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Sep 30, 2019:

1:02 PM Ticket #2455 (Graphics/Orient now a placebo) closed by Greg Couch: fixed: It now gives an error message -- in this case, "dV - unknown …
12:13 PM Ticket #2455 (Graphics/Orient now a placebo) created by grahamj@…: […]
11:46 AM Ticket #2453 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by pett: duplicate
11:42 AM Ticket #2449 (2nd "camera stereo" → glDrawBuffer: invalid operation) closed by Tom Goddard: duplicate: Same bug as #2446 but with Quadro P5000 graphics. Will add a note to …
11:16 AM Ticket #2454 (RFE: Labels preference for (3D) label height) closed by Tom Goddard: fixed: Done. New settings is under the Labels tab in preferences "Height of …
10:27 AM Ticket #2454 (RFE: Labels preference for (3D) label height) created by Elaine Meng: There is already a Labels category in preferences. Since each user is …

Sep 27, 2019:

9:47 PM Ticket #2453 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by chimerax-bug-report@…: […]
8:43 PM Ticket #2450 (Various segmentation problems) closed by Tom Goddard: fixed: Fixed error opening segmentation (.seg) file written by Chimera. Fixed …
5:00 PM Ticket #2452 (protons not properly stripped in 3qm8 heme) created by pett: The angle check is bad, possibly because alt locs are involved?
1:34 PM Ticket #2451 (Tiling not working for volumes) created by yanxin@…: […]
11:52 AM Ticket #2450 (Various segmentation problems) created by jaremko@…: […]

Sep 26, 2019:

12:48 PM Ticket #2449 (2nd "camera stereo" → glDrawBuffer: invalid operation) created by satyshur@…: […]
11:53 AM Ticket #2448 ("swapaa interactive spec same" buggy) closed by pett: fixed: It was a problem with the handling of "same" for swapaa interactive. …
11:46 AM Ticket #2447 (selection visible through opaque surface after BILD file opened) closed by Tom Goddard: not a bug: This is a feature, not a bug. A while back I made selection outlines …
11:39 AM Ticket #2448 ("swapaa interactive spec same" buggy) created by Elaine Meng: […]
11:30 AM Ticket #2447 (selection visible through opaque surface after BILD file opened) created by Elaine Meng: This is definitely an obscure situation, but reproducible... file as …
9:40 AM Ticket #2446 (Camera stereo → glDrawBuffer: invalid operation) created by satyshur@…: […]
9:30 AM Ticket #2445 (Undesirable center of rotation) created by satyshur@…: […]
8:36 AM Ticket #2444 (Weird import errors) created by chimerax-bug-report@…: […]

Sep 25, 2019:

3:46 PM Ticket #2443 ("graphics restart" failure) closed by Tom Goddard: duplicate: Same problem as #2442. Use ChimeraX daily build.
3:43 PM Ticket #2442 (camera stereo → glDrawBuffer: invalid operation) closed by Tom Goddard: can't reproduce: Please try the ChimeraX daily build. I believe I made a change a few …
3:12 PM Ticket #2443 ("graphics restart" failure) created by satyshur@…: […]
2:47 PM Ticket #2441 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by pett: duplicate: Hi Bryan, This bug was only in the daily build for less than a day …
2:26 PM Ticket #2442 (camera stereo → glDrawBuffer: invalid operation) created by satyshur@…: […]
2:11 PM Ticket #2441 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by hansenbry@…: […]
10:32 AM Ticket #2440 (GUI panels are all blank) closed by Tom Goddard: nonchimerax: From: Pascal Albanese UU Subject: Re: [chimerax-users] GUI not …
10:31 AM Ticket #2440 (GUI panels are all blank) created by p.albanese@…: On Sep 23, 2019, at 7:26 AM, Pascal Albanese UU wrote: Hi Chimera …

Sep 24, 2019:

7:12 PM Ticket #2439 (Linux crash) created by zhengw2013@…: […]
12:36 PM Ticket #2438 (should object models (e.g. from BILD) be selectable?) created by Elaine Meng: This has many of the same pros and cons as making labels selectable …
11:31 AM Ticket #2437 (ISOLDE/Clipper: 'NXmapHandler' object has no attribute 'set_display_style') closed by Tristan Croll: duplicate: Duplicate of #2214.
11:30 AM Ticket #2436 (ISOLDE/Clipper: 'Atoms' object has no attribute 'transform') closed by Tristan Croll: duplicate
7:34 AM Ticket #2437 (ISOLDE/Clipper: 'NXmapHandler' object has no attribute 'set_display_style') created by ne272@…: […]
6:58 AM Ticket #2436 (ISOLDE/Clipper: 'Atoms' object has no attribute 'transform') created by ne272@…: […]

Sep 23, 2019:

11:38 AM Ticket #2435 (Select menu protein, nucleic acid, ribose should be under Chemistry ...) created by Elaine Meng: protein, nucleic acid, ribose are chemically defined and make more …

Sep 22, 2019:

9:58 AM Ticket #2434 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by pett: duplicate: Hi Ulrich, Thanks for reporting this problem. It is fixed in the …

Sep 21, 2019:

6:21 AM Ticket #2434 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by ubaumann@…: […]

Sep 20, 2019:

3:50 PM Ticket #2432 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by Greg Couch: fixed: My apologies. The fix didn't make it into our central repository. …
2:58 PM Ticket #2432 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by hyli.pasteur@…: […]
1:36 PM Ticket #2430 (Problem playing microscopy timepoints) closed by Tom Goddard: can't reproduce: The current ChimeraX daily build records a 360sbs movie of …
1:18 PM Ticket #2431 (Crash in free_keys_object/subtype_dealloc) closed by pett: can't reproduce: pre-Qt 5.12.5
1:09 PM Ticket #2431 (Crash in free_keys_object/subtype_dealloc) created by chimerax-bug-report@…: […]
11:37 AM Ticket #2430 (Problem playing microscopy timepoints) created by vbindoka@…: […]
11:21 AM Ticket #2429 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by pett: duplicate: Hi Karim, Thanks for reporting this problem. It is fixed now, so if …
11:20 AM Ticket #2428 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by pett: fixed
11:18 AM Ticket #2427 (Crash due to NULL sseq.structure pointer) closed by pett: can't reproduce
8:16 AM Ticket #2429 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by karim.rafie@…: […]
4:40 AM Ticket #2428 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by chimerax-bug-report@…: […]
1:47 AM Ticket #2427 (Crash due to NULL sseq.structure pointer) created by chimerax-bug-report@…: […]

Sep 19, 2019:

6:55 PM Ticket #2426 (Use special wildcards {t},{c},{z} for opening microscopy TIFF series) closed by Tom Goddard: fixed: Done. I added special wildcards {t}, {c}, {z} that can be used in the …
6:35 PM Ticket #2426 (Use special wildcards {t},{c},{z} for opening microscopy TIFF series) created by goddard@…: […]
10:27 AM Ticket #2425 (ISOLDE cannot find symbol atomstruct::Residue::find_atom) created by chimerax-bug-report@…: […]
9:17 AM Ticket #2424 (Array of coordinates is None) created by chimerax-bug-report@…: […]
3:32 AM Ticket #2423 (Sequence viewer fails on edited chain) created by Tristan Croll: […]

Sep 18, 2019:

3:54 PM Ticket #2376 (File history and/or "open" command converting \t to tab) closed by Greg Couch: fixed: Fixed. Working on more general solution. Each *Arg class will …
3:49 PM Ticket #2422 (reorder file formats suffixes for open/save dialogs) closed by Greg Couch: fixed: This is not a problem on Linux, because the file suffixes are not …
1:41 PM Ticket #2419 (Model.positions is None) closed by Tom Goddard: can't reproduce: This error saving a ChimeraX session is because something was …
1:30 PM Ticket #2421 ('MDFF_Mgr' object has no attribute '_c_pointer') closed by pett: nonchimerax: Okey dokey. :-)
1:05 PM Ticket #2422 (reorder file formats suffixes for open/save dialogs) created by Greg Couch: Would like the list of file format suffixes in the open/save dialogs …
11:37 AM Ticket #2421 ('MDFF_Mgr' object has no attribute '_c_pointer') created by Tristan Croll: […]
11:33 AM Ticket #2420 (Error with nucleotide/ring graphics after session restore) created by wenfeili@…: […] error2.png
11:22 AM Ticket #2418 (File→Open: unhashable type: 'set') closed by pett: duplicate: Hi Thor, This problem was just fixed, so if you get the most recent …
11:20 AM Ticket #2417 (File→Open: unhashable type: 'set') closed by pett: duplicate
11:19 AM Ticket #2416 (File→Open: unhashable type: 'set') closed by pett: fixed: Conrad fixed this one yesterday. --Eric
11:18 AM Ticket #2415 (File→Open: unhashable type: 'set') closed by pett: duplicate
10:49 AM Ticket #2419 (Model.positions is None) created by wenfeili@…: […] Screenshot from 2019-09-18 10-49-06.png
10:43 AM Ticket #2386 (Registration window obscured) closed by Conrad Huang: nonchimerax: This is Qt bug #49576, …
12:13 AM Ticket #2418 (File→Open: unhashable type: 'set') created by thor.thorsen@…: […]

Sep 17, 2019:

9:28 PM Ticket #2409 (File→Open: unhashable type: 'set') closed by Conrad Huang: fixed: Fixed in d1cafaf2d. Code added to report formats …
2:17 PM Ticket #2417 (File→Open: unhashable type: 'set') created by chimerax-bug-report@…: […]
1:26 PM Ticket #2405 (2dlabels creation/deletion sometimes not shown in Model Panel) closed by pett: fixed: Okay, model panel updates properly when "global tool unhide" occurs
12:47 PM Ticket #2416 (File→Open: unhashable type: 'set') created by Tristan Croll: […]
12:33 PM Ticket #2415 (File→Open: unhashable type: 'set') created by chimerax-bug-report@…: […]
11:43 AM Ticket #2414 (File→Open: unhashable type: 'set') closed by pett: duplicate: duplicate of #2409
11:37 AM Ticket #2413 (Crash in free_keys_object/subtype_dealloc) closed by pett: can't reproduce
8:27 AM Ticket #2414 (File→Open: unhashable type: 'set') created by chimerax-bug-report@…: […]
12:01 AM Ticket #2411 (Template fetching broken?) closed by Greg Couch: worksforme: Looks like a temporary failure. Just worked for me from home.
12:00 AM Ticket #2412 (Superfluous argument quoting) closed by Greg Couch: fixed: Fixed. _whitespace only find leading whitespace. Added …

Sep 16, 2019:

9:03 PM Ticket #2413 (Crash in free_keys_object/subtype_dealloc) created by chimerax-bug-report@…: […]
4:39 PM Ticket #2179 (Non-graphics windows blank after structure load) closed by pett: can't reproduce
4:23 PM Ticket #2375 (Shell tab-completion attempts import of non-Python libs) closed by pett: nonchimerax: I don't think there's anything I can do about this.
3:20 PM Ticket #2410 (self._positions is None) closed by Tom Goddard: duplicate: Duplicate. Fixed a while ago.
2:10 PM Ticket #2412 (Superfluous argument quoting) created by pett: The changes to argument processing/logging now cause unneeded …
2:05 PM Ticket #2411 (Template fetching broken?) created by pett: […]
11:48 AM Ticket #2406 (Bad startup-command error handling) closed by pett: fixed: Hi Daniel, There is something wrong with the commands you told …
11:36 AM Ticket #2404 (Toolbar context menu Hide Tool and Help don't work in full-window mode) closed by pett: duplicate: Largely a duplicate of #2297. Noted in #2297 to check this ticket to …
11:30 AM Ticket #2403 (Bad error reporting for startup-command errors) closed by pett: fixed
11:19 AM Ticket #2401 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') closed by pett: duplicate

