Timeline



Apr 12, 2018:

3:41 PM Ticket #1014 (mmCIF not assigning ss_id correctly) closed by pett
fixed: ss_ids are now normalized before first use: 0 for coil, helix/strand …
12:59 PM Ticket #1086 (Show modified residues in smart display?) created by Tom Goddard
Xiaokun Shu opened his GFP structure 2duf and the chromophore (:C12) …
10:54 AM ChangeLog edited by Elaine Meng
(diff)

Apr 11, 2018:

3:28 PM ChangeLog edited by Elaine Meng
(diff)
12:29 PM Ticket #1085 ("name frozen" target reported to contain models after those models ...) created by Elaine Meng
If a frozen user-defined target includes parts of more than one model …
11:59 AM Ticket #1084 ("name delete all" gives traceback: 'is_selector_reserved' is not defined) created by Elaine Meng
"name delete all" deletes built-in targets, whereas it should just …
11:59 AM Ticket #1082 (Ability to temporarily disable specific mouse modes) closed by Tom Goddard
wontfix: There are plenty of commands that can modify structures (e.g. deleting …
3:57 AM Ticket #1083 (Add missing sidechains) created by Tristan Croll
Would be great to have this as a command. Could be a simple wrapper …
3:54 AM Ticket #1082 (Ability to temporarily disable specific mouse modes) created by Tristan Croll
Up until now I've been disabling the entire mouse modes toolbar any …

Apr 10, 2018:

8:22 AM Ticket #1081 (Bug in unit testing) created by Tristan Croll
Not sure why I was suddenly hit with this, other than that I'm …

Apr 9, 2018:

5:39 PM Ticket #1075 (label (single?) color not saved in session) closed by pett
fixed
4:02 PM Ticket #1080 (Feature needed for ConSurf) created by fabian.glaser@…
1) Read Clustal ALN alignments 2) Show alignment headers 2b) Make …
1:30 PM Ticket #1079 (distance label format not saved in session) closed by pett
fixed
12:11 PM Ticket #1079 (distance label format not saved in session) created by Elaine Meng
distance label is colored black when I save the attached session, but …
12:07 PM Ticket #1078 (better mouse mode icon location specification) created by pett
The current scheme for mouse mode icons isn't very extensible since …
10:07 AM Ticket #1077 (Working with InterSphinx) created by Tristan Croll
(Hope I'm asking the right person!) I'm finally getting around to …
8:25 AM Ticket #1076 (Signs of memory leak during toolshed install) created by Tristan Croll
OK, this is doing my head in somewhat. In my ISOLDE source, if I add …

Apr 7, 2018:

1:59 PM Ticket #617 (Registration support) closed by Conrad Huang
fixed: Still need to link toolshed access with extending registration …

Apr 6, 2018:

2:55 PM Ticket #1075 (label (single?) color not saved in session) created by pett
I had adjusted label colors by using the color-well button in the …
10:53 AM Ticket #1073 (ChimeraX bug | No such file or directory | Desktop/) closed by Tom Goddard
fixed: Fixed. Image save and movie save toolbar buttons will save in current …
12:00 AM Milestone 0.6 completed
== Chimera Features * user registration tool (should be done soon …

Apr 5, 2018:

5:18 PM Ticket #690 (Custom atom/residue properties?) closed by pett
fixed: The under-the-hood revamp is complete and it seems to work with …
3:04 PM 2018-04-05 created by Conrad Huang
2:33 PM ChangeLog edited by Conrad Huang
(diff)
2:11 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:26 PM Ticket #1074 (selection highlighting nearly invisible for non-terminal stick atoms) created by Elaine Meng
ChimeraX selection highlighting of non-endcap atoms in stick style is …
2:30 AM Ticket #1073 (ChimeraX bug | No such file or directory | Desktop/) created by ramiro.magno@…
[…]

Mar 29, 2018:

5:54 PM ChangeLog edited by Elaine Meng
(diff)
2:41 PM 2018-03-29 created by Conrad Huang
2:35 PM Ticket #1072 (Document mmCIF output tables) created by Conrad Huang
Need technical document describing tables included in ChimeraX mmCIF …
1:56 PM DeveloperMeetings edited by Conrad Huang
(diff)

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" …
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