![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Jan 8, 2019:
- 11:16 AM Ticket #1539 (AddH: incorrect removal from hbond_info) closed by
- fixed: Metals being noted as "acceptors" also needed coordinators noted as donors.
- 10:47 AM Ticket #1594 (Eventually parsing of save-image keyword 'transparentBackground' goes south) closed by
- fixed
- 10:26 AM Ticket #1592 (select by minimum/maximum length selects non-pseudobonds) closed by
- fixed: Ok. If minimumLength or maximumLength is specified with the select …
- 10:00 AM Ticket #1591 (Molecular surface session restore: can't set attribute) closed by
- duplicate: duplicate of #1425
- 8:27 AM Ticket #1594 (Eventually parsing of save-image keyword 'transparentBackground' goes south) created by
- […]
- 7:58 AM ChangeLog edited by
- (diff)
Jan 7, 2019:
- 4:48 PM Ticket #1593 (multi-level "sel back/forward") created by
- Implement multi-level selection-only undo/redo as "sel back/forward" …
- 2:22 PM Ticket #1590 (Session restore of graphics: self._positions is None) closed by
- can't reproduce: Ok. Seems likely that there was an error on saving the session then. …
- 1:36 PM Ticket #1592 (select by minimum/maximum length selects non-pseudobonds) created by
- The select command minimumLength and maximumLength options were …
- 11:32 AM Ticket #1591 (Molecular surface session restore: can't set attribute) created by
- […]
Jan 5, 2019:
Jan 4, 2019:
- 8:00 PM Ticket #1588 (glDrawBuffer(GL_FRONT): invalid operation) closed by
- can't reproduce: Will wait for another report before putting in extra debug code.
- 7:57 PM Ticket #1569 (OpenGL startup error: invalid enumerant) closed by
- can't reproduce: Appears to be inadequate graphics driver giving an error on startup on …
- 10:51 AM Ticket #1589 (Selection demotion: Drawing: can't set attribute) closed by
- fixed: Fixed.
Jan 3, 2019:
- 4:09 PM Ticket #1589 (Selection demotion: Drawing: can't set attribute) created by
- […]
- 11:28 AM Ticket #1549 (AddH: More than 2 coplanar positions specified!) closed by
- fixed
- 9:53 AM Ticket #1588 (glDrawBuffer(GL_FRONT): invalid operation) created by
- […]
Jan 2, 2019:
- 4:50 PM Ticket #1585 ("open browse" file browser does not allow multi-file selection and opening) closed by
- fixed: Fixed by expanding upon 'RepeatOf's hacked argument parsing.
- 12:45 PM Ticket #694 (Add C-alpha trace depictions) closed by
- fixed: Chain trace display for atomic structures is on by default now.
- 11:37 AM Ticket #863 (collate message as HTML) closed by
- fixed
- 10:14 AM Ticket #1586 (Seq Viewer: unproved enter() call on region browser) closed by
- duplicate: previously fixed
- 4:34 AM Ticket #1587 (Registration internal error) created by
- […]
Dec 29, 2018:
Dec 28, 2018:
- 4:17 PM Ticket #1585 ("open browse" file browser does not allow multi-file selection and opening) created by
- per summary
- 1:31 PM Ticket #1583 (Updating 3D label triggers: KeyError: 'setting changed') closed by
- duplicate: Fixed 5 days after the date of the version in the bug report.
- 1:12 PM Ticket #1581 (NameError when deleting from command history) closed by
- duplicate: Fixed a few days ago.
- 1:08 PM Ticket #1572 (Some kind of resizing crash) closed by
- can't reproduce
Dec 27, 2018:
- 12:23 PM Ticket #1584 (multi-file open incorrectly logged) created by
- If I use menu: File... Open and use click + Shift-click to choose …
Dec 26, 2018:
Dec 23, 2018:
- 11:15 PM Ticket #1582 (Volume Viewer deleted twice(?)) created by
- […]
- 5:15 AM Ticket #1581 (NameError when deleting from command history) created by
- […]
Dec 22, 2018:
- 9:43 AM Ticket #1580 (Make VR grip button move models) created by
- With oculus touch controllers users often press the grip button …
- 9:41 AM Ticket #1579 (Make selection mouse mode issue command) created by
- Make selection mouse mode issue an equivalent command when mouse …
- 9:39 AM Ticket #1578 (Make bond rotation mouse mode issue command) created by
- Want bond rotation mouse mode to issue equivalent command when mouse …
- 9:37 AM Ticket #1577 (Make volume crop mouse mode issue a command) created by
- Want volume bounds mouse mode to issue an equivalent command when …
- 9:36 AM Ticket #1576 (Make clip mouse mode issue command) created by
- Make translate and rotate clip planes mouse modes issue a command …
- 9:35 AM Ticket #1575 (Make volume threshold change on histogram issue command) created by
- When user changes volume contour level or solid rendering transfer …
- 9:33 AM Ticket #1574 (Make swapaa mouse mode issue command) created by
- When mouse button released after using swapaa mouse mode issue an …
- 9:30 AM Ticket #1573 (Turn off depth cueing for VR meeting head and hands) created by
- In a VR meeting other people's head and hands vanish due to depth …
- 8:53 AM Ticket #1572 (Some kind of resizing crash) created by
- […]
Dec 21, 2018:
- 5:58 PM Ticket #1570 (Chain info incorrect when microheterogenicity) closed by
- fixed: Found it. In Structure::_delete_atoms it asks for the residue's chain …
- 4:19 PM Ticket #1571 (Undo selection buggy) created by
- […]
- 1:28 PM Ticket #1544 (AddH: z_align endpoints must be distinct) closed by
- nonchimerax: The seems to be an error in the 1ggr entry. The coordinates of all …
- 1:06 PM Ticket #1570 (Chain info incorrect when microheterogenicity) created by
- For structures with microheterogenicity, the mmCIF reader produces two …
- 11:07 AM Ticket #1568 (unknown command coordset) closed by
- fixed
- 10:56 AM Ticket #1569 (OpenGL startup error: invalid enumerant) created by
- […]
- 8:14 AM Ticket #1568 (unknown command coordset) created by
- […]
Dec 20, 2018:
- 5:19 PM Ticket #1030 (make "info" report metadata; upon opening file, provide "info" ...) closed by
- fixed: Okay, #2 implemented, though it only shows the principal citation.
- 4:36 PM ChangeLog edited by
- (diff)
- 2:27 PM ChangeLog edited by
- (diff)
- 1:15 PM Ticket #1566 (Return pressed in help browser is also captured by command line) closed by
- fixed: Well, "fixed" by having floating windows not forward keystrokes to the …
- 11:39 AM Ticket #1567 (glDrawBuffer: invalid enumerant) closed by
- can't reproduce: OpenGL error in drag select setting draw buffer to GL_FRONT on Windows …
- 11:21 AM Ticket #1567 (glDrawBuffer: invalid enumerant) created by
- […]
- 10:54 AM Ticket #1562 (Contradiction in Collection documentation) closed by
- fixed: The current documentation in molarray.py already says: "Collections …
- 10:11 AM Ticket #1564 (Crash involving QDockWidget) closed by
- can't reproduce
- 8:39 AM Ticket #1566 (Return pressed in help browser is also captured by command line) created by
- When logging into the ToolShed, pressing <Enter> after entering my …
- 7:54 AM Ticket #1565 (Can't upload bundle to ToolShed) created by
- I get the following error: […] If, in my bundle_info.xml I change …
- 7:20 AM Ticket #1564 (Crash involving QDockWidget) created by
- […]
- 6:40 AM Ticket #1563 (Various ChimeraX startup switches ineffective in Windows) created by
- The following commands just drop back to the shell with no apparent …
- 2:47 AM Ticket #1562 (Contradiction in Collection documentation) created by
-
Minor thing, but...
In docstring for
atomic.Collection(and similar …
Dec 19, 2018:
- 9:08 PM Ticket #1561 (Bundle build system does not recompile changed C++ files) created by
- Changing a C++ file in a bundle (such as histogram.cpp in …
- 6:10 PM Ticket #1559 (vr update trigger: missing head image) closed by
- duplicate: VR head image file path is wrong -- I guess with the escaped spaces. …
- 4:57 PM Ticket #1560 (Need command style guide) created by
- Would like to have guidance for outside developers on how to construct …
- 2:32 PM Ticket #1559 (vr update trigger: missing head image) created by
- […]
- 1:55 PM Ticket #1558 (Apparent infinite recursion of find_close_points_boxes) closed by
- duplicate: Fixed a few days ago. Get the ChimeraX daily build or 0.8 release. …
- 1:37 PM Ticket #1558 (Apparent infinite recursion of find_close_points_boxes) created by
- […]
- 11:57 AM ChangeLog edited by
- (diff)
- 11:32 AM Ticket #1555 (Error trying to delete from command history) closed by
- fixed: Hi Katherine, Thanks for reporting this error. I have committed a …
- 11:28 AM Ticket #1554 (glClear: invalid enumerant) closed by
- duplicate: Duplicate. Probably bad graphics driver. Intel graphics, Windows 7, …
- 10:51 AM Ticket #1557 (Bad bond selection) created by
- When using the tilde operator, bonds remain selected when they …
- 10:30 AM Ticket #1556 (save command option to exclude hydrogens) closed by
- wontfix: I'm not going to implement this for two reasons: 1) As of yesterday, …
- 8:22 AM Ticket #1556 (save command option to exclude hydrogens) created by
- Wanting to save only heavy atoms from a model with hydrogens is a very …
- 5:34 AM Ticket #1555 (Error trying to delete from command history) created by
- […]
- 2:52 AM Ticket #1554 (glClear: invalid enumerant) created by
- […]
Dec 18, 2018:
- 5:45 PM Ticket #1547 (Symmetry position atom: LinAlgError("Singular matrix")) closed by
- fixed
- 2:53 PM Ticket #1552 (glClear: invalid enumerant) closed by
- can't reproduce: Graphics driver or WIndows 7 problem. Looks like same reporter as …
- 2:30 PM Ticket #1403 (AddH: skip falsely terminal heavy atoms of standard residues) closed by
- fixed: Fix available in next daily build
- 2:23 PM Ticket #1553 (MeetingServer: Must call either listen, or connect, not both) created by
- […]
- 1:01 PM Ticket #1552 (glClear: invalid enumerant) created by
- […]
- 11:16 AM Ticket #1551 (Model.get_selected() doesn't consider child Drawings) closed by
- fixed: Ok. This behavior was intentional. If a Model has Drawing children it …
- 11:02 AM Ticket #1550 (glClear: invalid enumerant) closed by
- can't reproduce: Appears to be inadequate OpenGL 3.3 producing an error on …
- 8:24 AM Ticket #1551 (Model.get_selected() doesn't consider child Drawings) created by
- The symptoms mainly show up in the Model Panel "Selected" column. If a …
- 5:16 AM Ticket #1550 (glClear: invalid enumerant) created by
- […]
Dec 17, 2018:
- 5:53 PM Milestone 0.8 completed
- == Chimera Features * mask map with surface #1337 * map statistics …
- 5:18 PM ChangeLog edited by
- (diff)
- 4:44 PM Ticket #1549 (AddH: More than 2 coplanar positions specified!) created by
- […]
- 3:48 PM Ticket #1548 (KeyError while writing mmCIF) created by
- […] 1f8p_assembly.cif
- 2:37 PM Ticket #1547 (Symmetry position atom: LinAlgError("Singular matrix")) created by
- […] 1dwx_assembly.cif
- 1:42 PM Ticket #1545 (AddH: 'Atom' object has no attribute 'oslIdent') closed by
- fixed: Hydrogen-addition has its own internal bug reporting when "cannot …
- 1:39 PM Ticket #1543 (Help Viewer: "help help:user": KeyError: 'href') closed by
- fixed: Fixed on Oct 25th.
- 1:07 PM Ticket #1541 (AddH: skip falsely terminal heavy atoms of standard residues) closed by
- duplicate: Truncated arginine; duplicate of #1403
- 11:37 AM Ticket #1538 (NameError: name 'p' is not defined) closed by
- fixed: Hi Sarah, Also. this problem was fixed in April, but only affects …
- 9:50 AM Ticket #1546 ("Nightly build" system for Tool Shed) created by
- It would be great if the Tool Shed had a facility to upload regular …
- 7:03 AM Ticket #1545 (AddH: 'Atom' object has no attribute 'oslIdent') created by
- […]
- 6:58 AM Ticket #1544 (AddH: z_align endpoints must be distinct) created by
- […]
- 6:52 AM Ticket #1543 (Help Viewer: "help help:user": KeyError: 'href') created by
- […]
- 6:52 AM Ticket #1542 (Handle microheterogenicity in PDB files) created by
- […]
- 6:50 AM Ticket #1541 (AddH: skip falsely terminal heavy atoms of standard residues) created by
- […]
- 5:47 AM Ticket #1540 (AddH: no lone pairs on acceptor) created by
- […]
- 5:39 AM Ticket #1539 (AddH: incorrect removal from hbond_info) created by
- […]
Dec 16, 2018:
Dec 14, 2018:
- 4:06 PM Ticket #1536 (Saving prefs: unhashable type: 'weakproxy') closed by
- fixed: Using a proxy for settings object is problematic because it is …
- 1:52 PM Ticket #1536 (Saving prefs: unhashable type: 'weakproxy') created by
- […]
- 1:24 PM Ticket #1535 (Bild: 'Place' object has no attribute 'tranform_normals') closed by
- duplicate: Duplicate of #1533.
- 9:59 AM ChangeLog edited by
- (diff)
- 12:55 AM Ticket #1535 (Bild: 'Place' object has no attribute 'tranform_normals') created by
- […]
Dec 13, 2018:
- 11:53 PM Ticket #1534 (Machine-friendly REST interface) created by
- I've been learning how to use the existing REST ChimeraX interface, …
- 6:10 PM Ticket #1530 (volume surfaceSmoothing command: cannot import name ...) closed by
- fixed: Fixed. Surface smoothing C++ code had not been ported from Chimera to …
- 5:28 PM Ticket #1529 (Interrupt of (slow?) drawing) closed by
- can't reproduce: No idea what the problem was -- they hit ctrl-C probably in the shell …
- 4:15 PM Ticket #1533 (ChimeraX bug report submission) closed by
- fixed: Fixed. Typo when converting geometry transform function call.
- 2:57 PM Ticket #1516 (command-line breaks when a command is a prefix of another command ...) closed by
- fixed: clip vs clipper will be handled by having the standard commands bundle …
- 2:50 PM Ticket #1533 (ChimeraX bug report submission) created by
- […] simple.bild
- 2:47 PM 2018-12-13 created by
- 2:11 PM DeveloperMeetings edited by
- (diff)
- 12:13 PM Ticket #1532 (Improve deferring of subcommand registration) created by
- When a subcommand of a deferred command is registered, the parent …
- 11:49 AM Ticket #1325 (RFE: include named targets in sessions) closed by
- fixed: Should be fixed by deddf4186.
- 7:09 AM Ticket #1531 (session.models.assign_id() failure) created by
-
Clipper's
Symmetry_Managerclass is designed to take over control of … - 4:48 AM Ticket #1530 (volume surfaceSmoothing command: cannot import name ...) created by
- […]
- 4:42 AM Ticket #1529 (Interrupt of (slow?) drawing) created by
- […]
Dec 12, 2018:
- 4:20 PM Ticket #1528 (Better chain tracing for prolines with side chain shown) created by
- Oliver requested in ticket #694 that chain traces that include …
- 3:35 PM Ticket #1526 (mmCIF _entity category not properly formatted) closed by
- fixed: Now quote a string if a quote is anywhere in it.
- 2:32 PM Ticket #1512 (No suitable models found for ViewDockX) closed by
- fixed: Fixed in ea93d0e6d and 38ed87e9c. Instead of …
- 12:48 PM Ticket #1527 (RFE: include named targets in sessions) closed by
- duplicate: Hi George, This is a known issue that we hope to fix sooner rather …
- 12:43 PM Ticket #1525 (Help Viewer: _generate_index() missing 1 required positional ...) closed by
- fixed: Reproduced by clicking on documentation link for a command and then …
- 11:52 AM Ticket #1527 (RFE: include named targets in sessions) created by
- […]
- 8:41 AM Ticket #1526 (mmCIF _entity category not properly formatted) created by
- […] 2qaf_h.cif
- 7:17 AM Ticket #1516 (command-line breaks when a command is a prefix of another command ...) reopened by
- ... or not. Not sure why it stopped happening for a while, but it …
- 5:46 AM Ticket #1525 (Help Viewer: _generate_index() missing 1 required positional ...) created by
- […]
Dec 11, 2018:
- 7:19 PM Ticket #225 (Command to modulate colors) closed by
- fixed
- 7:17 PM Ticket #259 (Tools should not save in sessions by default) closed by
- fixed: By default tools do not save in sessions -- has been that way for …
- 7:11 PM Ticket #465 (atomic Collection.subtract() does not preserve element order) closed by
- fixed
- 7:09 PM Ticket #503 (Allow selection atoms through holes in mesh surface) closed by
- fixed: Selecting atoms through meshes was added a couple years ago.
- 7:02 PM Ticket #709 (Better sequential stereo rendering parameters) closed by
- fixed: Changed zooming in sequential stereo about a year ago to follow the …
- 6:59 PM Ticket #710 (Allow switching into sequential stereo after startup) closed by
- fixed: Added about a year ago. Just use "camera stereo" command. It creates …
- 6:57 PM Ticket #727 (Recently used colors?) closed by
- invalid: I don't see any specific enough suggestion in this request to …
- 6:48 PM Ticket #775 (add matrix/place attr to C++ Structure) closed by
- fixed
- 6:44 PM Ticket #786 (need method to reset view to default state) closed by
- not a bug: No specific use case for resetting viewing parameters on close has …
- 6:28 PM Ticket #990 (Preference setting for orthographic camera mode) closed by
- fixed: This can be done using Preferences / Startup command list adding the …
- 6:26 PM Ticket #991 (Command to set exact zoom factor for image data) closed by
- fixed: This is done by the zoom pixelSize option, added long ago.
- 6:25 PM Ticket #1020 (OpenGL 3.3 not available) closed by
- nonchimerax: Inadequate OpenGL.
- 6:24 PM Ticket #1024 (Add infrastructure such as locks to support C++ thread use) closed by
- not a bug: I think it is impractical to have ChimeraX atomic data changes require …
- 6:17 PM Ticket #1042 (Open file dialog spews debugging info on Windows) closed by
- fixed: No longer observe this in ChimeraX from Dec 11, 2018.
- 6:14 PM Ticket #1078 (better mouse mode icon location specification) closed by
- fixed: Made each bundle that defines a mouse mode keep the icon in its own …
- 6:12 PM Ticket #1087 (Add mouse mode to position 2d labels) closed by
- fixed: Done a few months ago.
- 6:11 PM Ticket #1111 (VR meeting moving molecule moves other person's user interface pane) closed by
- fixed: Fixed motion of user interface panel.
- 6:09 PM Ticket #1136 (Allow drag on VR gui panel to adjust volume thresholds) closed by
- fixed: Drags were added a few months ago. It is not so nice to use because …
- 6:04 PM Ticket #1283 (Use alt key to emulate middle mouse with trackpad on Windows laptops) closed by
- fixed: Made Alt left click emulate right mouse, and Alt Ctrl left click …
- 5:43 PM Ticket #1523 (Infinite recursion opening mol2 file) closed by
- fixed: Fixed. This structure has 20 atoms exactly on top of each other …
- 3:59 PM Ticket #1524 (Retain PQR charge information) created by
- The atomic code currently discards the charge information that the …
- 3:54 PM Ticket #1310 (Help link in Log wrong URL for "bumps" command) closed by
- fixed
- 3:44 PM Ticket #1523 (Infinite recursion opening mol2 file) created by
- […] parm_fb15.mol2
- 2:39 PM Ticket #1426 (mlp: No module named 'chimerax.core.commands.surface') closed by
- fixed
- 2:37 PM Ticket #1446 (Crash exiting ChimeraX when VR running) closed by
- can't reproduce: Tried 3 times on the same macOS system and it did not crash. But I …
- 2:12 PM Ticket #1452 (crosslinks network "select pseudobonds" only selects end atoms) closed by
- fixed: Fixed. Made it select pseudobonds and atoms at end of pseudobonds.
- 2:01 PM Ticket #1458 (Problem reading TIFF image stack) closed by
- can't reproduce
- 2:00 PM Ticket #1504 ('close' with VR on: object of type 'NoneType' has no len()) closed by
- fixed: Fixed. Code was not checking for new VR grouping model being deleted.
- 1:47 PM Ticket #1481 (alt_loc crashes) closed by
- fixed: Cython methods that call C++ methods than can throw exceptions need to …
- 12:52 PM Ticket #1508 (device vr true: openvr.OpenVRError: b'VRInitError_Init_HmdNotFound') closed by
- worksforme: Hi Wilian, I see you were using ChimeraX 0.7 from August for this …
- 12:49 PM Ticket #1520 (AddH: 'Structure' object has no attribute 'delete_residue') closed by
- fixed: Hi Lukas, Thanks for reporting this. Fixed now! --Eric
- 11:43 AM Ticket #1510 (Crash as DockWidet changes size) closed by
- can't reproduce: Hi Jozef, Thanks for the info. It _could_ have been gesture-event …
- 8:07 AM Ticket #1522 (ViewDockX: No suitable models found for ViewDockX) created by
- […]
- 7:27 AM Ticket #1516 (command-line breaks when a command is a prefix of another command ...) closed by
- fixed: Whatever you did, the problem appears to be gone in today's build. …
- 4:01 AM Ticket #1521 ('devel install' failing for RedHat rpm builds) created by
- Trying to get closer to the bottom of #1516 by building Clipper using …
- 3:07 AM Ticket #1520 (AddH: 'Structure' object has no attribute 'delete_residue') created by
- […]
Dec 10, 2018:
- 7:14 PM Ticket #1517 (Crash while reading in a volume) closed by
- 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
- fixed: Fixed. Specifying a non-existent face image in the meeting command …
- 3:26 PM Ticket #1515 (Make StructureArg more flexible) closed by
- fixed: Done.
- 1:53 PM Ticket #1519 (Restrict open/save keyword handling to those relevant for that format) created by
- Currently all keywords registered for open (or save) apply regardless …
- 1:36 PM 2018-12-10 edited by
- (diff)
- 1:25 PM 2018-12-10 created by
- 12:16 PM DeveloperMeetings edited by
- (diff)
- 12:03 PM Ticket #1518 (Clipper: No matching distribution found) created by
- […]
- 11:46 AM Ticket #1514 (StructureArg parsing: name 'AnnotationError' is not defined) closed by
- 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
- […]
- 6:36 AM Ticket #1516 (command-line breaks when a command is a prefix of another command ...) created by
- I *think* this has been triggered because I defined a set of commands …
- 5:33 AM Ticket #1515 (Make StructureArg more flexible) created by
- 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
- fixed: Never mind. All sorted out.
- 4:43 AM Ticket #1511 (Crash in ISOLDE MDFF_Mgr destructor) closed by
- 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
- […]
Dec 9, 2018:
- 2:06 PM Ticket #1513 (Add crystallographic reflection files to command-line open) created by
- I'm currently working on integrating ISOLDE and Clipper into the …
- 11:36 AM Ticket #1512 (No suitable models found for ViewDockX) created by
- […]
- 10:11 AM Ticket #1511 (Crash in ISOLDE MDFF_Mgr destructor) created by
- […]
- 7:12 AM Ticket #1510 (Crash as DockWidet changes size) created by
- […]
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See TracTimeline
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