Sep 15, 2019:

6:38 PM Ticket #2410 (self._positions is None) created by chimerax-bug-report@…: […]
6:32 AM Ticket #2409 (File→Open: unhashable type: 'set') created by chimerax-bug-report@…: […]

Sep 14, 2019:

2:16 PM Ticket #2408 (Cannot use Lenobo explorer for VR) created by rlehal@…: […]
12:40 AM Ticket #2407 (Problem saving session involving Clipper) created by coutandin@…: […]

Sep 13, 2019:

1:57 PM Ticket #2370 ((atomic) model: self.positions is None) closed by Tom Goddard: can't reproduce: It appears some ChimeraX tool tried to save a closed model in the …
1:54 PM Ticket #2399 (Crash handling Qt event) closed by Tom Goddard: nonchimerax: This is a crash in the OpenGL graphics driver. Apple's OpenGL …
10:58 AM Ticket #2402 (ViewDockX should facilitate correct receptor vs. ligand classification ...) closed by Elaine Meng: fixed: Fixed in Maestro tool version 1.3 as discussed in the comments for #2343.
10:45 AM Ticket #2343 (ViewDockX up/down arrow actions should log the corresponding commands) closed by Conrad Huang: fixed: Okay, receptors from Maestro files no longer get ViewDock attributes …
10:08 AM Ticket #2406 (Bad startup-command error handling) created by coutandin@…: […]

Sep 12, 2019:

11:44 PM Ticket #2395 (open of filetype in unloaded bundle should let user install bundle) closed by Conrad Huang: fixed: Fixed in f10025b5b. The text can probably stand some …
4:39 PM Ticket #2405 (2dlabels creation/deletion sometimes not shown in Model Panel) created by Elaine Meng: Image attached: I created a label with symbols and another with text, …
3:51 PM Ticket #2404 (Toolbar context menu Hide Tool and Help don't work in full-window mode) created by Elaine Meng: By full-window mode I mean when you use the icon to make the graphics …
2:06 PM Ticket #2403 (Bad error reporting for startup-command errors) created by chimerax-bug-report@…: […]
12:03 PM Ticket #2402 (ViewDockX should facilitate correct receptor vs. ligand classification ...) created by Elaine Meng: Suggestions are that ViewDockX should either: (A) read the …
12:38 AM Ticket #2401 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') created by chimerax-bug-report@…: […]

Sep 11, 2019:

5:15 PM Ticket #2400 (KeyError from item chooser) closed by pett: duplicate: Hi, I believe this problem was fixed on 8/14, so just after the …
9:17 AM Ticket #2400 (KeyError from item chooser) created by s.gutierrez@…: […]
8:33 AM Ticket #2398 (2D label fading broken) closed by pett: duplicate: Hi Gabor, This problem was fixed just yesterday, so as you noticed it …
7:56 AM Ticket #2399 (Crash handling Qt event) created by ubaumann@…: […]
12:40 AM Ticket #2398 (2D label fading broken) created by papai@…: […]

Sep 10, 2019:

7:59 PM Ticket #2397 (Crash in save-image dialog?) closed by Tom Goddard: nonchimerax: Appears to have crashed on mouse button release on a QToolButton that …
7:52 PM Ticket #2396 (Crash in graphics driver (chrome backend?) after ctypes call) closed by Tom Goddard: nonchimerax: Crash in Mac graphics driver. Unfortunately Apple graphics drivers …
4:25 PM Ticket #2298 (2dlabels fading broken) closed by pett: fixed
8:29 AM ChangeLog edited by Elaine Meng: (diff)
7:39 AM Ticket #2397 (Crash in save-image dialog?) created by chimerax-bug-report@…: […]
2:53 AM Ticket #2396 (Crash in graphics driver (chrome backend?) after ctypes call) created by kakayast@…: […]

