Timeline



Jun 15, 2015:

4:38 PM Ticket #100 (Deleting a pseudobond group crashes) closed by pett
fixed
3:24 PM 2015-6-15 edited by Elaine Meng
(diff)
3:12 PM DeveloperMeetings edited by Conrad Huang
(diff)
1:07 PM EarlyReleaseRequirements edited by Conrad Huang
(diff)
12:57 PM 2015-6-15 created by Conrad Huang

Jun 12, 2015:

4:23 PM Ticket #103 (Atomspec specifying one model in hierarchy) created by Tom Goddard
Atomspec parsing should be able to return the list of specified models …

Jun 11, 2015:

12:34 PM Ticket #102 (Strange atom spec parsing of model ids with commas) created by Tom Goddard
An atom spec "#1.1,2" is giving no models although there are open …

Jun 9, 2015:

4:18 PM Ticket #101 ('delete' command with nothing open throws error) closed by Tom Goddard
fixed: Fixed. AtomSpecResullts.atoms was None if no atoms specified. I …
3:27 PM Ticket #101 ('delete' command with nothing open throws error) created by pett
"del :3-30" raises this traceback: Traceback (most recent call last): …

Jun 8, 2015:

3:15 PM Ticket #100 (Deleting a pseudobond group crashes) created by Tom Goddard
Appears that PBGroup.clear() and Group.dtor_code() both delete the …
3:05 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:49 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:46 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:30 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:27 PM Needed Command Functionality edited by Elaine Meng
(diff)
11:05 AM Ticket #99 (unable to clear status line before executing command) created by Greg Couch
Doing the naive logger.status(""), before executing a command in …

Jun 5, 2015:

3:54 PM Ticket #98 (Too many PDB missing LINK residue error messages) created by Tom Goddard
Opening a PDB file with LINK residues referring to atoms that don't …

Jun 4, 2015:

3:04 PM 2015-6-4 edited by Conrad Huang
(diff)
12:16 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:15 PM 2015-6-4 created by Conrad Huang

Jun 2, 2015:

6:10 PM Ticket #89 (Atom deletion is very slow) reopened by Tom Goddard
Deleting chain 0 (65,000 atoms) from pdb 1jj2 (100,000) takes 95 …
1:08 PM Ticket #87 (Deleting atoms causes crash in atomstruct::Atom.remove_bond()) closed by pett
fixed: Needed to iterate through a _copy_ of the atom's bond list as I remove …
1:07 PM Ticket #89 (Atom deletion is very slow) closed by pett
fixed: Implemented delete_atoms(). Still need to properly delete pseudobonds.
11:06 AM Ticket #97 (Make one pseudobond manager per session) created by Tom Goddard
Currently there is one pseudobond manager for all sessions in the C++ …

Jun 1, 2015:

7:03 PM Ticket #96 (Make orthoplanes and box volume display use lighting) created by Tom Goddard
Currently orthoplanes does not use lighting. Graham Johnson suggested …
6:48 PM Ticket #95 (Ambient occlusion makes solid style volume a white cube) closed by Tom Goddard
fixed: Fixed. Only draw depth of opaque models.
6:36 PM Ticket #95 (Ambient occlusion makes solid style volume a white cube) created by Tom Goddard
Enabling multishadows with command "light soft" causes solid style …
6:34 PM Ticket #94 (Soft lighting with solid volume rendering gives OpenGL error) closed by Tom Goddard
fixed: Fixed. Fixed this error. Now soft lighting makes solid volumes …
6:16 PM Ticket #90 (Error when exiting with command-q) closed by pett
fixed: On Mac, wasn't making the binding to the callback that in turn calls …
5:23 PM Ticket #94 (Soft lighting with solid volume rendering gives OpenGL error) created by Tom Goddard
Traceback (most recent call last): File …
5:05 PM Ticket #91 (Copy from Log panel gives error) closed by pett
fixed: Fixed by skipping the event if the widget doesn't support the …
3:58 PM Ticket #93 (Drag and drop panel gives an error) created by Tom Goddard
Dragging and dropping the Log panel or Mouse Modes panel or Side View …
3:24 PM Needed Command Functionality edited by Elaine Meng
(diff)
3:23 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:55 PM Ticket #92 (Error with selection and silhouette edges) closed by Tom Goddard
fixed: This glBlitFramebuffer() error is caused by using render buffer …
2:43 PM Ticket #92 (Error with selection and silhouette edges) created by Tom Goddard
Get the following traceback when silhouette edges enabled and atom …
2:40 PM Ticket #91 (Copy from Log panel gives error) created by Tom Goddard
Using key command-c to copy selected text from the Log panel gives the …
2:28 PM Ticket #90 (Error when exiting with command-q) created by Tom Goddard
Exiting with key press command-q on Mac gives an error to the shell …

May 29, 2015:

7:26 PM Ticket #89 (Atom deletion is very slow) created by Tom Goddard
When deleting atoms from a molecule each atom delete causes all …
7:20 PM Ticket #88 (Pseudobonds are not deleted when atoms are deleted) created by Tom Goddard
When deleting chain A of 2bbv (delete /a) a crash follows when …
7:17 PM Ticket #87 (Deleting atoms causes crash in atomstruct::Atom.remove_bond()) created by Tom Goddard
Opening 1grl and then deleting chain A with command "delete /a" causes …
4:49 PM Ticket #86 (Chimera hangs after splash screen) created by Tom Goddard
Today about 5 of 25 starts of Chimera 2 (from a shell) resulted in the …
4:41 PM Ticket #54 (Make an icon for the Chimera 2 app) closed by Tom Goddard
fixed: Conrad made an icon which is the Chimera icon with a 2 over it.
4:40 PM Ticket #71 (Will command keywords be written with camel-case in user documentation?) closed by Tom Goddard
fixed: Yes camel case for the docs was decided at a Chimera meeting a week ago.
4:22 PM Ticket #66 (Log scrolls to top when resized) closed by pett
fixed: Apparently HistoryBack() on the HTML window keeps the scrolling at …
4:05 PM Ticket #43 (parse_mmCIF_file() tries to import structaccess within C++ and fails) closed by pett
wontfix: Moot now that PDBio will no longer be creating blobs.
4:03 PM Ticket #67 (Error dialog taller than screen, no obvious way to close it) closed by pett
fixed: Long errors by removing their central lines and replacing them with "…"
4:01 PM Ticket #76 (Typing p or n in command line activates history without ctrl key) closed by pett
fixed
3:53 PM Ticket #77 (Can't paste into command-line with Cmd-V) closed by pett
fixed: Required the implementation of an Edit menu

