Timeline



Dec 10, 2018:

7:14 PM Ticket #1517 (Crash while reading in a volume) closed by Tom Goddard
can't reproduce: Although the user says they were opening a volume the crash happened …
6:30 PM Ticket #1509 ('vr update' produces a lot of errors if the 'head' file isn't found) closed by Tom Goddard
fixed: Fixed. Specifying a non-existent face image in the meeting command …
3:26 PM Ticket #1515 (Make StructureArg more flexible) closed by Tom Goddard
fixed: Done.
1:53 PM Ticket #1519 (Restrict open/save keyword handling to those relevant for that format) created by Eric Pettersen
Currently all keywords registered for open (or save) apply regardless …
1:36 PM 2018-12-10 edited by Elaine Meng
(diff)
1:25 PM 2018-12-10 created by Conrad Huang
12:16 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:03 PM Ticket #1518 (Clipper: No matching distribution found) created by Greg Couch
[…]
11:46 AM Ticket #1514 (StructureArg parsing: name 'AnnotationError' is not defined) closed by Eric Pettersen
fixed: Tristan, Thanks for the heads up. When atomic argument parsing moved …
11:24 AM Ticket #1517 (Crash while reading in a volume) created by chimerax-bug-report@…
[…]
6:36 AM Ticket #1516 (command-line breaks when a command is a prefix of another command ...) created by Tristan Croll
I *think* this has been triggered because I defined a set of commands …
5:33 AM Ticket #1515 (Make StructureArg more flexible) created by Tristan Croll
A minor thing, but I'd like to propose the below modification to …
5:25 AM Ticket #1513 (Add crystallographic reflection files to command-line open) closed by Tristan Croll
fixed: Never mind. All sorted out.
4:43 AM Ticket #1511 (Crash in ISOLDE MDFF_Mgr destructor) closed by Tristan Croll
duplicate: This is a known bug, fixed in my development builds. I'll be releasing …
4:19 AM Ticket #1514 (StructureArg parsing: name 'AnnotationError' is not defined) created by tic20@…
[…]

Dec 9, 2018:

2:06 PM Ticket #1513 (Add crystallographic reflection files to command-line open) created by Tristan Croll
I'm currently working on integrating ISOLDE and Clipper into the …
11:36 AM Ticket #1512 (No suitable models found for ViewDockX) created by chimerax-bug-report@…
[…]
10:11 AM Ticket #1511 (Crash in ISOLDE MDFF_Mgr destructor) created by guillermo.montoya@…
[…]
7:12 AM Ticket #1510 (Crash as DockWidet changes size) created by j.r.lewandowski@…
[…]

Dec 7, 2018:

2:48 PM Ticket #1509 ('vr update' produces a lot of errors if the 'head' file isn't found) created by chimerax-bug-report@…
[…]
2:38 PM Ticket #1508 (device vr true: openvr.OpenVRError: b'VRInitError_Init_HmdNotFound') created by wilian.cortopassi@…
[…]

Dec 6, 2018:

6:12 PM Ticket #1507 (Advise user of fixed bugs when error occurs) created by Tom Goddard
Would be nice if our error dialog could check if the traceback …
5:32 PM Ticket #1505 (Surface capping and Side View both wrong) closed by Tom Goddard
not a bug: This is a bit weird but I don't think there is any bug here and the …
5:28 PM 2018-11-29 edited by Eric Pettersen
(diff)
4:15 PM Ticket #1188 (ChimeraX should ask before registering itself as default application ...) closed by Greg Couch
nonchimerax: ChimeraX never installs itself as the default viewer -- it uses …
2:19 PM Ticket #1506 (Non-existent attribute tests wong) created by Eric Pettersen
open 1gcn sel @@serial_num=255 The above selects everything, despite …
2:09 PM Ticket #1505 (Surface capping and Side View both wrong) created by olibclarke@…
[…] Screen Shot 2018-12-06 at 5.07.44 PM.png​
1:11 PM Ticket #1165 (Ramachandran plot in ISOLDE (libbz2.so.1.0 not found)) closed by Greg Couch
fixed: matplotlib doesn't refer to libbz anymore.
10:16 AM Ticket #1427 (offscreen rendering fails) closed by Greg Couch
fixed: (libGLX, mentioned below was incorrect. Library should have been …

Dec 5, 2018:

5:05 PM Ticket #1504 ('close' with VR on: object of type 'NoneType' has no len()) created by chimerax-bug-report@…
[…]
3:49 PM Ticket #1503 (Side View wrong) closed by Tom Goddard
fixed: Fixed. Side view code was modifying camera position in an incorrect …
3:10 PM Ticket #1503 (Side View wrong) created by olibclarke@…
[…] Screen Shot 2018-12-05 at 6.09.00 PM.png​
12:40 PM Ticket #1502 (menu undo/redo not logged) closed by Conrad Huang
fixed: Fixed in d25c8fac1. Menu items for undo/redo were …
11:28 AM ChangeLog edited by Elaine Meng
(diff)
11:24 AM Ticket #1502 (menu undo/redo not logged) created by Elaine Meng
when I use the menu to undo, nothing is added to the Log. Shouldn’t …

