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Timeline
Oct 30, 2018:
- 11:31 PM Ticket #1399 (Crash reading PDB file) created by
- […]
- 4:31 PM Ticket #1397 (All sessions broken) closed by
- fixed: msgpack-python was explicitly being installed in prereqs/msgpack, in …
- 4:29 PM Ticket #1393 (Crash reading PDB file with non-ASCII characters) closed by
- fixed: Hi Tom, Thanks for reporting the bug. Fixed in the next daily build. …
- 3:11 PM Ticket #1395 (Sequence session-restore failure: get_class() missing 1 required ...) closed by
- fixed: Pushed a fix; can't test until #1397 fixed
- 2:34 PM ChangeLog edited by
- (diff)
- 1:05 PM Ticket #1398 (Open pdbdev 10: File is not a zip file) created by
- […]
- 12:58 PM Ticket #1397 (All sessions broken) created by
- The changes to support tinyarray now cause all session restores to …
- 12:31 PM ChangeLog edited by
- (diff)
- 11:18 AM Ticket #638 (Linux OpenBLAS library threading problems) closed by
- fixed: Applied workaround in 5f7cc9259. Should be in daily build …
- 1:43 AM Ticket #1396 (PC requires restart to launch ChimeraX a second time) created by
- […]
- 1:41 AM Ticket #1395 (Sequence session-restore failure: get_class() missing 1 required ...) created by
- […]
Oct 29, 2018:
- 10:50 PM Ticket #1392 (Problem parsing mmCIF: unexpected left bracket) closed by
- not a bug: That file is illegal according to the CIF standard. [ and ] are …
- 7:21 PM Ticket #1393 (Crash reading PDB file with non-ASCII characters) created by
- […] DQ8trans_012_AKM-GKP.pdb
- 5:51 PM Ticket #1392 (Problem parsing mmCIF: unexpected left bracket) created by
- […] 1bep_assembly.cif
- 3:46 PM Ticket #1368 (Camera 360tb crash) closed by
- fixed: Works for me. Probably a bug that was fixed within days after your …
- 3:41 PM Ticket #1391 (Report map statistics) closed by
- fixed: Added "measure mapstats" command. measure mapstats [volumes] [step …
- 3:10 PM Ticket #1391 (Report map statistics) created by
- Add command to report map min, max, mean, standard deviation, rms for …
- 3:04 PM Ticket #1337 (Port volume mask command) closed by
- fixed: Tested all keyword options of "volume mask" and "volume onesmask" …
- 3:04 PM Ticket #1163 (Sample Error Tool) closed by
- wontfix: The documentation is still being overhauled, but the "Sample Tool" …
- 2:56 PM 2018-10-29 edited by
- (diff)
- 2:52 PM Ticket #1114 (Error when saving session) closed by
- can't reproduce
- 2:40 PM Ticket #1298 (No module named 'pip.wheel') closed by
-
fixed: Fixed in f1fb8fb5e.
Using
pkg_resourcesinstead of … - 2:18 PM Ticket #1390 (Need merged view of help documentation) created by
- With documentation moving to the bundle that implements the …
- 1:59 PM Ticket #780 (Prerequisite dependency versions listed in two places) closed by
- fixed: All of core's Python package dependencies are now in prereqs/pips. …
- 1:45 PM Ticket #1389 (port Chimera's Select menu) created by
- as per summary
- 1:05 PM 2018-10-29 created by
- 12:04 PM DeveloperMeetings edited by
- (diff)
- 11:26 AM Ticket #1387 (No module named 'wheel.install') closed by
- fixed: Fixed in f1fb8fb5e. Updating to new version of …
- 11:08 AM Ticket #1388 (RFE: start/end for atomspec numerical ranges (or asterisk to mean them)) created by
- For command-line atomspecs, would be great if the words "start" and …
Oct 26, 2018:
- 4:58 PM Ticket #1383 (Incorrect backbone bonding opening PDB) closed by
- fixed: When I removed 'is_het' as a residue attribute, some code that tested …
- 4:18 PM Ticket #1384 ('hide sidechain' should not hide CA atoms) closed by
- not a bug: After much discussion it was decided to keep CA in the sidechain …
- 2:54 PM Ticket #1386 (Shell: error → unusable) closed by
- fixed: Apparently you can force installation of older prereqs. I forced …
- 8:42 AM Ticket #638 (Linux OpenBLAS library threading problems) reopened by
- Sorry for letting this drop off the radar, but it turns out it's still …
- 7:54 AM Ticket #1387 (No module named 'wheel.install') created by
- […] error.log
Oct 25, 2018:
- 6:47 PM Ticket #1297 (Handle tinyarray in session save/restore) closed by
- fixed: Added support for tinyarray.ndarray_float, .ndarray_int, and …
- 6:18 PM Ticket #1386 (Shell: error → unusable) created by
- […]
- 6:12 PM Ticket #1385 (Session restore ValueError: Places place_array argument must have type ...) closed by
- fixed: Fixed. Code I put in a couple days ago now verifies that Place …
- 5:35 PM Ticket #1015 (help/cxcmd support in Sphinx docs) closed by
- fixed: Fixed in f4891d102. Added static JS file that is …
- 4:48 PM Ticket #1208 (Error closing Active Tools tool) closed by
- wontfix: Active Tools has been retired.
- 4:46 PM Ticket #966 ('make app-install' hangs when ToolShed website is down) closed by
- fixed: The preferred way to build and installed bundles is now: ChimeraX.exe …
- 4:45 PM Ticket #1385 (Session restore ValueError: Places place_array argument must have type ...) created by
- […] goo.cxs
- 4:13 PM FAI edited by
- (diff)
- 4:06 PM Ticket #1382 (CageBuilder session restore failure) closed by
- duplicate: Fixed a month or two ago.
- 3:34 PM Ticket #1069 (Trigger error messages difficult to debug) closed by
- fixed: Excellent suggestion, finally implemented.
- 3:19 PM Ticket #1318 (Apparently bogus help viewer error) closed by
- fixed: Identified as developer debug message in log.
- 2:46 PM Ticket #1313 (misleading error message) closed by
- not a bug: I don't consider this a bug. In the log window, the part of the …
- 2:22 PM Ticket #668 (Movie encode failure in Linux build) closed by
- fixed: CentOS rpm works.
- 1:58 PM Ticket #1381 (Help failure generating index) closed by
- fixed: Ignore <a name="toolbars">
- 1:50 PM Ticket #1354 (Trouble reading gzipped cif file: unexpected data value near line 1) closed by
- fixed: Need to use temporary file
- 10:24 AM Ticket #1384 ('hide sidechain' should not hide CA atoms) created by
- Not much more to say, really - at the moment this command leaves the …
- 10:03 AM Ticket #1383 (Incorrect backbone bonding opening PDB) created by
- If I download 2x0s.pdb and open it, there is a bond between Ser102 and …
- 9:29 AM Ticket #1379 (Failure on OSX 10.11) closed by
- not a bug: Download page notes that it doesn't work on 10.11 or earlier
- 3:10 AM Ticket #1382 (CageBuilder session restore failure) created by
- […]
Oct 24, 2018:
- 1:23 PM Ticket #1381 (Help failure generating index) created by
- […]
- 2:18 AM Ticket #1380 (Command to print Python equivalent of command-line input) created by
- It can be quite a challenge at times to track down the Python …
Oct 23, 2018:
- 2:20 PM Ticket #1379 (Failure on OSX 10.11) created by
- […]
- 11:52 AM Ticket #1378 (Bounds calculation fails under certain conditions) closed by
- fixed: Fixed. I'm amazed this mistake didn't effect more code, but I guess …
- 11:46 AM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) closed by
- fixed: Fixed. Put in order = 'C' in Place constructor. Interesting. I …
- 10:02 AM Ticket #1378 (Bounds calculation fails under certain conditions) reopened by
- Belay that. After confusing the hell out of myself, the culprit turns …
- 9:18 AM Ticket #1377 (Crash reading PDB file) closed by
- can't reproduce
- 9:10 AM Ticket #1378 (Bounds calculation fails under certain conditions) closed by
- nonchimerax: ... ah. Poking at this some more, it looks like I might have a memory …
- 7:40 AM Ticket #1378 (Bounds calculation fails under certain conditions) created by
-
Root cause first:
Places.array()returns afloat64array, while … - 4:01 AM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) reopened by
- I've changed my code to use float32 arrays for transforms, but that …
Oct 22, 2018:
- 8:41 PM Ticket #1377 (Crash reading PDB file) created by
- […]
- 7:14 PM Ticket #1376 (Crash during geometry change on a DockWidget) closed by
- can't reproduce
- 5:48 PM Ticket #1365 (Bad geometry can crash graphics on ribbon generation) closed by
- fixed: Instead of throwing an error out of the dssp code, it _logs_ an error …
- 4:11 PM Ticket #1374 (VR startup error when hand controller button held down at start) closed by
- fixed: Fixed. This error on VR startup happened when a VR hand controller …
- 3:40 PM Ticket #1376 (Crash during geometry change on a DockWidget) created by
- […]
- 3:36 PM Ticket #1371 (Geometry coming out incorrect on first attempt) closed by
- fixed: Fixed. My matrix optimizations reuse Place instances and their numpy …
- 3:16 PM Ticket #1288 (Toolshed error) closed by
- fixed: Added fix in f4d609e06.
- 3:08 PM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) closed by
- can't reproduce: The problem is likely because you Places(opengl_array=tf) requires a …
- 2:53 PM Ticket #1375 (implement wildcarding for atom specs) created by
- As per: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/2018-10-22 …
- 2:13 PM Ticket #1370 (Any error breaks shell instance) closed by
- fixed: Fixed. The broken shell was running IPython 7.0.1 while older working …
- 1:18 PM 2018-10-22 edited by
- (diff)
- 11:59 AM 2018-10-22 edited by
- (diff)
- 11:57 AM 2018-10-22 created by
- 11:42 AM DeveloperMeetings edited by
- (diff)
- 10:49 AM Ticket #1369 (Problem opening pdbdev 10) closed by
- fixed: "open 10 from pdbdev" worked correctly on Windows and Mac in the …
- 9:21 AM Ticket #1374 (VR startup error when hand controller button held down at start) created by
- […]
- 8:04 AM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) created by
-
Seems to be another change in the
DrawingAPI that I'm struggling to … - 6:38 AM Ticket #1372 (Crash during QTimer (status line?)) created by
- […]
- 3:52 AM Ticket #1371 (Geometry coming out incorrect on first attempt) created by
- This is something new (code has been working perfectly for months). …
- 3:24 AM Ticket #1370 (Any error breaks shell instance) created by
- Working with today's daily build, if I do anything that causes any …
Oct 21, 2018:
Oct 20, 2018:
- 1:55 PM Ticket #1368 (Camera 360tb crash) created by
- […] [[Image(...)]]
Oct 19, 2018:
Oct 18, 2018:
- 3:58 PM Ticket #1367 (volume command does not work on submodel specs (multiple contour levels)) created by
- If multiple contour levels are shown for a single volume model, using …
- 3:24 PM 2018-10-18 created by
- 2:11 PM DeveloperMeetings edited by
- (diff)
Oct 17, 2018:
- 3:53 PM Ticket #1366 (Chimerax bug) closed by
- fixed: Fixed in the next daily release.
- 2:31 PM Ticket #1366 (Chimerax bug) created by
- […]
- 1:54 PM Ticket #602 (Need user interface to be able to choose window configuration) closed by
- fixed: Can control default side new tools appear on, and which side an …
- 4:47 AM Ticket #1365 (Bad geometry can crash graphics on ribbon generation) created by
- Arising out of working through CASP assessments... one model had a …
Oct 16, 2018:
- 4:13 PM Ticket #1364 (Coordset slider gui should sync with coordset command) created by
- After making a morph a slider appears to play the morph. If instead …
- 4:10 PM Ticket #1363 (coordset stop command) created by
- Need a command to stop coordset from playing. This becomes an issue …
- 3:02 PM Ticket #917 (RFE Log context menu allows switching between help links and execution ...) closed by
- fixed: All done.
- 10:48 AM Ticket #618 (ChimeraX bug reporting) closed by
- fixed: Tom Goddard implemented this
Oct 15, 2018:
- 3:44 PM Ticket #572 (Failed dependency in last night's Linux build) closed by
- fixed: Latest QtWebEngineWidgets, ChimeraX uses Qt 5.9.6, does not depend on …
- 3:33 PM Ticket #473 (Create Linux installer and distribute necessary system libraries) closed by
- fixed: Now distribute a CentOS / Red Hat 7 rpm.
Oct 12, 2018:
Oct 11, 2018:
- 6:50 PM Ticket #1362 (Not all bugs offering "Report Bug" option) created by
- […]
- 1:45 PM Ticket #1359 (RFE Command History preference to show all executed commands or only ...) closed by
- fixed: Sticky option controlling all vs. typed is in context menu
- 11:44 AM Ticket #1361 (PDBio: bad format char in arg-parsing string) closed by
- duplicate
- 10:38 AM Ticket #1209 (cartoon preset undisplays too much) closed by
- wontfix: Closing this since the requested behavior is problematic in other …
Oct 10, 2018:
- 2:45 PM Ticket #1361 (PDBio: bad format char in arg-parsing string) created by
- […]
- 11:41 AM Ticket #1344 (Sequence Viewer annoying horizontal scroll behavior) closed by
- fixed: I believe these behaviors are for the most part fixed. The only …
Oct 9, 2018:
- 2:34 PM Ticket #1229 (Eliminate is_het res attribute) closed by
- fixed
- 1:09 PM Ticket #1360 (Starting VR on Linux gives traceback) closed by
- fixed: Added simple error message saying SteamVR is not installed or failed …
- 1:01 PM Ticket #1342 (Atoms.aniso_u(6) hides data) closed by
- fixed: I've made Atoms.aniso_u and Atoms.aniso_u6 raise a ValueError …
- 11:54 AM WikiStart edited by
- (diff)
- 11:25 AM Ticket #1358 (Some kind of dock widget crash) closed by
- can't reproduce
- 11:24 AM Ticket #1357 (Some kind of dock widget crash) closed by
- can't reproduce
Oct 8, 2018:
- 5:38 PM Ticket #1346 (Same model used multiple times in model hierarchy) closed by
- fixed: Okay, fixed the slow table rebuild as well (was asking for selected …
- 3:07 PM Ticket #1360 (Starting VR on Linux gives traceback) created by
- […]
- 2:18 PM 2018-10-08 edited by
- (diff)
- 1:58 PM Ticket #1359 (RFE Command History preference to show all executed commands or only ...) created by
- This preference would be controlled by option(s) in the Command …
- 1:33 PM 2018-10-08 edited by
- (diff)
- 11:40 AM Ticket #1358 (Some kind of dock widget crash) created by
- […]
- 11:40 AM Ticket #1357 (Some kind of dock widget crash) created by
- […]
- 11:33 AM 2018-10-08 edited by
- (diff)
- 10:38 AM Ticket #1356 (Write PDB: 'polymeric_res_names' arg is not a sequence) closed by
- fixed: Now fixed. In next daily build.
