Timeline



May 17, 2020:

12:38 PM Ticket #3214 (Tube helices broken on Windows, Scipy cannot import _uarray) closed by Greg Couch
fixed: I agree that the installer asking to restart the computer is annoying. …
12:22 PM Ticket #3235 (Could not start space navigator) created by ed.luk@…
[…]
12:08 PM Ticket #3214 (Tube helices broken on Windows, Scipy cannot import _uarray) reopened by Tom Goddard
I tested the May 16 Windows build and tube helices worked. But …
1:50 AM Ticket #3234 (ISOLDE Tool Shed install button not appearing) created by Tristan Croll
Bug report received as email from Wenxin Xi, Chinese Academy of …
12:00 AM Ticket #3233 (Remove bogus 1-star reviews) created by goddard@…
[…]

May 16, 2020:

11:58 PM Ticket #3232 (Tool Shed download problem) created by goddard@…
[…]
9:20 PM Ticket #3231 (Underscores in atom/residue names) created by goddard@…
[…]
9:18 PM Ticket #3229 (Atom names with underscores not parsed in commands) closed by Tom Goddard
invalid: I'm going to rereport this with current ChimeraX build since this bug …
9:16 PM Ticket #3230 (Checking if bug report includes all logged commands) closed by Tom Goddard
not a bug
9:10 PM Ticket #3230 (Checking if bug report includes all logged commands) created by goddard@…
[…] Screen Shot 2020-05-16 at 9.10.28 PM.png
8:55 PM Ticket #3229 (Atom names with underscores not parsed in commands) created by goddard@…
[…]
12:10 PM Ticket #3228 (Preference setting for model id numbers) created by dgutierrez@…
Would be helpful if new model numbers were always one larger than …
8:35 AM Ticket #3227 (Cannot import _uarray) created by manuela.lanzafame@…
[…]
6:44 AM Ticket #3226 (Make mesh surfaces not cast shadows) created by Tristan Croll
[…] soft_lighting_map_issues.tar.gz
3:23 AM Ticket #3225 (Failure reading DCD: unexpected end of data) created by Tristan Croll
[…]
2:14 AM Ticket #3224 (Cartoon pick: index is out of bounds) created by chimerax-bug-report@…
[…]
2:14 AM Ticket #3223 (glClearColor: invalid enumerant) created by pradeep.hiriyur.nagaraj@…
[…]
12:31 AM ChangeLog edited by Greg Couch
(diff)

May 15, 2020:

9:07 PM Ticket #3214 (Tube helices broken on Windows, Scipy cannot import _uarray) closed by Greg Couch
fixed: Windows release candidates will now include the Visual C++ runtime and …
2:43 PM Ticket #3220 (Volume viewer broken; registration checking still broken) closed by Greg Couch
fixed: Fixed. Triple checked previous patch to see if this was systemic or …
2:40 PM Ticket #3217 (Saving mmCIF: citation is None) closed by Greg Couch
duplicate: That is consistent. The bug was happened when a mmCIF model was read …
1:21 PM Ticket #3222 (During ChimeraX quit: Could not make graphics context current) created by Tristan Croll
[…]
10:29 AM Ticket #3219 (Tether atom spec balloon wrong) closed by Tom Goddard
fixed: Fixed. Tethers never had support for showing atomspec balloons, they …
8:51 AM Ticket #3215 (Resized Windows text + Ramachandran plato crashes ChimeraX) closed by Tristan Croll
fixed: Wow - believe it or not, you're the second person in a week to figure …
8:15 AM Ticket #3221 (Chain mix up using ISOLDE) created by Tristan Croll
[…]
3:12 AM Ticket #3220 (Volume viewer broken; registration checking still broken) created by caillancm@…
[…]
1:58 AM Ticket #3219 (Tether atom spec balloon wrong) created by Tristan Croll
[…]

May 14, 2020:

11:57 PM Ticket #3218 (Duplicate residues created in Chain) created by goddard@…
[…] 7bv2_extended.pdb
8:20 PM Ticket #3217 (Saving mmCIF: citation is None) created by goddard@…
[…]
5:29 PM Ticket #3216 (open/save need to be aware of uninstalled formats) created by pett
Also Info.plist. So toolshed needs to be enhanced to allow access to …
3:59 PM Ticket #3194 (remove bare excepts) closed by Greg Couch
fixed: All of the bare excepts have been replace with "except Exception".
12:06 PM Ticket #3215 (Resized Windows text + Ramachandran plato crashes ChimeraX) created by rowechris@…
[…] ChimeraX_Application Errors_CR.evtx
10:38 AM Ticket #3211 (Scipy can't import _uarray) closed by Greg Couch
duplicate: Duplicate of #3214.
10:30 AM Ticket #3172 (Space Navigator does not start on Mac) closed by Tom Goddard
fixed: Fixed. Tested today's mac build and space navigator worked.
10:23 AM Ticket #3212 (Drawing silhouette: glFramebufferTexture2D: invalid operation) closed by Tom Goddard
can't reproduce: OpenGL InvalidOperation error in glFramebufferTexture2D when drawing …
10:07 AM Ticket #3214 (Tube helices broken on Windows, Scipy cannot import _uarray) created by goddard@…
[…]
10:03 AM Ticket #3209 (Graphics hardware error) closed by Tom Goddard
nonchimerax: Crashed in Mac OpenGL graphics driver. Apple OpenGL drivers are prone …
9:58 AM Ticket #3208 (Cartoon pick: index is out of bounds) closed by Tom Goddard
duplicate: Was fixed April 21. Reporter is using April 14 build.
9:13 AM Ticket #3213 (REST: broken pipe) created by g.m.carstairs@…
On May 14, 2020, at 8:07 AM, Mungo Carstairs (Staff) …
8:44 AM Ticket #3206 (wrong version in download) closed by pett
wontfix: Was responded to on the chimera-users list
7:16 AM Ticket #3212 (Drawing silhouette: glFramebufferTexture2D: invalid operation) created by chimerax-bug-report@…
[…]
5:26 AM Ticket #3211 (Scipy can't import _uarray) created by chimerax-bug-report@…
[…]

May 13, 2020:

10:19 PM Ticket #3210 (develop stragegy for updating JavaScript toolkits embedded in ui module) created by Greg Couch
The UI module provides several JavaScript toolkits, namely bootgrid …
7:15 PM Ticket #3209 (Graphics hardware error) created by andrew.alexander@…
[…]
7:08 PM Ticket #3208 (Cartoon pick: index is out of bounds) created by chimerax-bug-report@…
[…]
3:49 PM Ticket #3207 (Re: [chimerax-users] wrong version in download) closed by Greg Couch
wontfix
3:31 PM Ticket #3207 (Re: [chimerax-users] wrong version in download) created by Greg Couch
[…]
2:38 PM Ticket #3204 (Save mmCIF: citation is None) closed by Greg Couch
fixed: Fixed. Thanks for report this.
1:18 PM Ticket #3205 (Can't save settings file (in use by another process)) closed by pett
fixed: Hi Stephen, This only happened the very first time you started …
1:07 PM Ticket #3206 (wrong version in download) created by christinelgee@…
[…]
1:07 PM Ticket #3159 (Registration traceback) closed by Conrad Huang
fixed: Fixed in [changset:1a20a02de]. Temporarily set locale to en_us when …
10:41 AM Ticket #3205 (Can't save settings file (in use by another process)) created by stephen.thong@…
[…]
9:45 AM Ticket #3204 (Save mmCIF: citation is None) created by dirk.fahrenkamp@…
[…]
9:24 AM Ticket #3203 (Crash creating OpenGL context) closed by Tom Goddard
can't reproduce: No idea how QOpenGLContext::create() can crash. One Qt bug report …
9:10 AM Ticket #3202 (CUDA_ERROR_UNKNOWN starting ISOLDE simulation) closed by Tristan Croll
wontfix: Would require further feedback from the user to debug.
9:00 AM Ticket #3203 (Crash creating OpenGL context) created by chimerax-bug-report@…
[…]
8:29 AM Ticket #3202 (CUDA_ERROR_UNKNOWN starting ISOLDE simulation) created by chimerax-bug-report@…
[…]
6:25 AM Ticket #3201 (Out of memory error starting ISOLDE simulation) closed by Tristan Croll
wontfix
5:34 AM Ticket #3201 (Out of memory error starting ISOLDE simulation) created by chimerax-bug-report@…
[…]

May 12, 2020:

9:27 PM Ticket #3199 (Map segmentation coloring array size mismatch) closed by Tom Goddard
fixed: Fixed. Image style rendering was sometimes using a region size that …
6:29 PM Ticket #3200 (configfile/configparser not handling encoding) created by zhaowenxu@…
[…]
6:19 PM Ticket #3199 (Map segmentation coloring array size mismatch) created by goddard@…
[…]
6:16 PM Ticket #3198 (Segmentation map coloring in opaque mode gives error) closed by Tom Goddard
fixed: Fixed. Segment colors array was not correctly converted to opaque colors.
5:48 PM Ticket #3198 (Segmentation map coloring in opaque mode gives error) created by goddard@…
[…]
4:53 PM Ticket #3197 (command to change chain IDs) created by dirk.fahrenkamp@…
per summary; can leverage work from #2528
1:58 PM Ticket #3195 (Open PDB file in already running ChimeraX) closed by Tom Goddard
fixed: Fixed. ChimeraX was getting the Qt FileOpen event but ignored it …
11:49 AM Ticket #3193 ("web fetch" format not recognized) closed by pett
fixed: Okay, I have quashed this bug, so that file-history entry should work …
11:30 AM Ticket #3196 (Add chimerax --send startup option) created by Tom Goddard
Want to be able to open a file in a currently running ChimeraX from a …
11:22 AM Ticket #3195 (Open PDB file in already running ChimeraX) created by Tom Goddard
On Mac double clicking a PDB file starts ChimeraX and shows it, but …
11:19 AM Ticket #3153 (Mac ChimeraX not registered to open PDB, mmCIF, MRC, ....) reopened by pett
11:08 AM Ticket #3153 (Mac ChimeraX not registered to open PDB, mmCIF, MRC, ....) closed by Greg Couch
fixed: Confirmed additional data formats are in the distributed application's …
11:00 AM Ticket #3194 (remove bare excepts) created by Greg Couch
All bare excepts, "except:" should be removed from ChimeraX. Instead, …
10:42 AM Ticket #3193 ("web fetch" format not recognized) created by huatiger3@…
[…] 2020-05-12_chimerax_1_tutorial_fail.pdf
10:42 AM Ticket #3192 (Faster decompression of maps in session files) created by Tom Goddard
Maps saved in session files are compressed with gzip. Compression and …
10:36 AM Ticket #3189 (Keyboard interrupt during session restore (hang reading volume data?)) closed by Tom Goddard
not a bug: The full exception is in the bug report. A session file was opened, …
10:13 AM Ticket #3191 (remove dead I/O code) created by Greg Couch
At least remove the dead I/O code from the core. It is very confusing …
9:50 AM Ticket #3188 (glDrawBuffer: invalid operation) closed by Tom Goddard
can't reproduce: This is the third report by the same user of this error in 5 months on …
9:48 AM Ticket #3187 (Can't save settings file (in use by another process)) closed by pett
can't reproduce: Hi Steffen, Thanks for getting back to me. This feels like a problem …
9:39 AM Ticket #3190 (Bug reporter test) closed by Tom Goddard
fixed: Works.
9:37 AM Ticket #3190 (Bug reporter test) created by goddard@…
[…]
9:31 AM Ticket #3189 (Keyboard interrupt during session restore (hang reading volume data?)) created by chimerax-bug-report@…
[…]
8:35 AM Ticket #3186 (Save options widgets deleted) closed by pett
duplicate: Hi Thomas, Very sorry for this problem. It was fixed on Friday and is …
8:33 AM Ticket #3185 (Crash getting global interpreter lock) closed by pett
can't reproduce
5:44 AM Ticket #3188 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…
[…]
4:15 AM Ticket #3187 (Can't save settings file (in use by another process)) created by hinz@…
[…]

May 11, 2020:

4:04 PM Ticket #3186 (Save options widgets deleted) created by tomasiak@…
[…]
3:34 PM Ticket #3185 (Crash getting global interpreter lock) created by chimerax-bug-report@…
[…]
11:50 AM Ticket #3184 (Save options widgets deleted) closed by pett
duplicate: Hi Rebecca, Very sorry for this problem. It was fixed on Friday and …
11:45 AM Milestone RC 1 completed
See Milestone 1.0
11:44 AM Ticket #3184 (Save options widgets deleted) created by voorhees@…
[…]
11:13 AM Ticket #1166 (Ribbon: operands could not be broadcast together with shapes) closed by Conrad Huang
wontfix: No feedback and ribbon code revamped by Tom Goddard.
11:12 AM Ticket #622 (Develop protocol for releasing standard bundles onto toolshed) closed by Conrad Huang
not a bug: The consensus is that we will *not* automatically put standard bundles …
11:04 AM Ticket #3183 (pb_scene_coord returning None) closed by Tom Goddard
duplicate: This was fixed a month ago. Use ChimeraX daily build.
11:04 AM Ticket #922 (Revise tutorials for new data format and bundle APIs) closed by pett
fixed: The new open/save APIs were documented before the RC1 release.
10:08 AM Ticket #3182 (Crash restoring Structure) closed by pett
duplicate: duplicate of #3181
10:07 AM Ticket #3181 (Crash restoring Structure) closed by pett
can't reproduce: Corrupted session? Unfortunately, would need the session file to make …
10:02 AM Ticket #3180 (Save options widgets deleted) closed by pett
duplicate: Hi Ulrich, Very sorry for this problem. It was fixed on Friday and is …
10:00 AM Ticket #3179 (Crash syncing threads) closed by pett
can't reproduce
9:57 AM Ticket #3178 (Error with GaudiViewX opening a .zip file) closed by pett
nonchimerax
9:55 AM Ticket #3177 (Save options widgets deleted) closed by pett
duplicate
9:54 AM Ticket #3176 (Save options widgets deleted) closed by pett
duplicate: Hi Caillan, Actually the problem is that the save dialog only works …
9:52 AM Ticket #3175 (Save options widgets deleted) closed by pett
duplicate: Hi Cailian, Very sorry for this problem. It was fixed on Friday and …
9:49 AM Ticket #3174 (Save options widgets deleted) closed by pett
duplicate: Hi Eva, Very sorry for this problem. It was fixed on Friday and is …
9:43 AM Ticket #3171 (Save options widgets deleted) closed by pett
duplicate: duplicate of #3166
9:30 AM Ticket #3170 (Ubuntu 20.04 (Linux) 64-bit download fails) closed by Greg Couch
fixed: Try again :-) It now works for me.
8:18 AM Ticket #2837 (Crash displaying ISOLDE ramachandran plot) closed by Tristan Croll
fixed: Fixed. Turns out this was being triggered by calling MatPlotLib's …
1:37 AM Ticket #3183 (pb_scene_coord returning None) created by vytautas.raskevicius@…
[…]

May 10, 2020:

9:31 PM Ticket #3182 (Crash restoring Structure) created by chimerax-bug-report@…
[…]
9:29 PM Ticket #3181 (Crash restoring Structure) created by chimerax-bug-report@…
[…]
11:48 AM Ticket #3180 (Save options widgets deleted) created by ubaumann@…
[…]
6:52 AM Ticket #3179 (Crash syncing threads) created by chimerax-bug-report@…
[…]

May 9, 2020:

4:52 PM Ticket #3178 (Error with GaudiViewX opening a .zip file) created by chimerax-bug-report@…
[…]
12:03 PM Ticket #3169 (No Report a Bug option for OpenGL error) closed by Tom Goddard
fixed: Fixed. Code was using logger.error() instead of logger.bug() when …
10:20 AM Ticket #3177 (Save options widgets deleted) created by chimerax-bug-report@…
[…]
9:55 AM Ticket #3176 (Save options widgets deleted) created by caillancm@…
[…]
8:24 AM Ticket #3175 (Save options widgets deleted) created by caillancm@…
[…]
5:40 AM Ticket #3174 (Save options widgets deleted) created by eva.bertosin@…
[…]

May 8, 2020:

11:25 PM Ticket #2936 (MemoryError saving session) closed by Greg Couch
fixed: Not sure if this is the same bug, but the msgpack size limits have …
11:21 PM Ticket #1918 (Documentation warnings) closed by Greg Couch
fixed: Changed code to only report "errors" found when building the merged …
10:24 PM Ticket #2573 (safe-save permission denied writing temp file) closed by Greg Couch
can't reproduce
10:23 PM Ticket #2700 (Can't open .pyc file) closed by Greg Couch
fixed: pyc files from different versions of Python are rejected with a …
8:54 PM Ticket #2855 (Command to run tests deprecated) closed by Greg Couch
fixed: Removing testing from bundle builder. Tests are done, separately, …
6:37 PM Ticket #3173 (BLAST PDB web services being removed November 2020) created by Tom Goddard
The PDB announced that legacy PDB web services will be discontinued …
5:06 PM Ticket #3172 (Space Navigator does not start on Mac) created by acheron24@…
[…]
4:47 PM Ticket #2785 (Nucleotides saving deleted Residue) closed by Greg Couch
duplicate: Duplicate of #2955. And fixed!
4:45 PM Ticket #2823 (Nucleotides trying to save dead Residue in session) closed by Greg Couch
duplicate: Duplicate of #2955. Finally able to reproduce and fix.
4:39 PM Ticket #3166 (Save options widgets deleted) closed by pett
fixed: Can't cache format-specific options because the dialog is destroyed …
3:13 PM Ticket #2994 (Nucleotides trying to save closed structure) closed by Greg Couch
duplicate: Duplicate of #2955. Finally able to reproduce and fix.
3:12 PM Ticket #2955 (Nucleotides trying to save closed structure) closed by Greg Couch
fixed: Fixed.
3:11 PM Ticket #3123 (self.positions is None) closed by Greg Couch
duplicate: Duplicate of #2955. Finally able to reproduce and fix.
3:11 PM Ticket #3164 (Nucleotides trying to save dead structure) closed by Greg Couch
duplicate: Duplicate of #2955. Finally able to reproduce and fix.
1:30 PM Ticket #3171 (Save options widgets deleted) created by chimerax-bug-report@…
[…]
12:52 PM Ticket #3170 (Ubuntu 20.04 (Linux) 64-bit download fails) created by huatiger3@…
[…]
11:57 AM Ticket #3161 (camera 360sbs: Shader does not have uniform variable "model_view_matrix") closed by Tom Goddard
fixed: Fixed
11:29 AM Ticket #3169 (No Report a Bug option for OpenGL error) created by goddard@…
[…]
10:21 AM Ticket #3168 (Support CHARMM/X-PLOR format PDB files) created by Tristan Croll
Like it or not, these are still a favourite with many in the molecular …
10:21 AM Ticket #3165 (Problem drawing selection outline: Invalid operation: glBlitFramebuffer) closed by Tom Goddard
duplicate: Fixed several days ago. Selection outline broken by default …
10:17 AM Ticket #3167 (Add crystalcontacts command) created by guillaume@…
From: Guillaume Gaullier Subject: [chimerax-users] How to display …
9:09 AM Ticket #3163 (Model panel problem) closed by pett
duplicate
7:09 AM Ticket #3166 (Save options widgets deleted) created by chimerax-bug-report@…
[…]
5:37 AM Ticket #3165 (Problem drawing selection outline: Invalid operation: glBlitFramebuffer) created by chimerax-bug-report@…
[…]
1:16 AM Ticket #3164 (Nucleotides trying to save dead structure) created by chimerax-bug-report@…
[…]

May 7, 2020:

11:23 PM Ticket #3163 (Model panel problem) created by chimerax-bug-report@…
[…]
8:14 PM Ticket #3157 (License string not "Sphinx compliant") closed by Greg Couch
fixed: Extra digit in enumeration requires nested paragraph to be indented …
6:00 PM Ticket #3162 (Incorrect commands easily lost) created by goddard@…
[…]
5:55 PM Ticket #3161 (camera 360sbs: Shader does not have uniform variable "model_view_matrix") created by gokhan_tolun@…
[…]
3:29 PM Ticket #3160 (Install updated bundle into 1.0) created by pett
Sometime prior to the 1.0 release, we need to verify that an updated …
3:27 PM Ticket #3159 (Registration traceback) created by Greg Couch
At the beginning of #3123 is a traceback in the Registration bundle. …
3:20 PM Ticket #3158 (Bogus Linux test failures) created by pett
The nightly build reports Linux test failures when there aren't any.
1:50 PM Ticket #3145 (File history unreadable) closed by Tom Goddard
can't reproduce: Saw this once before. Not sure how file history JSON file gets …
12:38 PM Ticket #1903 (Tabbed toolbar customization) closed by Greg Couch
fixed: Done, modulo macOS Qt errors rearranging sections.
12:36 PM Ticket #1149 (bundles need test suites) closed by Greg Couch
fixed: Developers need to add their own tests now :-)
12:12 PM Ticket #1482 (bundle-ize WebServices + improve docs) closed by Greg Couch
fixed
12:10 PM Ticket #3060 (Adding images and descriptions to RBVI bundles) closed by Elaine Meng
fixed: have apportioned the list to the corresponding programmers
11:58 AM Ticket #1173 (Ribbon normalization error) closed by Greg Couch
fixed: This appears to have been fixed.
11:12 AM Ticket #3150 (open/save severely hampered) closed by pett
fixed: Okay, I've committed a fix that works in my testing.
8:59 AM Ticket #3155 (Model panel problem) closed by pett
duplicate
8:58 AM Ticket #3154 (Model panel problem) closed by pett
can't reproduce: Seen this once before. I *believe* it indicates that a level in the …
3:15 AM Ticket #3157 (License string not "Sphinx compliant") created by Tristan Croll
Just a minor formatting issue, by the looks of it. On the license …
2:29 AM Ticket #3156 (Error initializing context: clGetPlatformIDs) created by gokhan_tolun@…
[…]

May 6, 2020:

9:37 PM Ticket #3155 (Model panel problem) created by chimerax-bug-report@…
[…]
9:37 PM Ticket #3154 (Model panel problem) created by chimerax-bug-report@…
[…]
6:32 PM Ticket #3153 (Mac ChimeraX not registered to open PDB, mmCIF, MRC, ....) created by goddard@…
[…]
3:29 PM Ticket #3131 (Read CCD CIFs directly) closed by pett
fixed: Error was only happening for fetch-only formats. SMILES suffered from …
2:50 PM Ticket #3137 (SeggerX and save dialog need updating) closed by Tom Goddard
fixed: Fixed. Ok, the Segger File / Save... menu now sets the Save dialog …
11:02 AM Ticket #3152 (Toolbar icon rollover → crash) created by Elaine Meng
[…]
9:25 AM Ticket #3148 (pb_scene_coord returning None) closed by Tom Goddard
duplicate: Error showing pseudobonds fixed a month ago. Use a ChimeraX daily …
8:46 AM Ticket #3151 (Close session: clipper: 'SymmetryManager' object has no attribute ...) closed by Tristan Croll
fixed: This should be fixed in the latest version (for ChimeraX 0.93). Could …
8:24 AM Ticket #3149 (arrays moved to bundle) closed by pett
fixed
8:19 AM Ticket #3147 (Crash moving window) closed by pett
can't reproduce
4:35 AM Ticket #3151 (Close session: clipper: 'SymmetryManager' object has no attribute ...) created by perth2000.geo@…
[…] errorWhenSavingSession.rtf
4:15 AM Ticket #3150 (open/save severely hampered) created by Tristan Croll
[…]
1:39 AM Ticket #3149 (arrays moved to bundle) created by Tristan Croll
[…]

May 5, 2020:

8:56 PM ChangeLog edited by Greg Couch
(diff)
5:11 PM Ticket #3148 (pb_scene_coord returning None) created by rohou.alexis@…
[…]
3:25 PM Ticket #3146 (balloon help does not respond to camera change) closed by Tom Goddard
not a bug: It's not a bug. The popup atom names appear when you move the mouse …
12:16 PM Ticket #3147 (Crash moving window) created by chimerax-bug-report@…
[…]
11:28 AM Ticket #3146 (balloon help does not respond to camera change) created by Tristan Croll
[…]
10:27 AM Ticket #3138 (Build out full side-chains for MD simulations) closed by pett
fixed: Does the template give the hybridization of the heavy atom? If so, …
10:00 AM Ticket #3139 (Thread-safe Atom deletion) closed by pett
wontfix: Glad I didn't need to add my own comments about what a bad idea this …
7:41 AM Ticket #3145 (File history unreadable) created by chimerax-bug-report@…
[…]
7:14 AM Ticket #3144 (Map local resolution estimation) created by Tristan Croll
This is a really popular (and useful) tool to have these days - if …
1:21 AM Ticket #3143 (Starting simulation: Error initializing context: clGetDeviceIDs) created by florejo@…
[…]

May 4, 2020:

5:00 PM Ticket #3142 (Identify regions of unoccupied density) created by tic20@…
Begin forwarded message: From: Tristan Croll Subject: Re: ISOLDE and …
4:53 PM Ticket #3141 (Measure fit of residue in map) created by tic20@…
Begin forwarded message: From: Tristan Croll Subject: Re: ISOLDE and …
4:51 PM Ticket #3140 (Compute zone triangle mask in C++ thread) created by tic20@…
I'm not sure what is being requested here. To mask a map isn't a copy …
4:31 PM Ticket #3091 (ToolInstance.delete(self) during session reset produces KeyError) closed by Greg Couch
fixed: Believe this is fixed the #2110 fix -- removed maintaining a numerical …
4:28 PM Ticket #2110 (ToolInstance id problem restoring session) closed by Greg Couch
fixed: Removed ToolInstance.id since it no longer needed.
4:23 PM Ticket #3139 (Thread-safe Atom deletion) created by tic20@…
Tristan suggests using a shared pointer for Atom to avoid deleting the …
4:18 PM Ticket #3138 (Build out full side-chains for MD simulations) created by tic20@…
Tristan wants to be able to add atoms to make complete side-chains …
3:29 PM Ticket #3130 (Session saving: surface color is None) closed by Tom Goddard
fixed: Fixed. Session saving failed because a surface colored by height had …
1:57 PM Ticket #3134 (Attempt to retrieve context when no valid context) closed by Tom Goddard
can't reproduce: OpenGL error rendering status bar on an expose event. It is pretty …
1:46 PM Ticket #3136 (Graphics driver crash) closed by Tom Goddard
nonchimerax: Mac graphics driver bug, crash reports "Graphics hardware encountered …
1:43 PM Ticket #3133 (glBlitFramebuffer: invalid operation) closed by Tom Goddard
duplicate: This bug was fixed last week. Get current ChimeraX daily build. It …
1:41 PM Ticket #3132 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') closed by Tom Goddard
duplicate: Fixed 4 weeks ago.
11:51 AM Ticket #3137 (SeggerX and save dialog need updating) created by jaremko@…
[…]
10:17 AM Ticket #3015 (Crash in Finder(?)) closed by pett
can't reproduce
10:15 AM Ticket #2873 (PyQt icon image not changing) closed by pett
can't reproduce: Seems to have disappeared with a different version of Qt.
7:22 AM Ticket #3136 (Graphics driver crash) created by chimerax-bug-report@…
[…]
5:01 AM Ticket #3135 (OpenMM: Error initializing context: clGetPlatformIDs) created by r.caliebe@…
[…]

May 3, 2020:

6:31 PM Ticket #3134 (Attempt to retrieve context when no valid context) created by chimerax-bug-report@…
[…]

May 2, 2020:

2:55 PM Ticket #3133 (glBlitFramebuffer: invalid operation) created by huatiger3@…
[…]
7:51 AM Ticket #3132 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') created by chimerax-bug-report@…
[…]

May 1, 2020:

6:47 PM Ticket #3131 (Read CCD CIFs directly) created by goddard@…
[…] CRO.cif
6:20 PM Ticket #3029 (Add Color to Actions Menu) closed by pett
fixed
4:09 PM Ticket #3130 (Session saving: surface color is None) created by mfschmid@…
[…]
9:50 AM Ticket #3127 (Clicking file history thumbnail fails, ccp4 format not supported) closed by pett
fixed: Fixed and have restarted the builds.
9:45 AM Ticket #3129 (Model panel confirm close) created by Tristan Croll
[…]
9:42 AM Ticket #3128 (Open dialog generates 'open2' command) created by novakw@…
[…]

Apr 30, 2020:

8:03 PM Ticket #3109 (Error drawing selection outline) closed by Tom Goddard
fixed: Fixed. Another reporter of this problem (ticket #3125) verified that …
7:58 PM Ticket #3125 (glBlitFramebuffer() error drawing selection outline) closed by Tom Goddard
fixed: Fixed in tonight's ChimeraX builds. The Linux VMware OpenGL driver …
7:28 PM Ticket #3127 (Clicking file history thumbnail fails, ccp4 format not supported) created by goddard@…
[…]
6:20 PM Ticket #3124 (open2/save2 still used by dialogs) closed by pett
fixed: The fix is in the build currently on the web site.
4:34 PM Ticket #3126 (Nucleotide stub takes 10 minutes to display for ribosome) created by goddard@…
[…]
4:23 PM Ticket #3125 (glBlitFramebuffer() error drawing selection outline) created by florejo@…
[…]
3:16 PM Ticket #3124 (open2/save2 still used by dialogs) created by caillancm@…
[…]
2:27 PM Ticket #3123 (self.positions is None) created by caillancm@…
[…] non-rot-eco-4v9d-no-ssu.pdb
12:45 PM Ticket #3030 (Add Label to Actions Menu) closed by pett
fixed
11:00 AM Ticket #3122 (sse.py → scipy cannot import _uarray) closed by Tom Goddard
nonchimerax: scipy could not import one of its private compiled libraries _uarray …
1:02 AM Ticket #3122 (sse.py → scipy cannot import _uarray) created by chimerax-bug-report@…
[…]

Apr 29, 2020:

3:00 PM Ticket #3120 (setting fixed pixel height for labels → traceback) closed by Tom Goddard
fixed: Fixed. When the label command default_height option was added the …
2:48 PM Ticket #3121 (Better 2D label quality in saved images) closed by Tom Goddard
fixed: Fixed. 2d labels now adjust texture size for image saving and also …
2:40 PM Ticket #3121 (Better 2D label quality in saved images) created by goddard@…
[…]
2:15 PM Ticket #3119 (pseudobond's atoms pb_scene_coord is None(?)) closed by pett
duplicate: Hi Jeremy, Thanks for reporting this problem. It was fixed two days …
2:11 PM Ticket #3120 (setting fixed pixel height for labels → traceback) created by pett
[…]
1:26 PM Ticket #3117 (2D labels size wrong if saved image size not same as window size) closed by Tom Goddard
fixed: Fixed. 2D labels were stretched when saved image had different aspect …
12:54 PM Ticket #3119 (pseudobond's atoms pb_scene_coord is None(?)) created by jeremy.force@…
[…]
9:27 AM Ticket #3116 (computeSs documented as computeSS) closed by Elaine Meng
fixed: fixed in documentation for coordset, dssp, matchmaker, morph
9:17 AM Ticket #3118 (ISOLDE/OpenMM: trouble loading DLL) closed by Tristan Croll
fixed: This was caused by a bug in the Intel MKL library used by Numpy …
7:49 AM Ticket #3118 (ISOLDE/OpenMM: trouble loading DLL) created by chimerax-bug-report@…
[…]
7:22 AM Ticket #3117 (2D labels size wrong if saved image size not same as window size) created by vadim.kotov@…
[…] bug4.cxc
6:59 AM Ticket #3116 (computeSs documented as computeSS) created by vadim.kotov@…
[…] bug3.cxc

Apr 28, 2020:

1:58 PM Ticket #3062 (Adding images and descriptions to RBVI bundles) closed by pett
fixed: All the bundles assigned to me seem like they should be standard, and …
11:36 AM Ticket #2830 (Allow Toolshed uploads with dependencies on daily build bundles) closed by Greg Couch
fixed: Dependency check no longer prevents bundle submission.
11:28 AM Ticket #3113 (Surface caps: Array argument has non-numeric values) closed by Tom Goddard
duplicate: Fixed in July 31, 2019. Duplicate #2277
11:26 AM Ticket #3115 (Dead Volume Eraser still responding to events) closed by Tom Goddard
fixed: Fixed in tonight's ChimeraX builds. Map eraser mouse mode tried to …
6:29 AM Ticket #3115 (Dead Volume Eraser still responding to events) created by jporta@…
[…]
1:39 AM Ticket #3114 (Improve session-saving error information) created by Tristan Croll
[…]

Apr 27, 2020:

7:35 PM Ticket #3113 (Surface caps: Array argument has non-numeric values) created by chimerax-bug-report@…
[…]
4:18 PM Ticket #3112 (geometry.find_closest_points index problem(?)) closed by Tom Goddard
fixed: Fixed doc string. Now reads near1numpy int32 array A third array is …
10:54 AM Ticket #3111 (Errors restoring maps produces inconsistent state) closed by Tom Goddard
can't reproduce: There were many errors restoring this sessions where volume data …
8:39 AM Ticket #3110 (wrapped C/C++ object of type MultiColorButton has been deleted) closed by pett
can't reproduce
2:37 AM Ticket #3112 (geometry.find_closest_points index problem(?)) created by Tristan Croll
[…]

Apr 25, 2020:

4:30 PM Ticket #3111 (Errors restoring maps produces inconsistent state) created by chimerax-bug-report@…
[…]
3:49 PM Ticket #3110 (wrapped C/C++ object of type MultiColorButton has been deleted) created by chimerax-bug-report@…
[…]
11:34 AM Ticket #3109 (Error drawing selection outline) created by m_mlk@…
[…]

Apr 24, 2020:

7:26 PM Ticket #1532 (Improve deferring of subcommand registration) closed by Greg Couch
fixed
7:25 PM Ticket #2600 (Problem with "toolshed show") closed by Greg Couch
fixed: Done.
7:18 PM Ticket #1771 ("devel install" cannot link OpenMM.lib) closed by Greg Couch
fixed: Done.
4:33 PM Ticket #2250 (Simplify tool-author look up) closed by Conrad Huang
wontfix: For (2), until there is actually a high volume of new developers, just …
4:25 PM Ticket #3102 (volume subregion: 'NoneType' object has no attribute 'size') closed by Tom Goddard
fixed: Fixed. A clip cap of one map was colored by volume data value of …
4:23 PM Ticket #3022 (ISOLDE used with incompatible ChimeraX) closed by Greg Couch
fixed: 0.93 is out. This problem should not crop up with future versions.
3:52 PM Ticket #2771 (_openmm fails to load) closed by Greg Couch
fixed: Lastest numpy has the lastest MKL which has the fix. And is installed …
3:51 PM Ticket #2749 (ISOLDE installed into incompatible Ubuntu build of ChimeraX) closed by Greg Couch
fixed: Fixed by common Linux ABI
3:41 PM Ticket #2710 (Somewhat mysterious warning when building bundles) closed by Greg Couch
fixed: Testing has been removed from bundle builder.
3:34 PM Ticket #2694 (Autoscale ToolShed downloads graph widget) closed by Greg Couch
wontfix: Lost this functionality in the Python3 version of the toolshed. A CSV …
3:28 PM Ticket #2672 (Toolshed down) closed by Greg Couch
fixed
3:27 PM Ticket #2649 (Toolshed details does not display http link markup correctly.) closed by Greg Couch
fixed: Conrad fixed regex in Markdown.Converter.js.
3:05 PM Ticket #2618 (Web page to release bundles on Tool Shed is broken) closed by Greg Couch
fixed
2:01 PM Ticket #3025 (Installing bundle doesn't add its providers) closed by pett
fixed
1:27 PM Ticket #1666 (bundle_info.xml DataFormat classifier needs allow_directory option) closed by pett
fixed: The data-formats manager supports an "allow_directory" attribute.
1:14 PM Ticket #1976 ("is_default" does nothing in Open and Save ChimeraXClassifier) closed by pett
fixed: I believe the issue is moot at this point, but with the new …
12:57 PM Ticket #2592 (Can't install ISOLDE for everyone) closed by Greg Couch
duplicate: Work will be tracked in #2593.
12:39 PM Ticket #2444 (Weird import errors) closed by Conrad Huang
can't reproduce: Might be because user ran new version, resulting in new bundle cache, …
12:36 PM Ticket #2425 (ISOLDE cannot find symbol atomstruct::Residue::find_atom) closed by Greg Couch
fixed: Fixed by common Linux ABI.
12:33 PM Ticket #2174 (Could not install ISOLDE/Clipper: EnvironmentError) closed by Greg Couch
fixed: Can't install globally anymore.
12:30 PM Ticket #2087 (Problem with distutils-generated loader flags) closed by Greg Couch
fixed
12:27 PM Ticket #1961 (Toolshed US download map not colored) closed by Greg Couch
wontfix: GeoIP data costs real money now.
12:24 PM Ticket #1862 (Some funkiness installing wheels needing tilde expansion) closed by Greg Couch
fixed: Use os.path.expanduser() to expand ~.
12:16 PM Ticket #1845 ("toolshed install" errors reporting to status bar rather than log) closed by Greg Couch
duplicate: Work is happening in #3055.
12:14 PM Ticket #1819 (Problem with PyPI dependencies (or dependencies of dependencies?)) closed by Greg Couch
duplicate: Work is happening in #3055.
12:12 PM Ticket #1546 ("Nightly build" system for Tool Shed) closed by Greg Couch
duplicate: Duplicate of #1787.
12:09 PM Ticket #1786 (Naming of development bundles) closed by Greg Couch
fixed: We now conform to PEP 440 version numbers.
12:00 PM Ticket #1766 (Permission denied installing Clipper) closed by Greg Couch
fixed: No response.
11:58 AM Ticket #1686 ('ChimeraX -m pip install mdtraj' causes GUI to repeatedly flash up) closed by Greg Couch
wontfix: Conrad says "I can live with that".
11:57 AM Ticket #1672 (Library linking failure after ISOLDE install) closed by Greg Couch
fixed: Fixed by requiring all Linux binary bundles be built on the same …
11:55 AM Ticket #1650 (IncludeDir argument in bundle_info.xml no longer recognises $HOME) closed by Greg Couch
wontfix: Conrad says don't use $HOME.
11:53 AM Ticket #1640 ('toolshed install isolde reinstall true' attempts to install wrong ...) closed by Greg Couch
fixed: Workaround is use ~=VERSION in dependencies.
11:49 AM Ticket #1521 ('devel install' failing for RedHat rpm builds) closed by Greg Couch
fixed: The include files are now in the CentOS 7 rpm.
11:45 AM Ticket #1402 (Bundle's own compiled libraries should be at top of symbol search path) closed by Greg Couch
wontfix: Symbols from an already loaded library override subsequent loads.
11:35 AM Ticket #1278 (Option to only rebuild Python component of bundle) closed by Greg Couch
wontfix: setup.py might be smart enough to limit the compile to just the Python …
11:34 AM Ticket #1106 (Dependencies on other bundle's include dirs) closed by Greg Couch
duplicate: Dup of #1022.
11:33 AM Ticket #1104 (Installing ISOLDE gives traceback, needs user-friendly error message) closed by Greg Couch
fixed: ChimeraX no longer tries to install incompatible packages.
11:30 AM Ticket #1099 (PyPI dependency fail on 'make app-install') closed by Greg Couch
fixed: Using newer OpenSSL now.
11:28 AM Ticket #1089 (Option to recursively include contents of directory in bundle) closed by Greg Couch
fixed: Added <DataDir> option to <DataFiles> section in bundle_info.xml
11:25 AM Ticket #1022 (Allow Toolshed bundles to provide access to their C++ API) closed by Greg Couch
fixed: If bundle is dependent on another bundle, bundle_builder will add the …
11:23 AM Ticket #958 (Toolshed offers to install Linux bundle on Mac) closed by Greg Couch
fixed
11:05 AM Ticket #1646 (Clip broken + depth cueing question) closed by Tom Goddard
fixed: This problem was mostly solved by having the clip command warn when …
11:03 AM Ticket #3108 (Allow clip command to specify positions relative to center of rotation) created by olibclarke@…
Would like the "fromCenter true" option that Chimera has for setting …
10:59 AM Ticket #3107 (Enable depth cue with mesh lighting off) created by olibclarke@…
Currently depth cue is considered part of lighting and the setting …
10:59 AM Ticket #2805 (Update toolshed to Python3 and more recent django) closed by Greg Couch
fixed
10:57 AM Ticket #3106 (Side view shows wrong clip positions when near plane is behind far plane) created by olibclarke@…
Oliver Clarke accidentally put the near clip plane behind the far clip …
10:43 AM Ticket #2571 (No mail/feedback) closed by Greg Couch
can't reproduce: No response.
10:04 AM Ticket #3104 (Adjusting cage-builder edge length: 'NoneType' object has no attribute ...) closed by Tom Goddard
fixed: Fixed in tonight's ChimeraX build. The problem was not with edge …
9:33 AM Ticket #3103 (Strudel Score can't write its own config file) closed by pett
can't reproduce
9:22 AM Ticket #3105 (addh wrong hydrogen name on glycosylated Asn residues) created by Elaine Meng
When the asparagine is glycosylated, since there is only one hydrogen …
5:34 AM Ticket #3104 (Adjusting cage-builder edge length: 'NoneType' object has no attribute ...) created by esa-pekka.kumpula@…
[…]
5:08 AM Ticket #3103 (Strudel Score can't write its own config file) created by chimerax-bug-report@…
[…]
12:19 AM Ticket #2520 (ISOLDE synopsis in User Guide Index should link to ISOLDE website) closed by Greg Couch
fixed: Fixed getting generated user manual index with accessing via a href. …

Apr 23, 2020:

5:42 PM RestAPI edited by Tom Goddard
(diff)
5:39 PM RestAPI edited by Tom Goddard
(diff)
5:38 PM ChimeraXPhenix.docx attached to RestAPI by Tom Goddard
Tristan Croll, April 10, 2020 talks about advantages of Phenix / …
5:34 PM RestAPI edited by Tom Goddard
(diff)
5:31 PM RestAPI edited by Tom Goddard
(diff)
5:26 PM Remote interface discussion text.pdf attached to RestAPI by Tom Goddard
Tristan's October 1, 2019 description ChimeraX / Phenix communication
5:24 PM RestAPI created by Tom Goddard
5:14 PM Features edited by Tom Goddard
(diff)
2:20 PM Ticket #3102 (volume subregion: 'NoneType' object has no attribute 'size') created by chimerax-bug-report@…
[…]
1:46 PM Ticket #3101 (save mmCIF after opening PDB gives AttributeError: 'NoneType' object ...) closed by Greg Couch
duplicate: Duplicate of #3047. Fixed earlier today.
1:41 PM Ticket #2825 (Residue::find_atom() being looked for in isolde/libmolc.so) closed by Greg Couch
fixed: Now have common Linux ABI.
1:38 PM Ticket #3101 (save mmCIF after opening PDB gives AttributeError: 'NoneType' object ...) created by Elaine Meng
[…]
11:14 AM Ticket #3047 (Problem writing 'software' info to mmCIF) closed by Greg Couch
fixed
9:56 AM Ticket #3100 (IndexError during ribbon pick) closed by pett
duplicate: Hi Karim, Thanks for reporting this problem. It was fixed just a …
9:28 AM Ticket #3099 (auto-wipe some commands?) reopened by pett
Yeah, we're not fans of this particular paternalistic behavior. I …
9:12 AM Ticket #3099 (auto-wipe some commands?) closed by pett
wontfix: Yeah, actually neither the Actions menu nor the toolbar icons use the …
7:04 AM Ticket #3100 (IndexError during ribbon pick) created by karim.rafie@…
[…]
3:32 AM Ticket #3099 (auto-wipe some commands?) created by Tristan Croll
[…]

Apr 22, 2020:

5:00 PM Ticket #2634 (Crash clicking help-browser link) closed by Greg Couch
fixed: Does not crash on macOS 10.13 with current daily build that has Qt 5.12.8.
4:51 PM Ticket #2782 (Some help files crash ChimeraX) closed by Greg Couch
fixed: Unable to reproduce with daily build (Qt 5.12.8).
11:46 AM Ticket #3097 (Undeposited structure: 'NoneType' object has no attribute 'isupper') closed by pett
fixed: Fixed in the next build. The issue was with the HETNAM record for …
11:22 AM Ticket #3096 (Session restore failure: ValueError: int is not allowed for map key) closed by pett
duplicate: Hi Ondrej, This bug was fixed just yesterday, so if you get today's …
11:08 AM Covid19Grant edited by Tom Goddard
(diff)
11:07 AM Covid19Grant created by Tom Goddard
11:05 AM WikiStart edited by Tom Goddard
(diff)
11:03 AM WikiStart edited by Tom Goddard
(diff)
11:01 AM WikiStart edited by Tom Goddard
(diff)
10:33 AM Ticket #3098 (Add fitmap option to low pass filter before fitting) created by Tom Goddard
Would be convenient to have a fitmap command option to low pass filter …
7:39 AM Ticket #3097 (Undeposited structure: 'NoneType' object has no attribute 'isupper') created by Tristan Croll
[…]
12:10 AM Ticket #3096 (Session restore failure: ValueError: int is not allowed for map key) created by ogahura@…
[…]

Apr 21, 2020:

9:52 PM Ticket #2570 (Some help files crash ChimeraX) closed by Greg Couch
fixed: Just revised the daily build to use PyQt 5.12.3 with Qt 5.12.8. And I …
5:11 PM PhenixTools created by Tom Goddard
5:05 PM WikiStart edited by Tom Goddard
(diff)
4:11 PM Ticket #3084 (Inserted fragments should update missing-structure pseudobonds) closed by pett
fixed: The insertion now automatically updates the missing-structure …
3:14 PM Ticket #3059 (Toolshed bundle release page does not work) closed by Greg Couch
fixed: Works well enough for now.
2:38 PM Ticket #3095 (Crash in WebEngine trying to access Qt) closed by pett
can't reproduce: Hi Amedee, It looks like this crash occurred with the 0.8 version of …
2:28 PM Ticket #3093 (Error forming missing-structure pseudobonds to internally disconnected ...) closed by pett
fixed: Just pushed a fix.
2:18 PM Ticket #2625 (Problems with dependency version specifiers when uploading to Tool Shed) closed by Greg Couch
fixed: All of those version specifiers are now accepted.
12:19 PM Ticket #3095 (Crash in WebEngine trying to access Qt) created by adesgeorges@…
[…]
11:45 AM Ticket #3088 (Crash initializing OpenGL) closed by Tom Goddard
can't reproduce: Qt crashing trying to initialize some OpenGL on a window resize. …
11:21 AM Ticket #3086 (IndexError during ribbon pick) closed by Tom Goddard
fixed: Fixed. Sorted triangle ranges was not reset so had value from first …
10:41 AM Ticket #3094 (Ribbon error after deleting atoms) closed by Tom Goddard
fixed: Fixed. An empty ribbon residue range caused this error due to a bug …
10:29 AM Ticket #3089 (Session restore failure: ValueError: int is not allowed for map key) closed by Greg Couch
fixed: Fixed in the next daily build. Bug was due to change in msgpack 1.0 …
10:25 AM Ticket #3094 (Ribbon error after deleting atoms) created by goddard@…
[…]
10:04 AM Ticket #3090 (open2 not handling TIFF stack correctly) closed by pett
fixed: format-name checking also needed to check against prefixes
9:55 AM Ticket #3093 (Error forming missing-structure pseudobonds to internally disconnected ...) created by goddard@…
[…]
9:26 AM Ticket #3080 (ImportError: cannot import name 'RibbonDrawing' from ...) closed by Tom Goddard
duplicate: This was fixed 10 days ago. Get a current daily build. Problem is …
9:18 AM Ticket #3092 (pb_scene_coord returning None) closed by pett
duplicate: Hi Kasey, Thanks for reporting this problem. It has been fixed in …
9:04 AM Ticket #3087 (Sequence-association problem upon 'split') closed by pett
duplicate: Hi, I believe this problem is fixed in newer releases of ChimeraX. …
8:09 AM Ticket #3092 (pb_scene_coord returning None) created by kasey.jividen@…
[…]
7:58 AM Ticket #3091 (ToolInstance.delete(self) during session reset produces KeyError) created by chimerax-bug-report@…
[…]

