![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Jan 30, 2019:
- 4:03 PM Ticket #1665 (Bundles from other builds being used) closed by
- duplicate: duplicate of #1642
- 4:02 PM Ticket #1664 (Bundles from other builds being used) closed by
- duplicate: duplicate of #1642
- 3:14 PM Ticket #1666 (bundle_info.xml DataFormat classifier needs allow_directory option) created by
- Need ChimeraXClassifier DataFormat allow_directory option …
- 2:32 PM Ticket #1665 (Bundles from other builds being used) created by
- […]
- 2:28 PM Ticket #1664 (Bundles from other builds being used) created by
- […]
Jan 29, 2019:
- 5:58 PM Ticket #1662 (DICOM key error bitsAllocated) closed by
- fixed: I made the DICOM reader warn about and ignore these dicom files it …
- 1:20 PM Ticket #1659 (Crash due to NULL sseq.structure pointer) closed by
- duplicate: Need session file to reproduce
- 12:10 PM Ticket #1663 (DICOM value error 50 times but 2 found) closed by
- fixed: When opening a partial time series (files present for only 2 of 50 …
- 11:24 AM Ticket #1663 (DICOM value error 50 times but 2 found) created by
- Narrowed down the mouse data to at least one example, attached as zip …
- 11:10 AM Ticket #1662 (DICOM key error bitsAllocated) created by
- Narrowed down the problem with the head/neck study. Within the …
- 9:41 AM Ticket #1661 (Support adding state managers from bundles) created by
- Session state managers are useful mechanisms that provide a …
Jan 28, 2019:
- 6:38 PM Ticket #1660 (Unexpected None data given to StructureSeq.restore_snapshot()) created by
- […]
- 6:31 PM Ticket #1657 (DICOM singular matrix error) closed by
- nonchimerax: This DICOM data set has 88 planes, 87 of which are spaced at 4 mm in z …
- 6:28 PM Ticket #1659 (Crash due to NULL sseq.structure pointer) created by
- […]
- 6:15 PM Ticket #1656 (Structure sequence returns NULL structure pointer) closed by
- can't reproduce
- 5:37 PM Ticket #1658 (Structure sequence returns NULL structure pointer) created by
- […]
- 4:11 PM Ticket #1657 (DICOM singular matrix error) created by
- Narrowed this one down to a subset of the QIN LUNG CT data. Zip file …
- 3:58 PM Ticket #1656 (Structure sequence returns NULL structure pointer) created by
- […]
- 2:53 PM Ticket #1655 (Command history problems) created by
- […]
- 2:46 PM Ticket #1654 (Constant-size pivot indicator) created by
- […] Screen Shot 2019-01-28 at 5.45.21 PM.png
- 2:19 PM Ticket #1653 (Allow clip command distances specified from center of rotation) created by
- Current clip command specifies distances from center of bounding box. …
- 2:16 PM Ticket #1652 (Allow depth cue on unlit meshes) created by
- Oliver wants depth cue on unlit meshes. Begin forwarded message: …
- 11:51 AM Ticket #1651 (sseq_structure probably returning NULL) closed by
- can't reproduce
- 11:47 AM Ticket #1651 (sseq_structure probably returning NULL) created by
- […]
- 10:47 AM Ticket #1648 (draw() takes 3 positional arguments but 4 were given) closed by
- duplicate: Fixed months ago.
- 3:43 AM Ticket #1650 (IncludeDir argument in bundle_info.xml no longer recognises $HOME) created by
- Just updating Clipper/ISOLDE to use the ChimeraX daily builds. Up …
- 2:36 AM Ticket #1648 (draw() takes 3 positional arguments but 4 were given) created by
- […]
- 2:26 AM Ticket #1647 (UnicodeDecodeError installing ISOLDE) closed by
- duplicate: This is a known issue in the ChimeraX 0.8 release. Instructions on how …
Jan 27, 2019:
Jan 26, 2019:
- 2:44 PM Ticket #1646 (Clip broken + depth cueing question) created by
- […] Screenshot 2017-05-26 10.23.18.png
- 9:15 AM Ticket #1645 (Ribbons could be smoother) created by
- […] comparsion.jpg
Jan 25, 2019:
- 3:04 PM ChangeLog edited by
- (diff)
- 3:04 PM ChangeLog edited by
- (diff)
- 12:19 PM Ticket #1643 (FastVolumeSurface class not restorable) created by
- […]
- 11:32 AM Ticket #1642 (Bundles from other builds being used) created by
- […]
Jan 24, 2019:
- 3:22 PM Ticket #1641 (ChimeraX does not start: KeyError: 'ChimeraX_Clipper') closed by
- fixed: Working now in a build from scratch.
- 3:05 PM 2019-01-24 edited by
- (diff)
- 3:03 PM 2019-01-24 created by
- 2:03 PM DeveloperMeetings edited by
- (diff)
- 1:13 PM Ticket #1641 (ChimeraX does not start: KeyError: 'ChimeraX_Clipper') created by
- ChimeraX 0.8 will start but newer ChimeraX builds exit at start up -- …
- 12:34 PM Ticket #1638 (ISOLDE installation: UnicodeDecodeError) closed by
- duplicate: I've added instructions on how to work around the Unicode bug at …
- 11:49 AM Ticket #1639 (ISOLDE installation: UnicodeDecodeError) closed by
- fixed
- 11:21 AM ChangeLog edited by
- (diff)
- 7:35 AM Ticket #1640 ('toolshed install isolde reinstall true' attempts to install wrong ...) created by
- Just trying to find new ways to break things (and attempt to replicate …
- 7:01 AM Ticket #1639 (ISOLDE installation: UnicodeDecodeError) created by
- […]
- 6:08 AM Ticket #1638 (ISOLDE installation: UnicodeDecodeError) created by
- […]
- 4:29 AM Ticket #1637 (ISOLDE installation: UnicodeDecodeError) created by
- […]
- 3:27 AM Ticket #1636 (Installation problems with openSuSE Leap 15.0) created by
- […]
- 2:49 AM Ticket #1635 (Replace PyQt5 with PySide2) created by
- We currently require a paid commercial license for PyQt5 to be able to …
- 2:02 AM Ticket #1634 (Inconsistent ToolShed download statistics) created by
- On the ToolShed download statistics page for ISOLDE, there's a weird …
Jan 23, 2019:
- 4:52 PM Ticket #1610 (AddH: acc_phi_psi() takes 8 positional arguments but 9 were given) closed by
- duplicate: This is because of the mmCIF reader messing up the connectivity of …
- 2:42 PM Ticket #1629 (KeyError: 'ChimeraX_ISOLDE') closed by
- fixed: Fixed by same changes as #1628.
- 2:12 PM Ticket #1626 (Traceback and no redraw after dragging Volume Viewer "solid" display ...) closed by
- fixed
- 1:35 PM Ticket #1628 (ChimeraX fails to start after failed bundle install) closed by
- fixed: Fixed in b3d8cadc2. If cache data is not consistent with …
- 12:29 PM Ticket #642 (OpenMM bug) closed by
- fixed: The daily builds are now using OpenMM 7.3.
- 11:58 AM Ticket #1632 (TypeError: __getattr__() missing 1 required positional argument: ...) closed by
- fixed: Problem was that attr_registration.py defined a __getattr__ function …
- 11:08 AM Ticket #1582 (Volume Viewer deleted twice(?)) closed by
- can't reproduce: Tried several things but could not reproduce. We can catch the …
- 11:05 AM Ticket #1633 (Depict thermal ellipsoids) created by
- Same functionality as original Chimera
- 11:05 AM Ticket #1632 (TypeError: __getattr__() missing 1 required positional argument: ...) created by
- […]
- 10:42 AM Ticket #1587 (Registration internal error) closed by
- fixed: Fixed in 49e0c4149. When registration server is …
- 10:39 AM Ticket #1630 (ChimeraX bug report submission) closed by
- not a bug
- 8:25 AM Ticket #1631 (UnicodeDecodeError during ISOLDE install) created by
- […]
- 4:30 AM Ticket #1630 (ChimeraX bug report submission) created by
- […]
- 4:28 AM Ticket #1629 (KeyError: 'ChimeraX_ISOLDE') created by
- […]
- 12:08 AM Ticket #1628 (ChimeraX fails to start after failed bundle install) created by
- […]
Jan 22, 2019:
- 6:01 PM Ticket #1627 (Startup error: KeyError: 'ChimeraX_ISOLDE') created by
- […]
- 4:50 PM Ticket #1611 (AddH: list index out of range in roomiest()) closed by
- fixed: Fixed. AddH now treats CYS similarly to HIS (i.e. as "unspecified" …
- 12:34 PM Ticket #1623 (Session restore: msgpack: max_ext_len exceeded) closed by
- duplicate: Duplicate of #1616. Please try a newer daily build, dated 2019-01-17 …
- 12:15 PM Ticket #1626 (Traceback and no redraw after dragging Volume Viewer "solid" display ...) created by
- […]
- 6:30 AM Ticket #1624 (Wrong ChimeraX version when installing ISOLDE 1.0b1) closed by
- nonchimerax: ISOLDE 1.0b1 requires the ChimeraX 0.6 release. If you wait a day or …
Jan 21, 2019:
- 6:43 PM FAI edited by
- (diff)
- 5:59 PM Ticket #1624 (Wrong ChimeraX version when installing ISOLDE 1.0b1) created by
- […]
- 2:44 PM FAI edited by
- (diff)
Jan 19, 2019:
Jan 18, 2019:
- 4:37 PM Ticket #1622 (Need a method to clear atom's anisotropic B-factors) closed by
- fixed: a.aniso_u6 = None will now clear the aniso_u info.
- 4:01 PM Ticket #1621 (map planes slider doesn't go away when changed to non-plane with command) closed by
- fixed: Fixed. Changing a volume to show full region with a command now hides …
- 12:48 PM Ticket #1605 (Residue.atoms yields corrupted array after residue deleted) closed by
- fixed: The cost of the check seems to be negligible, so I have added it. …
- 12:25 PM Ticket #1256 (Module can't find shared lib) closed by
-
fixed: Appears to be fixed (after many iterations of
bundle_builder.py). - 6:49 AM Ticket #1622 (Need a method to clear atom's anisotropic B-factors) created by
- Not to set the entries to zero, but to clear the Atom.aniso_u field …
Jan 17, 2019:
- 3:17 PM Ticket #1621 (map planes slider doesn't go away when changed to non-plane with command) created by
- If I open a map file that initially displays as a single plane with a …
- 3:11 PM Ticket #1620 ("move planes" mouse mode behavior with multiple maps) created by
- I don't know if this is a request for enhancement or a bug report, but …
- 2:59 PM Ticket #1617 (Blast Protein lower case chain) closed by
- fixed: Fixed in 4c653742c. Blast database for PDB from NCBI uses …
- 1:38 PM Ticket #1618 (Session restore: msgpack: max_ext_len exceeded) closed by
- duplicate: Duplicate of #1616. Please send me a session file so I can test if …
- 11:58 AM Ticket #1619 (draw_xor_rectangle: draw() takes 3 positional arguments but 4 were given) closed by
- duplicate: Fixed months ago. Bug reported in Sept ChimeraX build.
- 10:05 AM Ticket #1619 (draw_xor_rectangle: draw() takes 3 positional arguments but 4 were given) created by
- […]
- 12:49 AM Ticket #1618 (Session restore: msgpack: max_ext_len exceeded) created by
- […]
Jan 16, 2019:
- 11:54 PM FAI edited by
- (diff)
- 5:28 PM Ticket #1617 (Blast Protein lower case chain) created by
- Blast results have lower case chains reported as a doubling of the …
- 4:40 PM Ticket #1613 (windowing mouse mode swap horizontal/vertical behavior) closed by
- fixed: Fixed. Made vertical drag do leveling and horizontal do windowing. …
- 4:26 PM Ticket #1615 (Drag select: glDrawBuffer(GL_FRONT): invalid operation) closed by
- fixed: Fixed. Drawing code pushed the silhouette framebuffer and then an …
- 3:49 PM Ticket #1616 (Session restore: msgpack: max_ext_len exceeded) created by
- […]
- 3:45 PM Ticket #1615 (Drag select: glDrawBuffer(GL_FRONT): invalid operation) created by
- […]
- 3:39 PM Ticket #1608 (Problem reshowing volume series) closed by
- can't reproduce: Not sure how you removed the threshold. Perhaps there is a bug where …
- 2:56 PM Ticket #1121 (Erroneous bonding at RNA chain break in PDB 5an9) closed by
- fixed: Apparently fixed by other previous changes/fixes.
- 10:52 AM ChangeLog edited by
- (diff)
- 9:33 AM Ticket #1614 (RFE: visual (text) feedback of window/threshold values) created by
- This could apply to both the graphics window in desktop use and in VR …
- 9:29 AM Ticket #1613 (windowing mouse mode swap horizontal/vertical behavior) created by
- Looks like both Horos and 3DSlicer windowing mouse modes use vertical …
Jan 15, 2019:
- 10:32 PM Ticket #1612 (DICOM unsupported value type) closed by
- fixed: Ok, can read this segmentation DICOM file now. This took more work …
- 1:35 PM Ticket #1540 (AddH: no lone pairs on acceptor) closed by
- fixed: Fixed by implementing tau test for aniline as an acceptor so that it …
- 12:41 PM Ticket #1612 (DICOM unsupported value type) created by
- […] 11-06-2014-1-96508.zip
- 11:34 AM Ticket #1561 (Bundle build system does not recompile changed C++ files) closed by
- fixed: Machine this bug occurred on had numpy 1.14.3 in ChimeraX. Updating …
- 7:55 AM Ticket #1611 (AddH: list index out of range in roomiest()) created by
- […]
- 7:55 AM Ticket #1610 (AddH: acc_phi_psi() takes 8 positional arguments but 9 were given) created by
- […]
- 3:50 AM Ticket #1608 (Problem reshowing volume series) created by
- […]
- 1:48 AM Ticket #1607 (Reading DCD: UnicodeDecodeError: unexpected end of data) created by
- […]
Jan 14, 2019:
- 6:00 PM Ticket #1606 (Singular matrix reading DICOM time series) closed by
- fixed: Error was caused by reading a DICOM time series which is not yet …
- 5:03 PM Ticket #1124 (Remove bot traffic from Toolshed download stats?) closed by
-
fixed: I've added a
robots.txtthat forbids mining all cxtoolshed pages. - 10:41 AM Ticket #1606 (Singular matrix reading DICOM time series) created by
- […] 10-01-2010-339068828-GBMintracranial-631.2.zip
- 4:42 AM Ticket #1605 (Residue.atoms yields corrupted array after residue deleted) created by
- If I have a model open: […]
Jan 11, 2019:
- 4:34 PM Ticket #1602 (Problem playing through multiple volume series: object of type ...) closed by
- fixed: Fixed. Attempting to use map series slider after first map in series …
- 3:44 PM Ticket #1603 (Multiple OpenGL errors) closed by
- nonchimerax: Inadequate graphics driver. Incomplete framebuffer errors are startup.
- 9:56 AM Ticket #1603 (Multiple OpenGL errors) created by
- […]
- 1:44 AM Ticket #1602 (Problem playing through multiple volume series: object of type ...) created by
- […]
Jan 10, 2019:
- 6:31 PM Ticket #1600 (Reading map: 'numpy.float64' object cannot be interpreted as an integer) closed by
- fixed: Fixed. Move planes mouse mode in orthoplanes mode was broken because …
- 3:13 PM Ticket #1601 (test notify-when-closed) closed by
- not a bug: Here we go!
- 3:12 PM Ticket #1601 (test notify-when-closed) created by
- 3:04 PM Ticket #1600 (Reading map: 'numpy.float64' object cannot be interpreted as an integer) created by
- […]
- 2:43 PM 2019-01-10 created by
- 2:08 PM DeveloperMeetings edited by
- (diff)
- 2:08 PM DeveloperMeetings2018 created by
- 1:45 PM Ticket #1599 (RFE: command (or other way) to restore initial display settings of a volume) created by
- Would be nice if there was a way to restore the thresholds and perhaps …
- 1:41 PM Ticket #1598 (RFE: command to report current volume-rendering settings) created by
- I keep wishing for some command to report the current rendering …
- 11:09 AM Ticket #1597 (error adding distance if Distances window previously closed) closed by
- fixed: Wasn't deregistering all trigger handlers when tool deleted
- 9:56 AM Ticket #1597 (error adding distance if Distances window previously closed) created by
- I had a few distances, showed the Distance tool, and then deleted all …
Jan 9, 2019:
- 5:11 PM Ticket #1596 (Volume Viewer interface not happy with non-Z planes) closed by
- fixed: Fixed. Volume viewer code was not switching back to showing full …
- 3:54 PM Ticket #1596 (Volume Viewer interface not happy with non-Z planes) created by
- If I use a command to show non-Z planes, e.g. vol #1 planes y,110 …
- 3:21 PM Ticket #1595 (glDrawBuffer(GL_FRONT): invalid operation) closed by
- duplicate: Fourth report of this error on different computer systems. Unclear …
- 2:25 AM Ticket #1595 (glDrawBuffer(GL_FRONT): invalid operation) created by
- […]
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
- […]
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