Dec 4, 2018:

6:09 PM Ticket #1501 (VR drag: Cannot multiply Place times "None") closed by Tom Goddard
fixed: Fixed. Error happened when one hand controller is turned on when the …
5:43 PM Ticket #1500 (Errorpalooza) closed by Tom Goddard
fixed: 4) Fourth traceback was from click on gui panel in VR and then hiding …
4:23 PM Ticket #1501 (VR drag: Cannot multiply Place times "None") created by chimerax-bug-report@…
[…]
2:17 PM Ticket #1500 (Errorpalooza) created by chimerax-bug-report@…
[…]
2:08 PM Ticket #1499 (Model splitting: KeyError: (15, 1)) closed by Tom Goddard
fixed: Fixed. Splitting an atomic model that was not at the top level of the …

Dec 3, 2018:

4:45 PM Ticket #1497 (OpenGL graphics error while starting up + glGenVertexArrays error) closed by Tom Goddard
nonchimerax: As the ChimeraX error said, update your graphics driver if possible: …
3:40 PM Ticket #1499 (Model splitting: KeyError: (15, 1)) created by chimerax-bug-report@…
[…]
2:57 PM Ticket #1467 (Cache should distinguish between database sources) closed by Conrad Huang
fixed: Fixed in 6e0a23e47. The "mmcif" bundle always used "PDB" …
2:23 PM Ticket #1473 ('cartoon style' doesn't update arrows unless arrowScale is explicitly ...) closed by Conrad Huang
fixed: Fixed in 6c1f064fc.
2:00 PM Ticket #1486 (Ribbon slowing graphics enormously for large models) closed by Conrad Huang
fixed: Added change in 028ed3a4e.
11:44 AM Ticket #1498 (Atom spec parsing: '<' not supported between instances of 'int' and ...) closed by Conrad Huang
fixed: Probably fixed by 256c79188. Atomspecs like #0-1 will …
11:04 AM Ticket #456 (Update surface zone when surface changes) closed by Tom Goddard
fixed: Surface zone update was added more than 6 months ago.
8:48 AM Ticket #1498 (Atom spec parsing: '<' not supported between instances of 'int' and ...) created by chimerax-bug-report@…
[…]

Dec 2, 2018:

7:54 AM Ticket #1497 (OpenGL graphics error while starting up + glGenVertexArrays error) created by elvis.marti@…
[…]

Dec 1, 2018:

9:39 PM Ticket #1493 (Help Viewer: "help help:user": KeyError: 'href') closed by Greg Couch
duplicate: Can't reproduce. Probably duplicate of #1381 which has been fixed in …

Nov 30, 2018:

3:34 PM Ticket #1494 (Cage Builder: name 'place_model' is not defined) closed by Tom Goddard
duplicate: Fixed a couple weeks ago. Your ChimeraX is from Nov 11 before the fix.
2:29 PM Ticket #493 (measure phi/psi/chi/omega angles) closed by Eric Pettersen
fixed: Residue phi/phi/omega/chi1-4 angles can be get/set via corresponding …
12:55 PM Ticket #1494 (Cage Builder: name 'place_model' is not defined) created by Scooter Morris
[…]
11:45 AM Ticket #1493 (Help Viewer: "help help:user": KeyError: 'href') created by chimerax-bug-report@…
[…]
10:44 AM Ticket #1492 (Crash doing *something* with a DockWidget) closed by Eric Pettersen
can't reproduce
10:29 AM Ticket #1492 (Crash doing *something* with a DockWidget) created by chimerax-bug-report@…
[…]

Nov 29, 2018:

7:06 PM 2018-11-29 edited by Conrad Huang
(diff)
6:41 PM ChangeLog edited by Tom Goddard
(diff)
6:39 PM Ticket #1475 (Make right mouse do translation) closed by Tom Goddard
fixed: Fixed. Made right mouse button do translation by default. Middle …
6:33 PM Ticket #1460 (linux swap interval code breaks offscreen rendering) closed by Tom Goddard
fixed: Fixed. Linked _graphics.so against libGLX.so on Linux. The vsync …
6:31 PM Ticket #1466 (Can't save offscreen image) closed by Tom Goddard
fixed: Fixed. The draw target for OSMesa needed to be GL_FRONT instead of …
5:58 PM 2018-11-29 edited by Conrad Huang
(diff)
5:46 PM 2018-11-29 edited by Conrad Huang
(diff)
5:00 PM Ticket #1488 (Old import of 'map') closed by Tom Goddard
fixed: Fixed. Bug in "color sample" command importing map module from …
4:28 PM Ticket #1164 (port filled rings from Chimera) closed by Greg Couch
fixed: Ported. For now commands are: […]
4:17 PM 2018-11-29 edited by Elaine Meng
(diff)
4:15 PM 2018-11-29 edited by Elaine Meng
(diff)
4:14 PM 2018-11-29 edited by Elaine Meng
(diff)
3:08 PM 2018-11-29 created by Conrad Huang
2:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:52 PM 2018-11-15 edited by Eric Pettersen
(diff)
1:51 PM 2018-11-15 edited by Eric Pettersen
(diff)
1:49 PM 2018-11-15 edited by Eric Pettersen
(diff)
1:10 PM Ticket #1491 (bundleinfo.xml tag for compiling executables) created by Eric Pettersen
Analogous to the CModule tag, I would like a CExecutable flag (or some …
11:49 AM Ticket #1490 (add support for displayedOnly to mmCIF writer) created by Greg Couch
It would be nice if the mmCIF writer, like the PDB writer, could limit …
11:40 AM Ticket #1489 (limit PDB output to only include HELIX and SHEET records for included atoms) created by Greg Couch
And example of when there should be no HELIX nor SHEET records: […] …
1:30 AM Ticket #1488 (Old import of 'map') created by chimerax-bug-report@…
[…]

Nov 28, 2018:

5:08 PM Ticket #1485 (Inadequate OpenGL) closed by Tom Goddard
can't reproduce: Strangely it seemed to get an OpenGL 3.3 context butt …
5:05 PM Ticket #1487 (Matrix reuse (optimization) problem) closed by Tom Goddard
fixed: Fixed. Problem is that Place instances are reused. So holding a …
1:58 PM Ticket #1487 (Matrix reuse (optimization) problem) created by Elaine Meng
This problem screws up saving moved structures to PDB files, and …
4:59 AM Ticket #1486 (Ribbon slowing graphics enormously for large models) created by Tristan Croll
There is a bug in the ribbon code of structure.py causing the number …

Nov 27, 2018:

5:16 PM 2018-11-15 edited by Eric Pettersen
(diff)
5:05 PM Ticket #1372 (Crash during QTimer (status line?)) closed by Eric Pettersen
can't reproduce: No response.
4:17 PM Ticket #1485 (Inadequate OpenGL) created by chimerax-bug-report@…
[…]
2:50 PM Ticket #851 (List ligands in log when opening structure) closed by Eric Pettersen
fixed: Now listed directly in log, though as a separate table.
11:19 AM 2018-11-15 edited by Eric Pettersen
(diff)
11:05 AM Ticket #1484 (Hiding labels: KeyError: 'setting changed') closed by Eric Pettersen
fixed
10:40 AM Ticket #1484 (Hiding labels: KeyError: 'setting changed') created by goddard@…
[…]
9:51 AM Ticket #1478 (OpenGL windows become unresponsive without error measasge) closed by Tom Goddard
can't reproduce: All indications were that ChimeraX was rendering graphics, but it did …

Nov 26, 2018:

4:25 PM Ticket #1483 (Allow web service request to be blocking) created by Eric Pettersen
Commands that invoke web services may well not want to return until …
3:17 PM Ticket #1477 (Volume Viewer: wrapped C/C++ object of type QFrame has been deleted) closed by Tom Goddard
can't reproduce: Appears to be a Toolshed bug in ChimeraX 0.7. User clicked close …
1:55 PM Ticket #1479 (Drawing not working) closed by Tom Goddard
duplicate: Log output for bug reported in #1478.
1:46 PM Ticket #1375 (implement wildcarding for atom specs) closed by Conrad Huang
fixed: Wildcard issues have been resolved here and in #1388
1:46 PM Ticket #1482 (bundle-ize WebServices + improve docs) created by Eric Pettersen
For better updatability and dependency declaration, core.WebServices …
11:39 AM Ticket #1481 (alt_loc crashes) created by Eric Pettersen
[…]
9:54 AM Ticket #1480 (Crash in isolde::MDFF_Mgr::destructors_done) closed by Tristan Croll
fixed: Never mind - I see my mistake. Now I'm wondering why it *doesn't* …
9:33 AM Ticket #1480 (Crash in isolde::MDFF_Mgr::destructors_done) created by tic20@…
[…] mdff.cpp​
8:48 AM Ticket #1479 (Drawing not working) created by tic20@…
[…]
8:24 AM Ticket #1478 (OpenGL windows become unresponsive without error measasge) created by Tristan Croll
Not sure what's happened here - Just messing about with visualisations …

Nov 23, 2018:

5:37 PM Ticket #1477 (Volume Viewer: wrapped C/C++ object of type QFrame has been deleted) created by chimerax-bug-report@…
[…]
11:08 AM ChangeLog edited by Elaine Meng
(diff)

Nov 22, 2018: