Timeline



Nov 19, 2018:

7:50 PM Ticket #1457 (Volume Viewer histogram/scrollbar problem) closed by Tom Goddard
fixed: Fixed hopefully. I found a Qt trick to always show the scrollbar on …
4:42 PM Ticket #1468 (Pressing Enter key in Volume Viewer entry field runs the last command) closed by pett
fixed: Fixed by not forwarding keystrokes if the focus widget is a QLineEdit …
3:59 PM Ticket #1456 (Ongoing/duplicate movie recording) closed by Tom Goddard
fixed: Fixed.
3:23 PM Ticket #1462 (Crash executing Python) closed by Tom Goddard
can't reproduce
3:08 PM Ticket #1468 (Pressing Enter key in Volume Viewer entry field runs the last command) created by Tom Goddard
Pressing the Enter key in the Volume Viewer contour level entry field …
2:50 PM Ticket #1454 (showPivot performance problems) closed by Tom Goddard
fixed: Fixed. Pivot indicator was casting shadows. Now it does not, so …
2:43 PM Ticket #1467 (Cache should distinguish between database sources) created by pett
For example, fetching from pdbe_updated shouldn't present the file hat …
1:25 PM Ticket #1463 (AddH on 1trz: Singular matrix) closed by pett
not a bug: Yes, as Tristan pointed out, it seems like an error in the model. …
1:22 PM ChangeLog edited by Elaine Meng
(diff)
12:19 PM Ticket #1466 (Can't save offscreen image) created by Greg Couch
After fixing many offscreen bugs, saving an image now fails with: …
11:47 AM Ticket #1465 (KeyError saving mmCIF) created by lpravda@…
[…] full.cif
8:53 AM Ticket #1464 (Addh on 1jj2: list index out of range) created by lpravda@…
[…]
8:42 AM Ticket #1463 (AddH on 1trz: Singular matrix) created by lpravda@…
[…]

Nov 18, 2018:

4:03 AM Ticket #1462 (Crash executing Python) created by maria.anastasina@…
[…]

Nov 17, 2018:

1:48 PM Ticket #1460 (linux swap interval code breaks offscreen rendering) created by Greg Couch
src/core/graphics/_graphics/linux_swap_interval.cpp links against …

Nov 16, 2018:

7:22 PM Ticket #1458 (Problem reading TIFF image stack) created by grahamj@…
[…]
7:07 PM Ticket #1457 (Volume Viewer histogram/scrollbar problem) created by grahamj@…
[…]
7:03 PM Ticket #1456 (Ongoing/duplicate movie recording) created by grahamj@…
[…]
6:54 PM Ticket #1455 (Something wrong with clipping for large models) closed by Tom Goddard
fixed: Fixed. Clipping was broken depending on the display style and …
5:11 PM Ticket #1433 (Allow for direct monitoring of setting changes) closed by pett
fixed: Settings instances fire a 'setting changed' trigger when changed, with …
2:13 PM Ticket #1455 (Something wrong with clipping for large models) created by olibclarke@…
[…] chimerax_clipping_bug.mov
9:52 AM Ticket #1453 (Crash deleting bonds) closed by pett
fixed: Hi Lukas, It looks like this crash occurred while you were issuing a …
6:37 AM Ticket #1454 (showPivot performance problems) created by olibclarke@…
[…]

Nov 15, 2018:

4:09 PM Ticket #1453 (Crash deleting bonds) created by lpravda@…
[…]
3:13 PM 2018-11-15 created by Conrad Huang
3:01 PM Ticket #1429 (Atom specifiers not handling chain case correctly) closed by Conrad Huang
fixed
2:10 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:54 PM Ticket #1452 (crosslinks network "select pseudobonds" only selects end atoms) created by Elaine Meng
crosslinks diagram edge context menu “Select N Pseudobonds” (same …
1:26 PM 2018-11-01 edited by pett
(diff)
12:23 PM Ticket #1172 (Problems encountered building bundle for Windows) closed by Conrad Huang
fixed: That's great! I can finally close this ticket.

Nov 14, 2018:

2:22 PM Ticket #1212 (opening 4b3o can produce KeyError generating chain descriptions) closed by pett
fixed: Seems to have "fixed itself" (reverse bitrot)
1:59 PM 2018-11-01 edited by pett
(diff)
12:58 PM Ticket #1440 (glBlitFramebuffer out of memory with large volume model) closed by Tom Goddard
not a bug: ChimeraX opened large volume data 5003, float32 values, at step 1 …
12:11 PM Ticket #1438 (Interfaces plugin should close when associated model closes) closed by Tom Goddard
fixed: I don't get a traceback clicking on the interfaces contact plot after …
11:25 AM Ticket #1451 (draw() takes 3 positional arguments but 4 were given) closed by Tom Goddard
fixed: Fixed more than a month ago.
11:18 AM Ticket #1450 (Crash with some event on a QDockWidget) closed by pett
can't reproduce
11:15 AM Ticket #1448 (Crash with some event on a QDockWidget) closed by pett
can't reproduce
9:06 AM Ticket #1451 (draw() takes 3 positional arguments but 4 were given) created by chimerax-bug-report@…
[…]
4:44 AM Ticket #1444 (Crash running OpenMM simulation) closed by Tristan Croll
can't reproduce: Hard to say what's going on here. I've tried out a few likely …
4:32 AM Ticket #1450 (Crash with some event on a QDockWidget) created by chimerax-bug-report@…
[…]
1:10 AM Ticket #1449 (Crash with some event on a QDockWidget) created by vikrambabuk@…
[…]

Nov 13, 2018:

11:36 PM Ticket #1448 (Crash with some event on a QDockWidget) created by chimerax-bug-report@…
[…]
7:15 PM Ticket #1447 (Multitouch trackpad does not work on Windows 10) created by Tom Goddard
Multitouch 2-finger rotation and 3-finger translation does not work on …
6:58 PM Ticket #1442 (Request to add Chimera1-like model "activity") closed by Tom Goddard
wontfix: ChimeraX moves individual models in a different way from Chimera. You …
5:24 PM 2018-11-01 edited by pett
(diff)
5:24 PM 2018-11-01 edited by pett
(diff)
5:20 PM 2018-11-01 edited by pett
(diff)
5:01 PM 2018-11-01 edited by pett
(diff)
4:54 PM 2018-11-01 edited by pett
(diff)
4:46 PM 2018-11-01 edited by pett
(diff)
4:43 PM 2018-11-01 edited by pett
(diff)
4:42 PM 2018-11-01 edited by pett
(diff)
4:34 PM 2018-11-01 edited by pett
(diff)
4:32 PM ChangeLog edited by Elaine Meng
(diff)
4:31 PM 2018-11-01 edited by pett
(diff)
3:39 PM Ticket #1446 (Crash exiting ChimeraX when VR running) created by goddard@…
[…]
1:41 PM Ticket #1445 ("Usage" needs to be more bulletproof) created by Conrad Huang
[…]
11:50 AM Ticket #1443 (Clipper: cannot import name 'ArrayGridData') closed by pett
fixed
10:55 AM Ticket #1435 (Molecular surface session restore: can't set attribute) closed by pett
duplicate: Hi Vikram. This was fixed about 6 days ago, so if you get the latest …
5:52 AM Ticket #1444 (Crash running OpenMM simulation) created by chimerax-bug-report@…
[…]
5:45 AM Ticket #1443 (Clipper: cannot import name 'ArrayGridData') created by chimerax-bug-report@…
[…]
4:36 AM Ticket #1442 (Request to add Chimera1-like model "activity") created by bhargav.saligram@…
[…]
4:17 AM Ticket #1441 (Crash using menu) created by mvc581@…
[…]
3:46 AM Ticket #1440 (glBlitFramebuffer out of memory with large volume model) created by bhargav.saligram@…
[…]
3:08 AM Ticket #1439 (Ability to spawn secondary View instance(s)) created by Tristan Croll
I can think of a number of situations where it would be really good to …
2:57 AM Ticket #1438 (Interfaces plugin should close when associated model closes) created by Tristan Croll
One arising from the Copenhagen workshop: if the model used to spawn …
1:48 AM Ticket #1437 (Crash docking/undocking window(?)) created by guillermo.montoya@…
[…]
1:14 AM Ticket #1436 (Crash in Qt event handling) created by bhargav.saligram@…
[…]
12:24 AM Ticket #1435 (Molecular surface session restore: can't set attribute) created by vikrambabuk@…
[…]

Nov 11, 2018:

1:22 PM Ticket #1410 (bundleinfo.xml DataFile not installed/found) closed by Conrad Huang
fixed: Fixed in b0a9858c3. about.html was neither created nor …

Nov 9, 2018:

3:33 PM Ticket #427 (Add multitouch trackpad rotation and translation) closed by Tom Goddard
fixed: Added 2-finger and 3-finger Mac trackpad drags to rotate, zoom and …
3:31 PM Ticket #1433 (Allow for direct monitoring of setting changes) created by pett
... so that the settings GUI doesn't have to be notified by every Tom, …
11:14 AM Ticket #1432 (Focus out from command line: QLineEdit::setSelection: Invalid start ...) closed by pett
fixed: Hi Brandon, Thanks for reporting this problem. It's harmless but …
8:48 AM Ticket #1432 (Focus out from command line: QLineEdit::setSelection: Invalid start ...) created by brandon.scott@…
[…]

Nov 8, 2018:

1:09 PM Ticket #1388 (RFE: start/end for atomspec numerical ranges (or asterisk to mean them)) closed by Conrad Huang
fixed: Fixed in 987564593. Looks like "*" used to work. Fixed …
12:59 PM Ticket #1388 (RFE: start/end for atomspec numerical ranges (or asterisk to mean them)) reopened by Elaine Meng
12:15 PM Ticket #1428 (ISOLDE: crash in Distance_Restraint_Mgr destructor) closed by Tristan Croll
fixed: Oops. A silly oversight on my part: destructor was calling the class's …
10:57 AM Ticket #1431 (Atom specifiers not handling chain case correctly) closed by pett
duplicate: This undoubtedly the same root problem as for your earlier report. …
10:39 AM Ticket #1430 (Atom specifiers not selecting upper case chain IDs) closed by pett
duplicate: Duplicate of #1429
10:09 AM Ticket #1431 (Atom specifiers not handling chain case correctly) created by pascal.albanese@…
[…]
9:25 AM Ticket #1430 (Atom specifiers not selecting upper case chain IDs) created by Scooter Morris
[…]
8:46 AM Ticket #1429 (Atom specifiers not handling chain case correctly) created by pascal.albanese@…
[…]
3:26 AM Ticket #1428 (ISOLDE: crash in Distance_Restraint_Mgr destructor) created by chimerax-bug-report@…
[…]

Nov 7, 2018:

10:30 AM Ticket #1425 (Molecular surface session restore: can't set attribute) closed by Tom Goddard
fixed: Fixed. Change made a week ago to allow measuring enclosed volume of …
9:57 AM Ticket #1427 (offscreen rendering fails) created by Lukas Pravda <lpravda@…>
Running 'chimerax-daily --nogui --offscreen' fails to get an offscreen …

Nov 6, 2018:

11:23 AM Ticket #1426 (mlp: No module named 'chimerax.core.commands.surface') created by beard2@…
[…]
6:26 AM Ticket #1425 (Molecular surface session restore: can't set attribute) created by Scooter Morris
[…] nucleosome.cxs

Nov 5, 2018:

7:03 PM Ticket #1419 (Crash in chem_group::find_5ring_OR2) closed by pett
fixed: Your feedback was very helpful in allowing me to track down this …
5:49 PM Ticket #1424 (Boolean attribute tests now failing) closed by Conrad Huang
fixed: Fixed in 8eaeff88d. A whole section code of dealing with …
3:58 PM Ticket #1424 (Boolean attribute tests now failing) created by Elaine Meng
[…]
3:27 PM Ticket #1412 (bug reporting doubles log commands) closed by Greg Couch
fixed: Fixed. Removed duplicate by scanning the log's HTML source and put a …
3:22 PM Ticket #1423 (ChimeraX bug report submission) closed by Greg Couch
fixed: Test of fix for #1412 showing that it is fixed!
3:18 PM Ticket #1423 (ChimeraX bug report submission) created by Greg Couch
[…]
3:17 PM Ticket #1388 (RFE: start/end for atomspec numerical ranges (or asterisk to mean them)) closed by Conrad Huang
fixed: Fixed in 8d2acd142. Code was using residue atomspec as …
1:49 PM Ticket #1422 (ChimeraX bug report submission) closed by Greg Couch
duplicate: Duplicate of #1412. Actually test of a bug fix that didn't work.
1:23 PM Ticket #1422 (ChimeraX bug report submission) created by Greg Couch
[…]
11:14 AM Ticket #1420 (Crash on OS X Mojave) closed by pett
can't reproduce
10:29 AM Ticket #1421 (Earlier detection of core incompatibilities) created by pett
It would be a significant enhancement if the Tool Shed could detect …
10:24 AM Ticket #1418 (Clipper incompatible with ChimeraX >= 0.7) closed by pett
not a bug: Hi Ricardo, As of right now, Clipper only works with ChimeraX version …

Nov 4, 2018:

11:49 PM Ticket #1420 (Crash on OS X Mojave) created by chimerax-bug-report@…
[…]
5:33 PM Ticket #1419 (Crash in chem_group::find_5ring_OR2) created by arik@…
[…]

Nov 2, 2018:

6:48 PM Ticket #1418 (Clipper incompatible with ChimeraX >= 0.7) created by ricardojstorquato@…
[…]
6:23 PM Ticket #1417 (ChimeraX bug report submission) closed by Tom Goddard
fixed
6:22 PM Ticket #1416 (ChimeraX bug report submission) closed by Tom Goddard
fixed
6:21 PM Ticket #1417 (ChimeraX bug report submission) created by goddard@…
[…]
6:18 PM Ticket #1416 (ChimeraX bug report submission) created by goddard@…
[…]
4:50 PM Ticket #1415 (ChimeraX bug report submission) closed by Tom Goddard
fixed: Working.
4:49 PM Ticket #1415 (ChimeraX bug report submission) created by goddard@…
[…]
4:48 PM Ticket #1414 (ChimeraX bug report submission) closed by Tom Goddard
fixed
4:47 PM Ticket #1414 (ChimeraX bug report submission) created by goddard@…
[…]
4:25 PM Ticket #1411 (OpenGL error when drawing mouse-drag rectangle: invalid operation) closed by Tom Goddard
can't reproduce: This error happens when you try to ctrl-click and drag to select …
3:56 PM Ticket #1407 (Transparency at the soft lightening) closed by Tom Goddard
fixed: Fixed. I also observed the part transparent ribbon became opaque when …
2:13 PM Ticket #1408 (Make drawings always have a "parent" attribute) closed by Tom Goddard
fixed: Fixed.
11:05 AM Ticket #1413 (Visualisation/handling of altlocs) created by Tristan Croll
Designating as "Core" and assigning to Eric, but is related to both …
10:13 AM Ticket #1412 (bug reporting doubles log commands) created by pett
Whatever mechanism is used to incorporate the log contents into bug …
7:18 AM Ticket #1411 (OpenGL error when drawing mouse-drag rectangle: invalid operation) created by pascal.albanese@…
[…]
6:51 AM Ticket #1410 (bundleinfo.xml DataFile not installed/found) created by chimerax-bug-report@…
[…]

Nov 1, 2018:

3:22 PM 2018-11-01 edited by Conrad Huang
(diff)
1:29 PM Ticket #1409 (Measure volume reports holes in molecular surfaces) closed by Tom Goddard
fixed: Fixed. Made measure volume use joined triangles for sharp-edge …
12:00 PM Ticket #1409 (Measure volume reports holes in molecular surfaces) created by Elaine Meng
The measure volume command reveals that the surface geometry of …
11:55 AM Ticket #1408 (Make drawings always have a "parent" attribute) created by pett
Currently a Drawing with no parent might have no "parent" attribute, …
11:30 AM ChangeLog edited by Elaine Meng
(diff)
2:35 AM Ticket #1407 (Transparency at the soft lightening) created by o.klykov@…
[…] [[Image(...)]] [[Image(...)]] …

Oct 31, 2018:

6:07 PM Ticket #1406 (Mark supported volume data APIs) created by Tom Goddard
Mark the essential volume APIs as supported, such as opening a volume, …
6:03 PM Ticket #1405 (Document supported geometry module APIs) closed by Tom Goddard
fixed: Added supported api notation to 83 geometry module methods, about 90% …
6:02 PM Ticket #1405 (Document supported geometry module APIs) created by Tom Goddard
Add Supported API to doc strings of geometry module functions.
5:06 PM Ticket #1404 (Bad bonds in mmCIF 1lpv) created by pett
The mmCIF form of the NMR entry 1lpv shows a variety of bogus long …
4:26 PM Ticket #1403 (AddH: skip falsely terminal heavy atoms of standard residues) created by lpravda@…
For standard residues that are incomplete, skip protonation for atoms …
2:22 PM Ticket #1401 (Cannot restore session: __init__() got an unexpected keyword argument 'raw') closed by pett
duplicate: Hi Oleg, Sorry about this problem. It is fixed in the most current …
2:17 PM Ticket #1399 (Crash reading PDB file) closed by pett
duplicate: previously fixed
12:53 PM 2018-11-01 created by Conrad Huang
12:47 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:33 PM Ticket #1400 (Volume.surface_level_for_enclosed_volume only correct for orthogonal ...) closed by Tom Goddard
fixed: Fixed. I added a voxel_volume() method to Grid_Data …
11:20 AM Ticket #1398 (Open pdbdev 10: File is not a zip file) closed by Tom Goddard
can't reproduce: I would not expect reinstalling ChimeraX to fix this problem. When I …
10:14 AM Ticket #1402 (Bundle's own compiled libraries should be at top of symbol search path) created by Tristan Croll
I *guess* this is a ToolShed issue? Short story: shared libraries …
9:39 AM Ticket #1401 (Cannot restore session: __init__() got an unexpected keyword argument 'raw') created by o.klykov@…
[…]
6:41 AM Ticket #1400 (Volume.surface_level_for_enclosed_volume only correct for orthogonal ...) created by Tristan Croll
At the moment, Volume.surface_level_for_enclosed_volume() starts: …

Oct 30, 2018:

11:31 PM Ticket #1399 (Crash reading PDB file) created by chimerax-bug-report@…
[…]
4:31 PM Ticket #1397 (All sessions broken) closed by Greg Couch
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 pett
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 pett
fixed: Pushed a fix; can't test until #1397 fixed
2:34 PM ChangeLog edited by Elaine Meng
(diff)
1:05 PM Ticket #1398 (Open pdbdev 10: File is not a zip file) created by mr.edvinas.stankunas@…
[…]
12:58 PM Ticket #1397 (All sessions broken) created by pett
The changes to support tinyarray now cause all session restores to …
12:31 PM ChangeLog edited by Elaine Meng
(diff)
11:18 AM Ticket #638 (Linux OpenBLAS library threading problems) closed by Conrad Huang
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 pascal.albanese@…
[…]
1:41 AM Ticket #1395 (Sequence session-restore failure: get_class() missing 1 required ...) created by pascal.albanese@…
[…]

Oct 29, 2018:

10:50 PM Ticket #1392 (Problem parsing mmCIF: unexpected left bracket) closed by Greg Couch
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 TSkillman@…
[…] DQ8trans_012_AKM-GKP.pdb
5:51 PM Ticket #1392 (Problem parsing mmCIF: unexpected left bracket) created by lpravda@…
[…] 1bep_assembly.cif
3:46 PM Ticket #1368 (Camera 360tb crash) closed by Tom Goddard
fixed: Works for me. Probably a bug that was fixed within days after your …
3:41 PM Ticket #1391 (Report map statistics) closed by Tom Goddard
fixed: Added "measure mapstats" command. measure mapstats [volumes] [step …
3:10 PM Ticket #1391 (Report map statistics) created by Tom Goddard
Add command to report map min, max, mean, standard deviation, rms for …
3:04 PM Ticket #1337 (Port volume mask command) closed by Tom Goddard
fixed: Tested all keyword options of "volume mask" and "volume onesmask" …
3:04 PM Ticket #1163 (Sample Error Tool) closed by Conrad Huang
wontfix: The documentation is still being overhauled, but the "Sample Tool" …
2:56 PM 2018-10-29 edited by Conrad Huang
(diff)
2:52 PM Ticket #1114 (Error when saving session) closed by Conrad Huang
can't reproduce
2:40 PM Ticket #1298 (No module named 'pip.wheel') closed by Conrad Huang
fixed: Fixed in f1fb8fb5e. Using pkg_resources instead of …
2:18 PM Ticket #1390 (Need merged view of help documentation) created by Greg Couch
With documentation moving to the bundle that implements the …
1:59 PM Ticket #780 (Prerequisite dependency versions listed in two places) closed by Greg Couch
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 pett
as per summary
1:05 PM 2018-10-29 created by Conrad Huang
12:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
11:26 AM Ticket #1387 (No module named 'wheel.install') closed by Conrad Huang
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 Elaine Meng
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 pett
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 pett
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 pett
fixed: Apparently you can force installation of older prereqs. I forced …
8:42 AM Ticket #638 (Linux OpenBLAS library threading problems) reopened by Tristan Croll
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 bwang@…
[…] error.log

Oct 25, 2018:

6:47 PM Ticket #1297 (Handle tinyarray in session save/restore) closed by Greg Couch
fixed: Added support for tinyarray.ndarray_float, .ndarray_int, and …
6:18 PM Ticket #1386 (Shell: error → unusable) created by Greg Couch
[…]
6:12 PM Ticket #1385 (Session restore ValueError: Places place_array argument must have type ...) closed by Tom Goddard
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 Conrad Huang
fixed: Fixed in f4891d102. Added static JS file that is …
4:48 PM Ticket #1208 (Error closing Active Tools tool) closed by Conrad Huang
wontfix: Active Tools has been retired.
4:46 PM Ticket #966 ('make app-install' hangs when ToolShed website is down) closed by Conrad Huang
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 Greg Couch
[…] goo.cxs
4:13 PM FAI edited by Greg Couch
(diff)
4:06 PM Ticket #1382 (CageBuilder session restore failure) closed by Tom Goddard
duplicate: Fixed a month or two ago.
3:34 PM Ticket #1069 (Trigger error messages difficult to debug) closed by Greg Couch
fixed: Excellent suggestion, finally implemented.
3:19 PM Ticket #1318 (Apparently bogus help viewer error) closed by Greg Couch
fixed: Identified as developer debug message in log.
2:46 PM Ticket #1313 (misleading error message) closed by Greg Couch
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 Greg Couch
fixed: CentOS rpm works.
1:58 PM Ticket #1381 (Help failure generating index) closed by Greg Couch
fixed: Ignore <a name="toolbars">
1:50 PM Ticket #1354 (Trouble reading gzipped cif file: unexpected data value near line 1) closed by Greg Couch
fixed: Need to use temporary file
10:24 AM Ticket #1384 ('hide sidechain' should not hide CA atoms) created by Tristan Croll
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 Tristan Croll
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 pett
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 chimerax-bug-report@…
[…]

Oct 24, 2018:

1:23 PM Ticket #1381 (Help failure generating index) created by chimerax-bug-report@…
[…]
2:18 AM Ticket #1380 (Command to print Python equivalent of command-line input) created by Tristan Croll
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 chimerax-bug-report@…
[…]
11:52 AM Ticket #1378 (Bounds calculation fails under certain conditions) closed by Tom Goddard
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 Tom Goddard
fixed: Fixed. Put in order = 'C' in Place constructor. Interesting. I …
10:02 AM Ticket #1378 (Bounds calculation fails under certain conditions) reopened by Tristan Croll
Belay that. After confusing the hell out of myself, the culprit turns …
9:18 AM Ticket #1377 (Crash reading PDB file) closed by pett
can't reproduce
9:10 AM Ticket #1378 (Bounds calculation fails under certain conditions) closed by Tristan Croll
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 Tristan Croll
Root cause first: Places.array() returns a float64 array, while …
4:01 AM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) reopened by Tristan Croll
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 chimerax-bug-report@…
[…]
7:14 PM Ticket #1376 (Crash during geometry change on a DockWidget) closed by pett
can't reproduce
5:48 PM Ticket #1365 (Bad geometry can crash graphics on ribbon generation) closed by pett
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 Tom Goddard
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 chimerax-bug-report@…
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3:36 PM Ticket #1371 (Geometry coming out incorrect on first attempt) closed by Tom Goddard
fixed: Fixed. My matrix optimizations reuse Place instances and their numpy …
3:16 PM Ticket #1288 (Toolshed error) closed by Conrad Huang
fixed: Added fix in f4d609e06.
3:08 PM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) closed by Tom Goddard
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 pett
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 Tom Goddard
fixed: Fixed. The broken shell was running IPython 7.0.1 while older working …
1:18 PM 2018-10-22 edited by Conrad Huang
(diff)
11:59 AM 2018-10-22 edited by Conrad Huang
(diff)
11:57 AM 2018-10-22 created by Conrad Huang
11:42 AM DeveloperMeetings edited by Conrad Huang
(diff)
10:49 AM Ticket #1369 (Problem opening pdbdev 10) closed by Tom Goddard
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 tlskillman@…
[…]
8:04 AM Ticket #1373 ("TypeError: Require contiguous 3x4 array" when Drawing has only one ...) created by Tristan Croll
Seems to be another change in the Drawing API that I'm struggling to …
6:38 AM Ticket #1372 (Crash during QTimer (status line?)) created by jjung@…
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3:52 AM Ticket #1371 (Geometry coming out incorrect on first attempt) created by Tristan Croll
This is something new (code has been working perfectly for months). …
3:24 AM Ticket #1370 (Any error breaks shell instance) created by Tristan Croll
Working with today's daily build, if I do anything that causes any …

Oct 21, 2018:

12:15 PM Ticket #1369 (Problem opening pdbdev 10) created by mr.edvinas.stankunas@…
[…]

Oct 20, 2018:

1:55 PM Ticket #1368 (Camera 360tb crash) created by tlskillman@…
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