Timeline



Mar 27, 2018:

4:36 PM Ticket #1070 (Stack trace on starting ChimeraX in Linux) closed by Greg Couch
fixed: Qt 5.9.5 is planned to be released in late March, i.e, this week. …
11:02 AM Ticket #1071 (vseries failure: list index out of range) created by sshakeel@…
[…]

Mar 25, 2018:

11:09 AM Ticket #1070 (Stack trace on starting ChimeraX in Linux) created by Tristan Croll
Looks like a particularly nasty PyQt bug, similar to that discussed at …

Mar 23, 2018:

1:41 PM Ticket #1066 (open 2xxx; light full - Bug or feature for PDB ID numbers starting ...) closed by pett
not a bug
11:40 AM Ticket #1068 (KeyError: 'string' in attribute registration code when hover over ...) closed by pett
fixed
4:42 AM Ticket #1069 (Trigger error messages difficult to debug) created by Tristan Croll
At present, if a callback raises an exception its _TriggerHandler …

Mar 22, 2018:

11:57 PM Ticket #1068 (KeyError: 'string' in attribute registration code when hover over ...) created by Tom Goddard
Mouse hover over pseudobond gives error. open 1zik hbonds hover mouse …
7:02 PM Ticket #1067 (Automatically extend registration when using toolshed) created by Conrad Huang
Registration expiration date should be extended automatically when …
2:05 PM Ticket #1066 (open 2xxx; light full - Bug or feature for PDB ID numbers starting ...) created by jsgro@…
[…]
11:15 AM Ticket #1065 (Swap sidechain occasionally yields incorrect geometry) closed by Tom Goddard
fixed: Fixed. The bizarre behavior where the added residue position would …
10:50 AM Ticket #1065 (Swap sidechain occasionally yields incorrect geometry) created by Tristan Croll
If I load up 5f4y with added hydrogens (not sure if that's relevant), …
5:25 AM Ticket #1064 (Add "byChain" option to fitmap command) created by Tristan Croll
Someone from my building came to me yesterday, asking for help in …

Mar 20, 2018:

2:45 PM Ticket #1062 (Recent changes break mmCIF writing) closed by pett
fixed: needed to resize(6) the vector, not reserve(6)
1:45 PM Ticket #1063 (Collections don't accept Numpy arrays with mismatched type) closed by Tom Goddard
not a bug: If high speed setting float32 atom coordinates is needed in the future …
1:25 PM Ticket #1061 (Account setup) closed by pett
nonchimerax: Hi Nina, This is chimerax-bugs@… you are sending this to, …
6:52 AM Ticket #1063 (Collections don't accept Numpy arrays with mismatched type) created by Tristan Croll
[…] This came up for me because I have a Collection class with a …

Mar 19, 2018:

5:52 PM Ticket #1007 (AtomicStructures not freed when closed) closed by pett
fixed: ctypes handling of non-array python objects was leaky
3:56 PM Ticket #1062 (Recent changes break mmCIF writing) created by Greg Couch
I'm debugging using 2adw. atom.aniso_u6 is sometimes returning an …

Mar 18, 2018:

7:53 PM Ticket #1061 (Account setup) created by peninnahrachel@…
[…]

Mar 16, 2018:

10:19 AM Ticket #970 (GUI occasionally fails to respond to window resize) closed by Tom Goddard
fixed: Resize problem fixed by update to PyQt 5.10. If you want to report …

Mar 15, 2018:

5:53 PM Ticket #1028 (nucleotides ladder: limit to only displayed residues?) closed by Greg Couch
fixed: Fixed. Also fixed bug where adding nucleotides after removing all …
4:53 PM Ticket #690 (Custom atom/residue properties?) reopened by pett
The current implementation has a session-restore race condition and …
3:17 PM 2018-03-15 created by Conrad Huang
2:07 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:58 PM Ticket #985 (persistent nucleotide slabs after deleting chain) closed by Greg Couch
fixed: Fixed. Added deletions to cases where the nucleotides are recomputed.
12:46 PM Ticket #1059 ("changes" trigger is not firing correctly) closed by pett
fixed: Tristan's proposed fix does indeed fix the problem.
11:42 AM Ticket #1060 (Error assigning atom coordinate from a tuple) closed by pett
fixed
11:22 AM Ticket #1060 (Error assigning atom coordinate from a tuple) created by Tom Goddard
IHM reader is broken by Cython changes because atom coordinate cannot …
10:41 AM Ticket #1058 (Collection caching bug?) closed by Tom Goddard
fixed: Fixed. If collection has fewer objects than in cached list then don't …
7:24 AM Ticket #1059 ("changes" trigger is not firing correctly) created by Tristan Croll
[…] I'm quite heavily reliant on the 'changes' trigger, so this is …

Mar 14, 2018:

4:53 PM Ticket #1058 (Collection caching bug?) created by pett
The Collection.iter method caches the objects it creates. This …
4:20 PM Ticket #690 (Custom atom/residue properties?) closed by pett
fixed: Pseudobond now supported, which finishes the classes I intend to …
2:52 PM ChangeLog edited by Tom Goddard
(diff)
2:49 PM ChangeLog edited by Tom Goddard
(diff)
1:21 PM Ticket #1051 (Convert atoms/elements ctypes interface to Cython interface) closed by pett
fixed
8:14 AM Ticket #1057 (Provide C++ API to _geometry functions) created by Tristan Croll
Most of the headers in core.geometry._geometry provide extern "C" …

Mar 9, 2018:

1:09 PM Ticket #1056 (Crash in read_pdb_file() C++ opening nuclear pore IHM model) closed by pett
can't reproduce: In my build, I opened it three times without error. Need more to go …
12:46 PM Ticket #1056 (Crash in read_pdb_file() C++ opening nuclear pore IHM model) created by Tom Goddard
Opening the attached IHM model causes ChimeraX to crash in C++ …
9:34 AM Ticket #1055 (First "show selAtoms" command is ignored) closed by Tom Goddard
duplicate: This was fixed yesterday, but the nightly builds all failed. …
8:56 AM Ticket #1055 (First "show selAtoms" command is ignored) created by Tristan Croll
After starting ChimeraX and loading a protein small enough to appear …

Mar 8, 2018:

3:54 PM 2018-03-08 edited by Elaine Meng
(diff)
2:48 PM ChangeLog edited by Elaine Meng
(diff)
2:41 PM 2018-03-08 created by Conrad Huang
2:05 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:36 PM Ticket #1053 (Registered selectors not working on first use) closed by Conrad Huang
fixed: Fixed in 3c8b57300. Previously, only functions could be …
12:27 PM ChangeLog edited by Elaine Meng
(diff)
12:10 PM ChangeLog edited by Elaine Meng
(diff)
12:06 PM Ticket #1054 (command "open" doesn't work on URLs without suffix) created by Elaine Meng
For example, open ​http://www.rbvi.ucsf.edu/chimera Missing filename …

Mar 7, 2018:

5:40 PM Ticket #1023 (Faster change tracking) closed by pett
fixed: The second set seems okay as well. I've committed them as well. --Eric
5:27 PM Ticket #913 (help command with absolute path to html does not work) closed by Greg Couch
fixed: I believe that changed. The command is now "open …
3:12 PM FAI edited by pett
(diff)
2:30 PM Ticket #914 (Write mmCIF file) closed by Greg Couch
fixed: Initial mmCIF writing is in. It is at level V7 mmCIFWriting.
1:43 PM mmCIFWriting edited by Greg Couch
(diff)

Mar 6, 2018:

5:42 PM Ticket #1053 (Registered selectors not working on first use) created by Tom Goddard
open 1a0m show selAtoms show selAtoms should show all the atoms on …
1:03 PM Ticket #1052 (Make starting directory ~/Desktop when launching from icon.) closed by Tom Goddard
fixed: Fixed. Implemented idea in previous comment.

Mar 5, 2018:

6:52 PM Ticket #1052 (Make starting directory ~/Desktop when launching from icon.) created by Tom Goddard
On macOS double clicking the ChimeraX icon starts it in directory "/" …
2:00 PM Ticket #1051 (Convert atoms/elements ctypes interface to Cython interface) created by Conrad Huang
Improve performance.
1:58 PM Ticket #1050 (Move core packages into bundles) created by Conrad Huang
Four packages should be moved from core to bundles: ui, atomic, map …
1:53 PM Ticket #908 (Stringdb bug) closed by Conrad Huang
fixed: Generate a better error message, instead of a Python traceback, when …

Mar 3, 2018:

5:35 PM mmCIFWriting edited by Greg Couch
(diff)

Mar 2, 2018:

4:38 PM Ticket #1049 (RE: VR ON bug in latest release) created by TSkillman@…
[…]
4:22 PM Ticket #1048 (Re: VR ON bug in latest release) created by goddard@…
[…]
4:13 PM Ticket #1047 (VR ON bug in latest release) created by TSkillman@…
[…]
4:13 PM Ticket #1046 (VR ON bug in latest release) created by TSkillman@…
[…]

Mar 1, 2018:

9:03 AM Ticket #1044 (Need "ribbon drawing finished" trigger) closed by Tristan Croll
not a bug: Ah - never mind. Turns out the 'frame drawn' trigger was what I was …

Feb 28, 2018:

12:27 PM Ticket #1045 (Nucleic matchmaker error) created by dgutierrez@…
[…] Screen Shot 2018-02-28 at 3.23.57 PM.png​

Feb 27, 2018:

4:40 AM Ticket #1044 (Need "ribbon drawing finished" trigger) created by Tristan Croll
To provide live symmetry visualisation for ribbons it looks to me like …
1:23 AM Ticket #1043 (Isolde error: no rotamers) closed by Tristan Croll
nonchimerax: Will continue any further discussion off-list.

Feb 26, 2018:

10:44 AM Ticket #1043 (Isolde error: no rotamers) created by dgutierrez@…
[…]
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