Timeline



Mar 25, 2019:

4:19 PM 2019-03-21 edited by Elaine Meng
(diff)
4:10 PM 2019-03-21 edited by Elaine Meng
(diff)
11:59 AM Ticket #1801 (error reading DICOM RTDOSE: tuple object not callable) created by Elaine Meng
for example, any of the RT DOSE subdirs in the same dataset as …
11:56 AM Ticket #1800 (error reading DICOM CT: TypeError: Cannot cast ufunc multiply output) created by Elaine Meng
for example, the CT subdirectory in the same dataset as attached to …
11:46 AM Ticket #1798 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Hi Klaas, This problem was fixed the day after the version you …
11:14 AM Ticket #1799 (error reading DICOM SEG models: IndexError: tuple index out of range) created by Elaine Meng
Reading these files was working fine for a while, but another change …
11:02 AM Ticket #1797 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Hi Kuen, This problem was fixed the day after the version you got(!), …

Mar 24, 2019:

1:31 PM Ticket #1798 ('Session' object has no attribute 'preset_mgr') created by klaas.yperman@…
[…]

Mar 23, 2019:

6:35 AM Ticket #1797 ('Session' object has no attribute 'preset_mgr') created by kpwulab@…
[…]

Mar 21, 2019:

4:24 PM 2019-03-21 edited by Elaine Meng
(diff)
4:23 PM 2019-03-21 edited by Elaine Meng
(diff)
4:17 PM 2019-03-21 edited by Elaine Meng
(diff)
4:16 PM 2019-03-21 edited by Elaine Meng
(diff)
4:16 PM 2019-03-21 edited by Elaine Meng
(diff)
3:20 PM 2019-03-21 created by Conrad Huang
2:05 PM DeveloperMeetings edited by Conrad Huang
(diff)
11:42 AM Ticket #1795 (self._positions is None) closed by Eric Pettersen
duplicate: Fixed last month.

Mar 20, 2019:

4:28 PM Ticket #1796 (Some kind of crash on the GPU) created by chimerax-bug-report@…
[…]
6:30 AM Ticket #1795 (self._positions is None) created by chimerax-bug-report@…
[…]

Mar 19, 2019:

5:28 PM Ticket #1793 (Add VR hand controller support for ISOLDE mouse modes) created by Tom Goddard
Add virtual reality hand controller support for ISOLDE mouse modes. …
4:27 PM Ticket #1792 (command "preset cartoon" TypeError: expected 1 arguments, got 0) closed by Eric Pettersen
fixed: Missed some parens in a custom-sortable-string class I implemented. …
4:18 PM Ticket #1792 (command "preset cartoon" TypeError: expected 1 arguments, got 0) created by Elaine Meng
[…]
12:49 PM Ticket #1791 (single-color space-filling preset lighting) closed by Eric Pettersen
fixed
11:07 AM Ticket #1791 (single-color space-filling preset lighting) created by olibclarke@…
[…] Screen Shot 2019-03-19 at 2.04.49 PM.png​

Mar 18, 2019:

3:10 PM 2019-03-07 edited by Tom Ferrin
(diff)
11:48 AM Ticket #1788 (Error handling: cannot unpack non-iterable NoneType object) closed by Eric Pettersen
fixed
11:21 AM ChangeLog edited by Elaine Meng
(diff)
10:42 AM Ticket #1790 (Crash handling event) closed by Eric Pettersen
can't reproduce: Seems to be entirely within Qt and graphics driver
10:26 AM Ticket #1790 (Crash handling event) created by chimerax-bug-report@…
[…]
5:42 AM Ticket #1788 (Error handling: cannot unpack non-iterable NoneType object) created by tic20@…
[…]
4:43 AM Ticket #1787 (Separate development builds on the Tool Shed) created by Tristan Croll
As per discussions last week, it would be great to have the ability to …
3:58 AM Ticket #1786 (Naming of development bundles) created by Tristan Croll
Setup Tools seems to be doing some automatic reformatting of bundles …

Mar 15, 2019:

2:57 PM Ticket #1785 (Have "view" not override center-of-view rotation mode) created by tic20@…
If rotation mode is center-of-view, have "view" command just continue …
2:38 PM Ticket #1784 (Spurious "command replacing existing command" log entries) created by Eric Pettersen
[…]
2:28 PM Ticket #1780 (Include .pyx file in distribution for reference purposes) closed by Eric Pettersen
fixed
2:12 PM Ticket #1783 (mmCIF: non-standard nucleotides disconnected in 5tna) created by Eric Pettersen
In 5tna, residue 2MG (:10) does not connect to either the nucleotide …
1:45 PM Ticket #1778 (ISOLDE installation: UnicodeDecodeError) closed by Eric Pettersen
duplicate
7:19 AM Ticket #1782 (Crash finding 6-member planar NR2 ring in 5vpx) created by lpravda@…
[…] 5vpx.cif​
7:17 AM Ticket #1781 (Crash finding 6-member planar NR2 ring in 5vrj) created by lpravda@…
[…] 5vrj.cif​

Mar 14, 2019:

5:45 PM benchmarking edited by Greg Couch
(diff)
5:37 PM Ticket #1780 (Include .pyx file in distribution for reference purposes) created by goddard@…
[…]
5:34 PM benchmarking edited by Greg Couch
(diff)
5:32 PM benchmarking edited by Greg Couch
(diff)
5:07 PM benchmarking edited by Greg Couch
(diff)
4:47 PM Ticket #1779 (ISOLDE picking: unsupported operand type(s) for -: 'NoneType' and ...) created by goddard@…
[…]
3:42 PM Ticket #1778 (ISOLDE installation: UnicodeDecodeError) created by goddard@…
[…]
3:13 PM benchmarking edited by Greg Couch
(diff)
2:54 PM benchmarking edited by Greg Couch
(diff)
2:07 PM benchmarking edited by Greg Couch
(diff)
2:06 PM benchmarking created by Greg Couch
12:52 PM DeveloperMeetings edited by Greg Couch
(diff)
12:18 PM Ticket #1777 (Model-specific lighting/materials) created by olibclarke@…
[…]
12:00 PM Ticket #1776 (Mottled ribbons) closed by Tom Goddard
not a bug: ChimeraX ambient occlusion is an approximation. To compute ambient …
10:46 AM Ticket #1772 (REST broken: KeyError: 'CONTENT-LENGTH') closed by Conrad Huang
fixed: The (next successful, probably dated March 14, 2019) daily build …
8:36 AM Ticket #1776 (Mottled ribbons) created by olibclarke@…
[…] Screen Shot 2019-03-14 at 11.33.49 AM.png​
8:33 AM Ticket #1775 (RFE: custom palettes) created by olibclarke@…
[…]

Mar 13, 2019:

9:37 PM Ticket #1774 (Various errors) created by chimerax-bug-report@…
[…]
7:07 PM Ticket #1598 (RFE: command to report current volume-rendering settings) closed by Elaine Meng
fixed: "volume settings" command has been added
5:31 PM ChangeLog edited by Tom Goddard
(diff)
5:27 PM Ticket #1773 (Optimize speed reading TIFF volume data) closed by Tom Goddard
fixed: Switched to reading TIFF volume with tifffile.py (version 2019.3.18) …
2:56 PM ChangeLog edited by Elaine Meng
(diff)
2:46 PM Ticket #1773 (Optimize speed reading TIFF volume data) created by Tom Goddard
Reading 3d images in TIFF format with Pillow is much slower than one …
1:06 PM Ticket #1772 (REST broken: KeyError: 'CONTENT-LENGTH') created by tic20@…
[…]
11:30 AM Ticket #1759 (Bond rotation slow when ribbon shown) closed by Conrad Huang
fixed: Verified to work in VR
10:08 AM Ticket #1771 ("devel install" cannot link OpenMM.lib) created by Tristan Croll
In Windows, the OpenMM .lib files are currently placed in …

Mar 12, 2019:

2:05 PM ChangeLog edited by Elaine Meng
(diff)
11:18 AM Ticket #1769 (IHM NameError: name 'mname' is not defined) closed by Tom Goddard
fixed: Fixed. Typo in recent code change involving opening map file.
11:01 AM Ticket #1770 (Add command to create pseudobonds.) created by Tom Goddard
Should have a command for creating pseudobonds, setting their color …
10:53 AM Ticket #1769 (IHM NameError: name 'mname' is not defined) created by brinda.vallat@…
[…]
9:53 AM Ticket #1768 (mmCIF export: chain ID KeyError) created by lpravda@…
[…] assembly.cif.gz​
9:46 AM Ticket #1767 (AddH: trying to bind bonded geometry of atom with no bonds) created by lpravda@…
[…] assembly.cif.gz​

Mar 11, 2019:

4:46 PM Ticket #1736 (Morph: No coordset id 1) closed by Tom Goddard
fixed: Fixed. Morph was making a copy of the first model and then adding …
11:18 AM Ticket #1765 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Hi Haoming, Sorry for the problem with the session restore. It was …
11:14 AM Ticket #1764 (UnicodeDecodeError installing ISOLDE) closed by Eric Pettersen
duplicate: This is a known bug affecting ChimeraX 0.8 in Windows. Please see …

Mar 9, 2019:

5:47 PM Ticket #1766 (Permission denied installing Clipper) created by rinku.jain@…
[…]
10:05 AM Ticket #1765 ('Session' object has no attribute 'preset_mgr') created by haom@…
[…] error.txt​

Mar 9, 2019:

1:03 PM Ticket #1764 (UnicodeDecodeError installing ISOLDE) created by filip.vanpetegem@…
[…]

Mar 8, 2019:

9:55 PM Ticket #1762 (Blend multichannel volume data on GPU) created by Tom Goddard
Would like to be able to blend multichannel volume data by keeping …
7:38 PM Ticket #1761 (Volume rendering artifacts from 8-bit colors) created by Tom Goddard
Volume rendering as a 3d image sometimes appears darker at step 1 …
4:16 PM Ticket #1760 (UnicodeDecodeError installing ISOLDE) closed by Eric Pettersen
duplicate
3:17 PM Ticket #1760 (UnicodeDecodeError installing ISOLDE) created by fage.cd@…
[…]

Mar 7, 2019:

3:02 PM 2019-03-07 created by Conrad Huang
2:06 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:45 PM Ticket #1759 (Bond rotation slow when ribbon shown) created by Tom Goddard
When rotating a sidechain bond with the mouse with ribbon display, the …
1:40 PM Ticket #1758 (Ribbon color change slow because it recomputes ribbon) created by Tom Goddard
Changing any ribbon residue color causes the shape of the entire …
1:07 PM Ticket #1757 (Need access to password protected web sites) created by Greg Couch
Currently, when one requests a password protected web site, e.g., …
11:58 AM Ticket #1669 (Toolshed updating list of tools: 'list' object has no attribute 'split') closed by Conrad Huang
fixed: Fixed by 9c80cac968. Daily builds after January 24, 2019 …
11:57 AM Ticket #1727 (Startup: AttributeError: 'list' object has no attribute 'split') closed by Conrad Huang
fixed: Fixed by 9c80cac968. Daily builds after January 24, 2019 …
11:04 AM Ticket #1756 (hide/show DICOM SEG gives AttributeError: 'NoneType' object has no ...) closed by Tom Goddard
fixed: Fixed. Error happened when number of blended dicom images changed.
10:55 AM Ticket #1755 (No cPickle in Python 3) closed by Eric Pettersen
not a bug: In Python 3, just use "pickle"
9:43 AM Ticket #1756 (hide/show DICOM SEG gives AttributeError: 'NoneType' object has no ...) created by Elaine Meng
Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 …
6:52 AM Ticket #1755 (No cPickle in Python 3) created by chimerax-bug-report@…
[…]
5:31 AM Ticket #1754 (ChromaDepth) created by Tristan Croll
I'm in bed with a cold and a little bored, and someone on the CCP4 …

Mar 6, 2019:

12:48 PM Ticket #1753 (cartoon style command interprets spec with atoms but without ...) created by Elaine Meng
I am prototyping possible presets and noticed that in certain cases …
7:23 AM Ticket #1752 (Focal blur) created by olibclarke@…
[…]

Mar 5, 2019:

2:33 PM Ticket #1729 (OpenGL buffer was not deleted before core.graphics.Buffer) closed by Tom Goddard
can't reproduce: Could not find any way for this to happen. Improved error message to …
2:32 PM toolbar-unification edited by Elaine Meng
(diff)
1:49 PM Ticket #1751 ('Alignment' object has no attribute 'suspend_notify_viewers') closed by Eric Pettersen
fixed: Hi Cody, Thanks for reporting this -- it hadn't been reported before. …
1:36 PM Ticket #1751 ('Alignment' object has no attribute 'suspend_notify_viewers') created by cody.warren@…
[…] 6atk.pdb​
1:31 PM Ticket #1750 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Hi Cody, Sorry for the problem with the session restore. It is fixed …
1:25 PM Ticket #1750 ('Session' object has no attribute 'preset_mgr') created by cody.warren@…
[…] MERS_DPP4_PDB4l72_PosSelection.cxs​
10:32 AM Ticket #1749 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Fixed/pushed.
10:30 AM Ticket #1747 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
duplicate: Hi Rohit, Sorry about this error. I have fixed it now and the fix …
10:28 AM Ticket #1746 ('Session' object has no attribute 'preset_mgr') closed by Eric Pettersen
fixed
9:19 AM Ticket #1749 ('Session' object has no attribute 'preset_mgr') created by goddard@…
[…]
8:45 AM Ticket #1748 (Extend solid rendering brightness curve) created by olibclarke@…
[…] Screen Shot 2019-03-05 at 11.36.49 AM.png​
8:06 AM Ticket #1747 ('Session' object has no attribute 'preset_mgr') created by rhsubram@…
[…]
4:33 AM Ticket #1746 ('Session' object has no attribute 'preset_mgr') created by chimerax-bug-report@…
[…]

Mar 4, 2019:

6:47 PM Ticket #1745 (Error opening DICOM with lossless JPEG image encoding) created by goddard@…
[…] image-000001.dcm​
4:00 PM Ticket #1742 (volume onesmask: local variable 'varray' referenced before assignment) closed by Tom Goddard
fixed: Fixed. Appears that the "volume onesmask" command was never tested, …
3:47 PM Ticket #1744 (undo does not undo cartoon xsection change of some residues) created by Elaine Meng
When a protein is first shown as ribbon, the strands have rectangular …

Mar 1, 2019:

4:17 PM toolbar-unification edited by Eric Pettersen