Timeline



Apr 24, 2018:

4:07 PM Ticket #1095 (alias can cause duplicates in "usage" output) created by Elaine Meng
"usage del" reports "delete pbonds" twice, once as a direct …
2:22 PM Ticket #1094 (traceback closing all models aftering coloring by ESP) closed by Tom Goddard
fixed: Fixed. Code to delete drawings forgot to delete auto recoloring …
12:34 PM Ticket #1094 (traceback closing all models aftering coloring by ESP) created by Elaine Meng
version UCSF ChimeraX version: 0.7 (2018-04-21) I tried subsets of …
12:12 PM Ticket #1093 (Problem creating ribbon graphics) closed by Tom Goddard
fixed: Fixed in tonight's ChimeraX builds. Zero length array of spline atoms …

Apr 20, 2018:

1:47 PM Ticket #1093 (Problem creating ribbon graphics) created by turmand@…
[…] smime.p7s​

Apr 19, 2018:

3:09 PM 2018-04-19 created by Conrad Huang
2:04 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:38 PM Ticket #1092 (rainbow broken) closed by Tom Goddard
fixed: Fixed. New color sequential subcommand forgot to handle case when no …
12:49 PM Ticket #1092 (rainbow broken) created by Elaine Meng
"rainbow" command (doesn't seem to matter what structure) gives …
4:30 AM Ticket #1091 ("View all" doesn't play well with "cofr center showpivot true") created by Tristan Croll
The pivot indicator is currently considered part of the scene when …

Apr 18, 2018:

5:43 PM Ticket #969 (Color subcommands for zone, map, etc.) closed by Tom Goddard
fixed: Done. Made color subcommands zone, sequential, electrostatic, sample, …
4:49 PM Ticket #1005 (Open File dialog gives lots of Debug output on Windows) closed by Tom Goddard
duplicate: Duplicate of #1042
4:47 PM Ticket #1049 (RE: VR ON bug in latest release) closed by Tom Goddard
duplicate: SteamVR bug, worked around it in ChimeraX a month ago.
4:46 PM Ticket #1048 (Re: VR ON bug in latest release) closed by Tom Goddard
duplicate: SteamVR bug, worked around it in ChimeraX a month ago.
4:46 PM Ticket #1047 (VR ON bug in latest release) closed by Tom Goddard
duplicate: SteamVR bug, worked around it in ChimeraX a month ago.
4:46 PM Ticket #1046 (VR ON bug in latest release) closed by Tom Goddard
duplicate: SteamVR bug, worked around it in ChimeraX a month ago.
4:45 PM Ticket #1040 (OpenGL version not recognized) closed by Tom Goddard
nonchimerax: Inadequate graphics provided by driver.
4:44 PM Ticket #1032 (attempting VR) closed by Tom Goddard
not a bug: No response. Assume split command is working now.
3:47 PM Ticket #1090 ("vr on": 'utf-8' codec can't decode byte: invalid continuation byte) closed by Tom Goddard
fixed: Fixed in tonight's builds. New SteamVR versions generate an benign …
9:30 AM Ticket #1090 ("vr on": 'utf-8' codec can't decode byte: invalid continuation byte) created by nicolas.floquet@…
[…]
7:21 AM Ticket #1089 (Option to recursively include contents of directory in bundle) created by Tristan Croll
Adding a copy of my Sphinx-generated documentation to the ISOLDE build …

Apr 16, 2018:

6:03 PM ChangeLog edited by pett
(diff)
1:50 PM 2018-04-16 edited by Tom Ferrin
(diff)
1:26 PM 2018-04-16 created by Tom Ferrin
1:17 PM Ticket #621 (Core bundle refactoring) closed by Tom Ferrin
duplicate: Superseded by #1050
12:17 PM DeveloperMeetings edited by Tom Ferrin
(diff)
11:25 AM Ticket #1034 (allow glycine CAs to be shown with ribbon) closed by Conrad Huang
wontfix
10:16 AM Ticket #1088 (Add a smart initial display toolbar button and preset command) created by Tom Goddard
Would like to be able reproduce the display style and color (ribbon, …
10:11 AM Ticket #687 (Pick atoms beneath density map surfaces) closed by Tom Goddard
fixed: About 6-12 months ago I made picking atoms through transparent volume …
10:08 AM Ticket #833 (Allow Drawing.position (or positions) = None) closed by Tom Goddard
wontfix: Won't allow position = None because this places a burden on all code …
10:03 AM Ticket #1087 (Add mouse mode to position 2d labels) created by Tom Goddard
Add mouse mode to position 2d labels
9:54 AM Ticket #988 (Fix volume linear interpolation) closed by Tom Goddard
fixed: Fixed a month ago.
9:52 AM Ticket #964 (Mirror VR on desktop display) closed by Tom Goddard
fixed: Fixed. vr command now turns of synchronization to vertical refresh …
4:10 AM Ticket #1076 (Signs of memory leak during toolshed install) closed by Tristan Croll
can't reproduce: Still not sure what was going on here, but it's not coming back. …
4:05 AM Ticket #1081 (Bug in unit testing) closed by Tristan Croll
not a bug

Apr 13, 2018:

12:22 PM Ticket #940 (Use newer OpenSSL on Mac OS X) closed by Conrad Huang
fixed: Fixed by using OpenSSL and setting SSL_CERT_FILE environment variable …
12:13 PM Ticket #736 (Need tool for managing active tools) closed by Conrad Huang
fixed: Implemented as Active Tools in Utilities category.
11:53 AM Ticket #1085 ("name frozen" target reported to contain models after those models ...) closed by Conrad Huang
fixed: Should be fixed in the daily build. Needed to refresh Objects …

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 …
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