3899 (Deleting bundle release from Toolshed hangs) created by goddard@…
[…] Screen Shot 2020-11-02 at 10.22.11 AM.png
10:02 AM Ticket #3894 (Crash in graphics driver) closed by Tom Goddard
can't reproduce: Crash in Apple intel graphics driver, 4 GB memory being used Graphics …
10:00 AM Ticket #3898 (Toolshed Python 3.8 bundle won't install in Python 3.7) created by goddard@…
[…]
9:57 AM Ticket #3895 (Crash loading font database) closed by pett
can't reproduce: Version 0.91
9:55 AM Ticket #3897 (subprocess.run being called with a BundleInfo instance argument) created by sitins07@…
[…]
9:48 AM Ticket #3896 (Bundle install fails with new version: "already installed") created by goddard@…
[…]

Nov 1, 2020:

12:21 PM Ticket #3895 (Crash loading font database) created by chimerax-bug-report@…
[…]
2:18 AM Ticket #3894 (Crash in graphics driver) created by chimerax-bug-report@…
[…]

Oct 30, 2020:

11:36 PM Ticket #3741 (devel install fails with new wheel version 0.35.1 module.) closed by Greg Couch
fixed
6:23 PM Ticket #3893 (Make EMDB fetch display author suggested contour level) created by Tom Goddard
Eric uses the following code to fetch the EMDB XML meta data to get …
3:51 PM Ticket #3500 (Problem simulating glycans) closed by Greg Couch
not a bug: Micah figured it out.
3:10 PM Ticket #3888 (Bad glycan connectivity after mmCIF save/restore) closed by Greg Couch
can't reproduce: Til next time…
10:49 AM ChangeLog edited by Elaine Meng
(diff)
10:49 AM ChangeLog edited by Elaine Meng
(diff)

Oct 29, 2020:

10:44 AM Ticket #3892 (chain merge not reordering residues) created by Tristan Croll
[…]

Oct 28, 2020:

8:29 PM Ticket #3891 (Session size 8x larger ChimeraX 1.0 vs 0.92) created by Tom Goddard
Opening 3j3q and saving a session makes a 50 Mbyte session file in …
5:06 PM Ticket #251 (Session save/restore slow) closed by pett
fixed: Just FYI, current timings with my build is 13 seconds to open the 3j3q …
4:40 PM Ticket #3890 (Move appropriate pip dependencies to bundles) created by Greg Couch
As a policy, how about moving the various pip requirements from …
4:24 PM ChangeLog edited by Elaine Meng
(diff)
4:22 PM ChangeLog edited by Elaine Meng
(diff)
4:07 PM Ticket #1741 (Qt crash) closed by pett
can't reproduce: We're using a much different version of Qt now, so would need to see …
1:50 PM Ticket #3830 (Crash (in modal dialog?)) closed by pett
can't reproduce: Can't reproduce this using ChimeraX 1.0 off a flash drive. Hopefully …
1:46 PM Ticket #3889 (Select→Chain organization not preserved through session save/restore) created by pett
Noticed it with 5y6p, but a less humongous example is 1www.
12:06 PM Ticket #3888 (Bad glycan connectivity after mmCIF save/restore) created by Tristan Croll
[…]
10:12 AM Ticket #3887 (Problem reading Hybrid-36 chain IDs for non-polymeric chain) created by Tristan Croll
[…]
10:07 AM Ticket #3886 (HELIX/SHEET records need to support Hybrid-36 chain IDs) created by Tristan Croll
[…]
7:14 AM Ticket #3885 (~sel wrong/unintuitive in some situations) created by Tristan Croll
[…]

Oct 27, 2020:

5:21 PM Ticket #3884 (Make non-VR meeting sync camera view) closed by Tom Goddard
fixed: Fixed. Meeting command now synchronizes camera view between …
9:47 AM Ticket #3882 (wrapped C/C++ object of type ChainMenuButton has been deleted) closed by pett
fixed: Don't call .deleteLater() on the chain widget -- let Python reference …
9:44 AM Ticket #3884 (Make non-VR meeting sync camera view) created by Tom Goddard
Meeting without VR would be more useful if it synchronized the view so …
7:22 AM Ticket #3883 (Largely trashed stack) created by aurore.andrieu@…
[…]
4:41 AM Ticket #3882 (wrapped C/C++ object of type ChainMenuButton has been deleted) created by chimerax-bug-report@…
[…]

Oct 26, 2020:

4:03 PM Ticket #2860 (Dead pseudobond group being saved in session) closed by pett
fixed: Fixed by other changes since the 0.91 release.
11:53 AM Ticket #3881 (VR toolbar gui) created by Tom Goddard
The toolbar panel is especially useful in VR but it is inconveniently …
11:50 AM Ticket #3880 (Show VR meeting participants name below face) created by Tom Goddard
For meetings where the participants don't know each other or where …
11:47 AM Ticket #3879 (Add a meeting settings panel) created by Tom Goddard
Would be helpful to have meeting graphical user interface where …
11:43 AM Ticket #3878 (Remember VR meeting proxy settings) created by Tom Goddard
It would be convenient to remember meeting command proxy settings (IP …
11:38 AM Ticket #3877 (Add VR meeting hands-off toggle button to avoid accidental model moves) created by Tom Goddard
It is very easy to accidentally press the grip button on Oculus touch …
11:30 AM Ticket #3876 (Gray out VR meeting participants not wearing headset) created by Tom Goddard
Would be nice to show face image and hands dimmed in VR meetings if a …
11:15 AM Ticket #3866 (Corrupted config file) closed by pett
fixed: ChimeraX now catches config-file parsing errors and reverts to …
11:08 AM Ticket #3875 (Setup a meeting name server) created by Tom Goddard
When joining a VR meeting one specifies the host address of the …
9:02 AM Ticket #3873 (Trashed stack) closed by pett
can't reproduce
6:36 AM Ticket #3874 (Error in error message reinstalling bundle) created by rwp33@…
[…]

Oct 24, 2020:

11:13 AM Ticket #3873 (Trashed stack) created by chimerax-bug-report@…
[…]

Oct 23, 2020:

4:40 PM Ticket #3833 (vseries play markers option is broken) closed by Tom Goddard
fixed: Fixed. I made vseries play use the "frame" attribute of markers. …
3:52 PM Ticket #3872 (Don't show console window when meeting command proxy option used) closed by Tom Goddard
fixed: Fixed. Need some Windows-specific subprocess.Popen mumbo-jumbo to …
3:37 PM Ticket #3872 (Don't show console window when meeting command proxy option used) created by goddard@…
[…]
3:33 PM Ticket #3871 (Add zone selection panel option to omit original selection) created by phil.cruz@…
Phil would like an checkbutton in the Select / Zone... panel to omit …
1:11 PM Ticket #3870 (bond.atomspec: NameError) created by Tony Schaefer
[…]
10:31 AM Ticket #3832 (Crash in glDrawElementsInstanced) closed by Tom Goddard
nonchimerax: Tested out of range triangle vertex index, details in #3869, does not …
10:27 AM Ticket #3868 (Graphics hardware encountered an error and was reset) closed by Tom Goddard
duplicate: Same crash as #3867.
10:26 AM Ticket #3867 (Graphics hardware encountered an error and was reset) closed by Tom Goddard
nonchimerax: This ChimeraX crash was in the Mac graphics driver and the crash …
10:20 AM Ticket #3869 (Test of out-of-range triangle vertex indices) closed by Tom Goddard
not a bug: It appears that macOS OpenGL does range check the vertex indices and …
10:08 AM Ticket #3869 (Test of out-of-range triangle vertex indices) created by goddard@…
[…]
9:19 AM Ticket #3863 (Linking two chains merges them) reopened by pett
Would it form the bond/pseudobond and raise an error, or not form it?

Oct 22, 2020:

4:53 PM Ticket #3865 (color by bfactor: NameError: 'session') closed by pett
fixed: Boo-boo in the code when consolidating attribute-name checking between …
4:40 PM Ticket #3864 (Session restore: destroying already-destroyed alignment) closed by pett
can't reproduce: Lots of changes since 0.91
4:29 PM Ticket #3868 (Graphics hardware encountered an error and was reset) created by siyuchen2021@…
[…]
4:28 PM Ticket #3863 (Linking two chains merges them) closed by pett
not a bug: It would seem that the two options when you explicitly create backbone …
4:02 PM Ticket #3867 (Graphics hardware encountered an error and was reset) created by siyuchen2021@…
[…]
3:34 PM NeteSOW edited by Tom Goddard
(diff)
3:33 PM NeteSOW edited by Tom Goddard
(diff)
2:43 PM Ticket #3866 (Corrupted config file) created by bab378@…
[…] ChimeraX_bug.PNG
2:18 PM NeteSOW edited by Elaine Meng
(diff)
2:10 PM NeteSOW edited by Elaine Meng
(diff)
2:03 PM NeteSOW edited by Elaine Meng
(diff)
12:45 PM Ticket #3865 (color by bfactor: NameError: 'session') created by Elaine Meng
[…]
12:39 PM Ticket #3864 (Session restore: destroying already-destroyed alignment) created by chimerax-bug-report@…
[…]
11:02 AM Ticket #3863 (Linking two chains merges them) created by Tristan Croll
[…]
10:53 AM NeteSOW edited by Tom Goddard
(diff)
10:50 AM NeteSOW edited by Tom Goddard
(diff)

Oct 21, 2020:

10:32 PM Ticket #3862 (Tracebacks when exiting on Windows during meeting) created by goddard@…
[…]
4:52 PM Ticket #3861 (Contacting Toolshed blocks startup) created by goddard@…
[…]
1:20 PM Ticket #3858 (Hybrid-36 chain assignment fails when 2-char chain ID includes a numeral) closed by pett
not a bug: You need a TER card between the end of chain H1 and the start of chain C1.
11:56 AM Ticket #3860 (setattr: 'OrderedSet' object is not subscriptable) closed by pett
fixed: Fixed in tomorrow's build. --Eric
10:16 AM Ticket #3859 (Re: Hybrid-36 chain assignment fails when 2-char chain ID includes a ...) closed by pett
duplicate
10:15 AM Ticket #3857 (Re: Hybrid-36 chain assignment fails when 2-char chain ID includes a ...) closed by pett
duplicate
7:47 AM Ticket #3860 (setattr: 'OrderedSet' object is not subscriptable) created by Tony Schaefer
[…]
7:42 AM Ticket #3859 (Re: Hybrid-36 chain assignment fails when 2-char chain ID includes a ...) created by Tristan Croll
[…]
7:41 AM Ticket #3858 (Hybrid-36 chain assignment fails when 2-char chain ID includes a numeral) created by Tristan Croll
[…] rc-dlh1-model1b.pdb
7:40 AM Ticket #3857 (Re: Hybrid-36 chain assignment fails when 2-char chain ID includes a ...) created by Tristan Croll
[…]

Oct 20, 2020:

5:59 PM Ticket #3856 (Many "Replacing opener..." warnings for SEQROW) closed by pett
fixed: Seems like TMI :-) but okay, Anyway, I have fixed the issue by only …
3:46 PM Ticket #3856 (Many "Replacing opener..." warnings for SEQROW) created by Tom Goddard
I bug report #3855 there apparently more than 30 warnings at startup …
3:41 PM Ticket #3855 (ModuleNotFoundError: No module named 'chimerax.surface.squaremesh') closed by Tom Goddard
fixed: Fixed. I forgot to add the squaremesh.py file to git.
3:10 PM Ticket #3855 (ModuleNotFoundError: No module named 'chimerax.surface.squaremesh') created by Elaine Meng
[…]
2:10 PM NeteSOW edited by Tom Goddard
(diff)
10:21 AM Ticket #3854 (Crash creating Python Residue) closed by pett
can't reproduce: Seemingly crashed as part of the garbage collection done while …
9:33 AM Ticket #3854 (Crash creating Python Residue) created by chimerax-bug-report@…
[…]
1:53 AM Ticket #3853 (Bug in chimeraX 1.1 version) created by irsa.abbasi29@…
[…]
1:29 AM Ticket #3852 (Attempt to install ISOLDE into ChimeraX 1.1.1) created by chimerax-bug-report@…
[…]

Oct 19, 2020:

11:29 PM NeteSOW edited by Greg Couch
(diff)
11:11 PM Ticket #1827 (Allow toolshed to be queried for providers) closed by Greg Couch
fixed: The manager and provider metadata is now in the toolshed and picked up …
7:36 PM Ticket #3851 (data_formats is not available yet) closed by Greg Couch
not a bug: Rebuilding everything from scratch fixed it. Unclear why partial …
6:30 PM Ticket #3851 (data_formats is not available yet) created by Greg Couch
When I start ChimeraX with the latest source code, I get: […]
6:21 PM ChangeLog edited by Elaine Meng
(diff)
6:10 PM Ticket #3850 (Crash showing tooltip on dual-display system) closed by Tom Goddard
can't reproduce: There have been ChimeraX 5 reports of this same crash, all in ChimeraX …
6:08 PM Ticket #3846 (Crash showing tool tip with two screens, macOS) closed by Tom Goddard
can't reproduce: See if we ever get this report in Qt 5.15 where it may be fixed.
5:40 PM ChangeLog edited by Elaine Meng
(diff)
4:30 PM Ticket #3850 (Crash showing tooltip on dual-display system) created by chimerax-bug-report@…
[…]
3:41 PM Ticket #3849 (AddH crash) closed by pett
fixed: Don't call ring.aromatic while IDATM types are in flux (which will …
10:20 AM Ticket #3847 (Various bugs after "rename" command) closed by Tom Goddard
duplicate: These errors are due to a bug in the rename command that was fixed a …
8:47 AM Ticket #3849 (AddH crash) created by Tristan Croll
[…] merged_raw.pdb

Oct 18, 2020:

10:44 AM Ticket #3848 (Crash in QtWebEngineCore) created by cassiezhang9@…
[…]
2:37 AM Ticket #3847 (Various bugs after "rename" command) created by sitins07@…
[…]

Oct 17, 2020:

12:36 PM Ticket #3846 (Crash showing tool tip with two screens, macOS) created by chimerax-bug-report@…
[…]

Oct 16, 2020:

6:09 PM Ticket #3845 (Handle low bandwidth in VR meetings) created by Tom Goddard
Want VR meetings to work for participants with lower bandwidth network …
4:38 PM Ticket #3842 (Meeting error in debugging code that checks for null bytes in messages) closed by Tom Goddard
fixed: Fixed. Duplicate of #3841 This was a bug in my debugging code that …
4:35 PM Ticket #3841 (VR problems) closed by Tom Goddard
fixed: Fixed second bug where a tool panel was shown after the VR user …
3:55 PM Ticket #3844 (Crash in glDrawElementsInstanced) closed by Tom Goddard
duplicate: Duplicate of #3832 by same anonymous reporter. Looked at last 10 …
3:06 PM Ticket #3391 ("defattr" format for 'save' command) closed by pett
fixed
2:54 PM Ticket #3844 (Crash in glDrawElementsInstanced) created by chimerax-bug-report@…
[…]
1:37 PM Ticket #3843 (transparency command does not work on nucleotides (target f)) created by Elaine Meng
Although I had not yet documented target f for the transparency …
1:21 PM Ticket #3840 (Font problems) reopened by pett
Was fooled by my mail client into thinking this was a duplicate.
1:19 PM Ticket #3840 (Font problems) closed by pett
duplicate: Duplicate of #3841
1:13 PM Ticket #3842 (Meeting error in debugging code that checks for null bytes in messages) created by goddard@…
[…]
1:13 PM Ticket #3841 (VR problems) created by phil.cruz@…
[…]
12:17 PM Ticket #3840 (Font problems) created by phil.cruz@…
[…]
10:57 AM Ticket #3698 (Libraries not found when generating bundle documentation) closed by Greg Couch
not a bug: I left out a step. It should be: […] That preloads the arrays …
10:04 AM Ticket #3839 (KeyError deleting models during 'close session') closed by Tom Goddard
duplicate: The ChimeraX session close error was caused by a bug in the rename …
9:57 AM Ticket #3838 (Multiple layers of transparency) closed by Tom Goddard
wontfix: Unfortunately ChimeraX graphics is not able to correctly show 2 or …
9:43 AM Ticket #3835 (glClear: invalid operation) closed by Tom Goddard
can't reproduce: Strange. Modern graphics RTX 2080 with current Oct 7, 2020 driver but …
9:00 AM Ticket #3837 (Show sequence viewer: name 'Atoms' is not defined) closed by pett
duplicate
8:58 AM Ticket #3836 (Blast: host aborted connection) closed by pett
can't reproduce: The host aborted the connection on the successful BLAST job before …
6:59 AM Ticket #3839 (KeyError deleting models during 'close session') created by ogahura@…
[…]
4:03 AM Ticket #3838 (Multiple layers of transparency) created by Tom Goddard
[…]
2:58 AM Ticket #3837 (Show sequence viewer: name 'Atoms' is not defined) created by chimerax-bug-report@…
[…]
1:39 AM Ticket #3836 (Blast: host aborted connection) created by chimerax-bug-report@…
[…]