Oct 7, 2018:
Oct 5, 2018:
- 4:37 PM Ticket #1345 ("Report a bug" should not be an option for errors that derive from NotABug) closed by
- fixed: Made an additional log level: LEVEL_BUG. Only this level puts the …
- 4:33 PM Ticket #1353 (Crash doing *something* with a DockWidget) closed by
- can't reproduce: Old version (0.1) as well
- 3:01 PM Ticket #1355 (Starts with Intel graphics instead of Nvidia graphics on Windows 10 laptop) closed by
- fixed: Added the NvOptimusEnablement symbol to ChimeraX.exe on Windows so it …
- 2:36 PM Ticket #1355 (Starts with Intel graphics instead of Nvidia graphics on Windows 10 laptop) created by
- […]
- 2:13 PM Ticket #1354 (Trouble reading gzipped cif file: unexpected data value near line 1) created by
- […]
- 1:42 PM Ticket #1352 (crossfade: FileNotFoundError) closed by
- fixed: The movie recording failed for a few reasons. First "movie crossfade" …
- 11:54 AM Ticket #1353 (Crash doing *something* with a DockWidget) created by
- […]
- 9:51 AM 2018-10-08 created by
- 9:40 AM DeveloperMeetings edited by
- (diff)
- 9:21 AM Ticket #1351 (Residue :0 atom spec does not work.) closed by
- fixed: Fixed in [changeset bce749297]. Missing residue spec is None, not …
Oct 4, 2018:
- 7:58 PM Ticket #1352 (crossfade: FileNotFoundError) created by
- […]
- 6:38 PM Ticket #1351 (Residue :0 atom spec does not work.) created by
- The atom-spec :0 does not specify any atoms even when residue :0 …
- 2:19 PM Ticket #1349 (error reading pseudobond file) closed by
- fixed
- 2:11 PM Ticket #1348 (mlp command broken) closed by
- fixed: Updating an import was missing when the surface bundle got moved out …
- 1:02 PM Ticket #1350 (Button to hide/show all maps, and button to hide/show all atomic structures) created by
- From: Oliver Clarke Subject: [Chimera-users] Maps/models …
- 12:41 PM Ticket #1349 (error reading pseudobond file) created by
- […] 5ego.pb
- 12:35 PM Ticket #1348 (mlp command broken) created by
- […]
- 11:27 AM ChangeLog edited by
- (diff)
- 11:23 AM ChangeLog edited by
- (diff)
- 11:22 AM ChangeLog edited by
- (diff)
- 10:19 AM Ticket #1347 (Crash in chem_group::find_5ring_OR2) closed by
- can't reproduce: Not the first report of this and it's just not enough info to diagnose …
- 7:56 AM Ticket #1347 (Crash in chem_group::find_5ring_OR2) created by
- […]
- 6:17 AM Ticket #1346 (Same model used multiple times in model hierarchy) created by
- If I do: […] ... then the loop runs crazily slow (after ~15 …
Oct 3, 2018:
- 5:38 PM ChangeLog edited by
- (diff)
- 5:13 PM Ticket #1345 ("Report a bug" should not be an option for errors that derive from NotABug) created by
- As summary. Pretty much the point of those error types (UserError, …
- 3:34 PM ChangeLog edited by
- (diff)
- 3:25 PM ChangeLog edited by
- (diff)
- 2:03 PM Ticket #1344 (Sequence Viewer annoying horizontal scroll behavior) created by
- I find it mpossible to get rid of horizontal scrollbar. My Mac …
- 12:47 PM Ticket #1343 (vr: VRInitError_Init_VRClientDLLNotFound) closed by
- nonchimerax: I never tried VR on Linux. It turns out the Python openvr library …
- 12:04 PM Ticket #1343 (vr: VRInitError_Init_VRClientDLLNotFound) created by
- […]
- 10:54 AM Ticket #1340 (PDBio: bad format char in arg-parsing string) closed by
- fixed: Hi, Thanks for reporting this problem. It is fixed now and the fix …
- 9:33 AM Ticket #1342 (Atoms.aniso_u(6) hides data) created by
- Would be really good to have these carry through to the output PDB …
- 4:04 AM Ticket #1341 (Friendlier alignment API) created by
- I found my way to what I needed by digging through the source of …
Oct 2, 2018:
- 7:57 PM Ticket #1340 (PDBio: bad format char in arg-parsing string) created by
- […]
- 4:56 PM Ticket #1339 (Status messages fetching file do not appear on Windows 10) created by
- When fetching a large file "open 4v6s from eds" (130 Mbytes) which …
Oct 1, 2018:
- 1:54 PM ChangeLog edited by
- (diff)
- 11:34 AM Ticket #1334 (Atom.aniso_u6 values in wrong order) closed by
- fixed: Not sure why the PDB uses the order it does, but nonetheless changed …
- 10:50 AM Ticket #1338 (draw() takes 3 positional arguments but 4 were given) closed by
- duplicate: Duplicate. Fixed last week.
- 4:01 AM Ticket #1338 (draw() takes 3 positional arguments but 4 were given) created by
- […]
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