Sep 9, 2019:

5:10 PM Ticket #2380 (surface hide/show wonky) closed by Tom Goddard: fixed: Fixed. Would be useful if the documentation clarified that "surface …
3:54 PM Ticket #2388 (surface coloring error after swapaa) closed by Tom Goddard: fixed: Fixed. Tried to use remembered molecular surface atom patch colors …
3:26 PM Ticket #2390 (Changing 2D label to be very large fails) closed by Tom Goddard: fixed: Fixed. Error was from label with empty text, resulting in 0 size …
2:00 PM Ticket #2395 (open of filetype in unloaded bundle should let user install bundle) created by Greg Couch: Like the case when a command is typed that is provided by a bundle …
12:46 PM Ticket #2391 (Surface cap not colored) closed by Tom Goddard: not a bug: To color a surface cap you would have to use the color zone command. …
12:38 PM Ticket #2393 (open 0069 fromDatabase emdb: MRC file is truncated) closed by Tom Goddard: not a bug: As the error message says, the MRC file was truncated. In fact I can …
11:37 AM Ticket #2392 (2D labels: local variable 'lm' referenced before assignment) closed by pett: duplicate: Hi Stephan, Thanks for reporting this problem. We fixed this issue …
9:45 AM Ticket #2394 (Residues added to protein chain save out of order in PDB) created by Tristan Croll: If I add a residue to a protein chain (e.g. to the N-terminus using …
7:35 AM Ticket #2393 (open 0069 fromDatabase emdb: MRC file is truncated) created by maria.anastasina@…: […]
3:45 AM Ticket #2392 (2D labels: local variable 'lm' referenced before assignment) created by tetterst@…: […]
1:16 AM Ticket #2391 (Surface cap not colored) created by susan.lea@…: […]

Sep 6, 2019:

3:45 PM Ticket #2390 (Changing 2D label to be very large fails) created by goddard@…: […]
3:06 PM Ticket #2384 (Excessive status output) closed by pett: fixed: Cut way back on the status message output by having swapaa silence the …
3:04 PM Ticket #2385 (Wrong default criteria) closed by pett: fixed: Upgraded the way the 'd' criteria is handled. If one map is open, …
2:13 PM Ticket #2389 (Graphics buffer deletion problem for "split" after "surface") closed by Tom Goddard: duplicate: Fixed yesterday but last night's builds failed. Duplicate of #2383.
2:04 PM Ticket #2381 (Add hbonds clear and distance clear subcommands) closed by pett: fixed: Implemented "dist/hb delete" as equivalents for ~dist/~hb
1:57 PM Ticket #2389 (Graphics buffer deletion problem for "split" after "surface") created by Elaine Meng: […]
1:12 PM Ticket #2387 (Alt loc issues) closed by pett: fixed: ChimeraX chooses alt locs by looking at connected groups of alt locs …
10:40 AM Ticket #2388 (surface coloring error after swapaa) created by goddard@…: […]
3:12 AM Ticket #2387 (Alt loc issues) created by Tristan Croll: […]
1:33 AM Ticket #2386 (Registration window obscured) created by rjr27@…: […]

Sep 5, 2019:

11:52 PM Ticket #2385 (Wrong default criteria) created by goddard@…: […]
11:37 PM Ticket #2384 (Excessive status output) created by goddard@…: […]
10:49 PM Ticket #2383 (surface close causes OpenGL buffer delete error) closed by Tom Goddard: fixed: Fixed. OpenGL buffers not deleted due to indentation error. Bug …
10:13 PM Ticket #2382 (mlp error: ValueError: list.remove(x): x not in list) closed by Tom Goddard: fixed: Fixed I think. Could not reproduce. The mlp command created volume …
5:56 PM Ticket #2383 (surface close causes OpenGL buffer delete error) created by goddard@…: […]
5:21 PM Ticket #2382 (mlp error: ValueError: list.remove(x): x not in list) created by goddard@…: […]
5:20 PM Ticket #2379 (traceback when closing seq viewer with multiple chains associated) closed by pett: fixed: A previous fix to stop a memory leak resulting in some data structures …
5:13 PM Ticket #2381 (Add hbonds clear and distance clear subcommands) created by goddard@…: […]
5:06 PM Ticket #2378 (Crash in free_keys_object/subtype_dealloc) closed by pett: can't reproduce: This crash seems to be reported roughly once a week, with no …
4:48 PM Ticket #2380 (surface hide/show wonky) created by pett: "surface show" seems busted. Ergo: open 3fx2 surface shows …
4:35 PM Ticket #2379 (traceback when closing seq viewer with multiple chains associated) created by goddard@…: […] seqbug.cxs
2:11 PM Ticket #2378 (Crash in free_keys_object/subtype_dealloc) created by chimerax-bug-report@…: […]
12:29 PM Ticket #2377 (Add command to assign VR buttons) closed by Tom Goddard: fixed: I added the command "vr button" to assign VR hand controller buttons …
12:18 PM Ticket #2377 (Add command to assign VR buttons) created by lucien.krapp@…: […]
3:17 AM Ticket #2376 (File history and/or "open" command converting \t to tab) created by juha.vahokoski@…: […]

Sep 4, 2019:

5:41 PM Ticket #2108 (Session adds non-statemanager to list of state managers) closed by pett: fixed: After a lot of headache-inducing code examination, concluded it would …
10:45 AM 2019-08-29 created by Conrad Huang
10:25 AM DeveloperMeetings edited by Conrad Huang: (diff)
3:37 AM Ticket #2375 (Shell tab-completion attempts import of non-Python libs) created by Tristan Croll: […]

Sep 3, 2019:

5:23 PM Ticket #2371 (FileNotFoundError re-reading map file) closed by Tom Goddard: duplicate: Newer ChimeraX versions give a user-friendly error message describing …
4:17 PM Ticket #2360 (Show clipping caps: Array argument has non-numeric values) closed by Tom Goddard: duplicate: Duplicate of #2277. Fixed a month ago.
2:40 PM Ticket #2369 (swapaa failure for non-rotameric side chains) closed by pett: fixed: Logic to check for no rotamers was no longer correct due to changes to …
2:14 PM Ticket #2367 (volume eraser: output array is read-only) closed by pett: duplicate: Hi Stephan, Thanks for reporting this problem. It was fixed 6 days …
2:10 PM Ticket #2366 (Bad pointer freed) closed by pett: duplicate: Seems to be the exact same crash as #2356. Would be nice to have more …
12:52 PM Ticket #2374 (ISOLDE: multiple different errors) created by chimerax-bug-report@…: […]
8:57 AM Ticket #2373 (Registration failure) created by chimerax-bug-report@…: […]
7:03 AM Ticket #2372 (Crash during script execution) created by papai@…: […] SAGA-intro.cxc
5:10 AM Ticket #2371 (FileNotFoundError re-reading map file) created by chimerax-bug-report@…: […]
2:51 AM Ticket #2370 ((atomic) model: self.positions is None) created by sitins07@…: […]
2:43 AM Ticket #2369 (swapaa failure for non-rotameric side chains) created by Tristan Croll: […]
2:38 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) created by Tristan Croll: More of a query than anything else: when adding a residue to a chain …
12:23 AM Ticket #2367 (volume eraser: output array is read-only) created by tetterst@…: […]
12:04 AM Ticket #2331 (Better session error reporting) closed by Greg Couch: fixed: Added code to keep track of where data is saved from in a session, and …

Aug 31, 2019:

3:33 PM Ticket #2366 (Bad pointer freed) created by chimerax-bug-report@…: […]

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