Oct 15, 2020:

7:12 PM Ticket #3835 (glClear: invalid operation) created by chimerax-bug-report@…
[…]
7:03 PM Ticket #3834 (Windows crash resizing main window) created by goddard@…
[…]
4:21 PM Ticket #3833 (vseries play markers option is broken) created by goddard@…
[…]
3:28 PM Ticket #3831 (Start Build Structure: name 'Atoms' is not defined) closed by pett
fixed: Hi Tony, Thanks for reporting this problem. Fixed now and the fix …
2:34 PM Ticket #3723 (Cannot rewrite settings file: "being used by another process") closed by Greg Couch
duplicate: This is probably fixed by #3205.
2:33 PM Ticket #3832 (Crash in glDrawElementsInstanced) created by chimerax-bug-report@…
[…]
1:26 PM Ticket #3631 (Move ChimeraX source code to GitHub) closed by Tom Goddard
fixed: Source code moved to github for the past month, working fine.
1:25 PM Ticket #3632 (Update to Qt 5.15) closed by Tom Goddard
fixed: Greg updated to Qt 5.15.
1:24 PM Ticket #3682 (Crash when screen removed) closed by Tom Goddard
fixed: The ChimeraX daily build is now using Qt 5.15.1 so this crash when …
12:50 PM Ticket #3831 (Start Build Structure: name 'Atoms' is not defined) created by Tony Schaefer
[…]
10:02 AM Ticket #3828 (SEQCROW writing JSON job list on exit: No such file or directory) closed by pett
fixed
9:15 AM Ticket #3829 (save PNG from toolbar: Unknown image file format "png image") closed by pett
duplicate
8:22 AM Ticket #3830 (Crash (in modal dialog?)) created by marco.salamina@…
[…]
6:10 AM Ticket #3829 (save PNG from toolbar: Unknown image file format "png image") created by chimerax-bug-report@…
[…]
5:18 AM Ticket #3828 (SEQCROW writing JSON job list on exit: No such file or directory) created by Tristan Croll
[…]

Oct 14, 2020:

11:13 PM Ticket #3756 (OpenMM 7.5 beta fails to load on Linux, C++ library not found) closed by Greg Couch
fixed: Updated prereqs/openmm/README.txt
2:59 PM Ticket #3363 (Visually distinguish old log output from new) closed by pett
fixed: Removed the textual indicator of the end of the embedded log and …
2:36 PM Ticket #3826 (_serialize.cpp: warning: 'tp_print' is deprecated) closed by Greg Couch
wontfix: Yes, this will be fixed by a future version of Cython, or it won't. …
2:25 PM Ticket #3809 (Log should show dates for saved sessions in local time, not UTC) closed by pett
can't reproduce
2:03 PM Ticket #3827 (Slow ChimeraX startup due to Toolshed) created by goddard@…
[…]
12:29 PM Ticket #3823 (shift-pick doesn't log command) closed by Tom Goddard
fixed: Fixed. I made shift-ctrl pick of an atom or residue log a select add …
12:24 PM Ticket #3826 (_serialize.cpp: warning: 'tp_print' is deprecated) created by goddard@…
[…]

Oct 13, 2020:

3:36 PM Ticket #3824 (RFE: add more settings to Labels category of Preferences dialog) created by Elaine Meng
Three somewhat interrelated suggestions: (A) Currently there is a …
1:45 PM ChangeLog edited by Elaine Meng
(diff)
11:44 AM Ticket #3777 (Selection ordering) closed by pett
fixed: Okay, now the 'sel' selector will return the atoms in the order they …
11:39 AM Ticket #3823 (shift-pick doesn't log command) created by pett
Simple picking with the mouse logs a select command. Shift-pick does …

Oct 12, 2020:

5:16 PM Ticket #3822 (VR Oculus Touch button is too easy to accidentally press) created by goddard@…
[…]
5:16 PM Ticket #3821 (Shell broken on Windows in Python 3.8) closed by pett
duplicate
5:15 PM Ticket #3820 (Shell broken on Windows in Python 3.8) closed by pett
fixed: You must have also not installed it! :-) Anyway, the fix is committed …
4:18 PM Ticket #3821 (Shell broken on Windows in Python 3.8) created by goddard@…
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4:04 PM Ticket #3819 (MemoryError decompressing map from session) closed by Tom Goddard
nonchimerax: Insufficient memory. Nothing ChimeraX can do about that. Same as …
3:19 PM Ticket #3820 (Shell broken on Windows in Python 3.8) created by goddard@…
[…]
2:49 PM Ticket #3819 (MemoryError decompressing map from session) created by anaschwarzer@…
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2:28 PM Ticket #3818 (Crash changing chain ID) closed by pett
fixed: Well, sort of fixed. The problem was that the type-guessing rules …
10:59 AM Ticket #3815 (Save-session crash) closed by Tom Goddard
nonchimerax: Based on your other two bug reports I would guess that the crash was …
10:43 AM Ticket #3817 (MemoryError restoring map from session) closed by Tom Goddard
not a bug: This MemoryError simply means your computer does not have enough …
10:36 AM Ticket #3816 (Unable to allocate buffer) closed by Tom Goddard
not a bug: This ChimeraX simply says your computer did not have enough memory. …
8:42 AM Ticket #3818 (Crash changing chain ID) created by Elaine Meng
[…]
6:00 AM Ticket #3817 (MemoryError restoring map from session) created by anaschwarzer@…
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Oct 11, 2020:

7:47 AM Ticket #3816 (Unable to allocate buffer) created by anaschwarzer@…
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7:45 AM Ticket #3815 (Save-session crash) created by anaschwarzer@…
[…]

Oct 9, 2020:

11:08 PM Ticket #3629 (cxconference server enables weak TLS ciphers) closed by Greg Couch
fixed: Removed AddTrust External CA Root cross-signing certificate for …
5:51 PM Ticket #3814 (HETATM not passed through to Modeller when requested) closed by pett
fixed: Okay, a fix for this will be in the next daily build.
4:22 PM Ticket #3629 (cxconference server enables weak TLS ciphers) reopened by Greg Couch
Actually, there is one more thing that needs to be done. The …
3:41 PM Ticket #3629 (cxconference server enables weak TLS ciphers) closed by Greg Couch
fixed: Fixed. Scooter installed src/mux.py as /usr/local/bin/cxconference on …
11:38 AM Ticket #3814 (HETATM not passed through to Modeller when requested) created by mmmtnez@…
As per summary. The problem is that the alignment transmitted to …
10:25 AM Ticket #3813 (Allow setting zone mouse mode label defaults) created by sarahjpiper89@…
From: Sarah Piper Subject: [chimerax-users] right mouse zone …

Oct 8, 2020:

7:41 PM Ticket #3767 (Ligand not surfaced) closed by Tom Goddard
not a bug: No response from reporter. Likely just did not understand how to …
7:39 PM Ticket #3740 (Ghost head and hands of person who left 3-person VR meeting) closed by Tom Goddard
fixed: Fixed. Made meeting send message to all participants when one …
5:55 PM Ticket #3528 (Obsolete Blast hits) closed by pett
fixed: It looks like NLM has removed the obsolete structures from the blast …
2:19 PM ChangeLog edited by Elaine Meng
(diff)
2:10 PM NeteSOW edited by Elaine Meng
(diff)
2:09 PM NeteSOW edited by Elaine Meng
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1:56 PM NeteSOW edited by Elaine Meng
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1:50 PM Ticket #3759 (Make ChimeraX 1.1.1 production release to fix startup on macOS Big Sur) closed by Greg Couch
fixed: Done. There is 1.1.1 release for just macOS that replaced the 1.1 release.
10:25 AM Ticket #3812 ("rename" bug) closed by Tom Goddard
fixed: Fixed. Moving a model which has child models to a lower position in …
9:37 AM Ticket #3812 ("rename" bug) created by caillancm@…
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Oct 7, 2020:

7:20 PM Ticket #3811 (Deprecation warnings in session code) created by goddard@…
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3:33 PM Ticket #3810 (glTF too bright in PowerPoint) closed by Tom Goddard
nonchimerax: I don't see anything we can do about PowerPoint's bad lighting.
12:07 PM Ticket #3810 (glTF too bright in PowerPoint) created by mikael.p.karjalainen@…
[…] 2egc gltf file.gltf
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