Apr 20, 2020:

9:57 PM Ticket #3090 (open2 not handling TIFF stack correctly) created by goddard@…
[…]
5:51 PM Ticket #3089 (Session restore failure: ValueError: int is not allowed for map key) created by chimerax-bug-report@…
[…]
5:47 PM Ticket #3088 (Crash initializing OpenGL) created by chimerax-bug-report@…
[…]
4:58 PM Ticket #3087 (Sequence-association problem upon 'split') created by perth2000.geo@…
[…] split model.html split model-1.html
4:41 PM Ticket #3044 (document pseudobond group create_type arg) closed by pett
fixed: Okay, that argument is documented now.
4:15 PM Ticket #3086 (IndexError during ribbon pick) created by chimerax-bug-report@…
[…]
2:44 PM Ticket #3078 (ribbon cross section: unsupported operand type(s) for *: 'float' and ...) closed by Tom Goddard
fixed: Fixed. The helix tube radius is normally calculated for each helix. …
2:15 PM Ticket #3085 (sequence viewer messed up when fragment inserted into missing-structure gap) created by Tristan Croll
Doesn't crash it, but the deleted residues appear as missing and their …
2:12 PM Ticket #3084 (Inserted fragments should update missing-structure pseudobonds) created by Tristan Croll
summary pretty much covers it
11:53 AM Ticket #3083 (partially numeric residue name not handled by atom spec) closed by Conrad Huang
fixed: Fixed in 6f9e798ad. "92D" looks like "residue 92 insert …
11:42 AM Ticket #3074 (Mac Catalina prevent toolbar image save to desktop) closed by Tom Goddard
can't reproduce: macOS Catalina asks permission to access Downloads, Desktop and …
10:24 AM Ticket #3083 (partially numeric residue name not handled by atom spec) created by pett
in structure 5val, "sel :92D" does not select the ligand.
9:58 AM Ticket #3082 (Molecular Docking problem) closed by pett
not a bug: Redirected to chimera-users
9:56 AM Ticket #3081 (ISOLDE cannot link Residue::find_atom) closed by pett
duplicate
9:29 AM Ticket #3077 (pb_scene_coord: Cannot multiply Place times "None") closed by pett
duplicate
9:21 AM Ticket #3076 (run .cxc file) closed by pett
not a bug: Hi, The 'runscript' command is for executing Python scripts, not …
8:37 AM Ticket #3082 (Molecular Docking problem) created by star.fs@…
[…]
8:25 AM Ticket #3081 (ISOLDE cannot link Residue::find_atom) created by chimerax-bug-report@…
[…]
4:09 AM Ticket #3080 (ImportError: cannot import name 'RibbonDrawing' from ...) created by ubaumann@…
[…]

Apr 19, 2020:

10:04 PM Ticket #3079 (Registration failure (while plato was down)) created by chimerax-bug-report@…
[…]
6:41 AM Ticket #3078 (ribbon cross section: unsupported operand type(s) for *: 'float' and ...) created by ogahura@…
[…]

Apr 18, 2020:

2:09 PM Ticket #3075 (Slow coloring of large molecular surfaces) closed by Tom Goddard
fixed: Fixed. 100x faster now on 6owg test case (0.3 seconds instead of 30 …
7:17 AM Ticket #3077 (pb_scene_coord: Cannot multiply Place times "None") created by chimerax-bug-report@…
[…]
3:07 AM Ticket #3076 (run .cxc file) created by perth2000.geo@…
[…]

Apr 17, 2020:

8:55 PM Ticket #3067 (Bug reporter losing log text) closed by Greg Couch
fixed: Fixed.
7:18 PM Ticket #3075 (Slow coloring of large molecular surfaces) created by goddard@…
[…]
6:12 PM ChangeLog edited by pett
(diff)
3:50 PM Ticket #3073 (empty surfaces slow things down) closed by Tom Goddard
not a bug: ~surface is an alias for "surface hide". (The command "alias …
2:54 PM Ticket #3069 (Delete backbone atom while ribbon displayed: Cylinder end-point and ...) closed by Tom Goddard
fixed: Fixed. Deleting a CA atom for a residue showing a ribbon caused this …
12:49 PM Ticket #3074 (Mac Catalina prevent toolbar image save to desktop) created by chimerax-bug-report@…
[…]
11:43 AM Ticket #3072 ("chains" that are not polymers) closed by pett
not a bug: Well, obviously a chain is a series of connected polymeric residues, …
11:31 AM Ticket #3073 (empty surfaces slow things down) created by Tristan Croll
[…]
11:18 AM Ticket #3070 (Inter-residue bonds should not select residues) closed by pett
fixed
10:35 AM Ticket #3066 (Actions menu: no visible models produces error) closed by pett
fixed
9:56 AM Ticket #3072 ("chains" that are not polymers) created by Tristan Croll
[…]
9:34 AM Ticket #3071 (Crash in ~Structure) closed by pett
can't reproduce: old version of ChimeraX
9:22 AM Ticket #3071 (Crash in ~Structure) created by chimerax-bug-report@…
[…]
8:19 AM Ticket #3070 (Inter-residue bonds should not select residues) created by Tristan Croll
[…]
12:29 AM Ticket #3069 (Delete backbone atom while ribbon displayed: Cylinder end-point and ...) created by Tristan Croll
[…]
Note: See TracTimeline for information about the timeline view.