May 28, 2015:

6:17 PM Ticket #85 (Open mmcif is 2x slower than yesterday, 3j3q) created by Tom Goddard
Opening mmcif 3j3q (2.4 million atoms) takes 16 seconds on my mac, but …
4:38 PM Ticket #75 (Closing side view panel gives error.) closed by pett
fixed: Changed the workaround to the more permanent fix of preventing the …

May 27, 2015:

5:55 PM Ticket #84 (End residue of secondary structure not found) closed by Greg Couch
fixed: Fixed in [develop 2e66f98].
5:36 PM Ticket #82 (Crash on exit) closed by pett
fixed: Needed to force destruction of chains and coord sets while the …
5:35 PM Ticket #68 (Make command keywords case insensitive) closed by Greg Couch
fixed: Resolved as user can type any case for keywords. And that the …
5:33 PM Ticket #78 (open command misleading error message) closed by Greg Couch
fixed: open xyzzy now gives the error: Missing filename suffix …
4:15 PM Ticket #84 (End residue of secondary structure not found) created by Tom Goddard
I get an unending stream of modal error dialogs saying "End residue of …
2:42 PM Ticket #80 (ReleaseMouse wx error) closed by pett
fixed: Fixed. The sequence of events for a double click is: button …
10:56 AM Ticket #83 (Importing PyTables HDF5 wrapper generates BytesWarning) created by Tom Goddard
Opening an HDF5 density map (file suffix .cmap) generates a couples …

May 26, 2015:

5:59 PM Ticket #81 (Atom spec #1.1 includes #1.2, 1.3, ...) closed by Tom Goddard
fixed: Fixed model hierarchy spec matching. Was matching if initial levels …
1:39 PM Ticket #82 (Crash on exit) created by Tom Goddard
Chimera 2 seems to crash on exit maybe 1 in 20 times. This crash was …
12:55 PM Ticket #81 (Atom spec #1.1 includes #1.2, 1.3, ...) created by Tom Goddard
With 3 molecular models #1.1, 1.2 and 1.3 the command color pink …
11:27 AM Ticket #80 (ReleaseMouse wx error) created by Tom Goddard
Starting Chimera 2 and repeatedly clicking in the empty graphics …

May 21, 2015:

5:22 PM Ticket #79 (Report errors to log instead of shell) closed by Tom Goddard
fixed: Done. Just writes to the logger using the info() method instead of …
5:20 PM Ticket #79 (Report errors to log instead of shell) created by Tom Goddard
Redirect tracebacks to the log panel. Tracebacks generated by menu …
3:14 PM EarlyReleaseRequirements edited by Conrad Huang
(diff)
2:57 PM DeveloperMeetings edited by Conrad Huang
(diff)
2:57 PM 2015-5-21 created by Conrad Huang

May 20, 2015:

6:10 PM Ticket #78 (open command misleading error message) created by Tom Goddard
The open command gives a misleading error message when opening a file …
5:03 PM Ticket #77 (Can't paste into command-line with Cmd-V) created by Tom Goddard
Pasting with focus in the command-line with Cmd-V (on Mac) does …
4:08 PM Ticket #76 (Typing p or n in command line activates history without ctrl key) created by Tom Goddard
Hard to use the command line now because typing a "p" or an "n" goes …
2:01 PM Ticket #75 (Closing side view panel gives error.) created by Tom Goddard
Pressing the close window button on the side view panel gives the …
1:58 PM Ticket #74 (Atom spec parsing eats following file path.) created by Tom Goddard
Parsing does not work for a command requiring an atom spec followed by …

May 19, 2015:

4:30 PM Ticket #73 (Selection outline shifted, zoom dependent) closed by Tom Goddard
fixed: Kind of fixed. Will likely require further study to understand the …
4:16 PM Ticket #73 (Selection outline shifted, zoom dependent) created by Tom Goddard
The selection outline on an atom doesn't exactly match the boundary of …
11:47 AM EarlyReleaseRequirements edited by Elaine Meng
(diff)
11:43 AM Needed Command Functionality edited by Elaine Meng
(diff)
9:54 AM Needed Command Functionality edited by Elaine Meng
(diff)
9:32 AM Needed Command Functionality edited by Elaine Meng
(diff)
9:06 AM Needed Command Functionality edited by Elaine Meng
(diff)
9:00 AM Needed Command Functionality edited by Elaine Meng
(diff)

May 18, 2015:

3:28 PM Needed Command Functionality edited by Elaine Meng
(diff)
3:12 PM Needed Command Functionality edited by Elaine Meng
(diff)
3:09 PM Needed Command Functionality edited by Elaine Meng
(diff)
3:07 PM Needed Command Functionality edited by Elaine Meng
(diff)
3:00 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:51 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:41 PM Needed Command Functionality edited by Elaine Meng
(diff)
2:12 PM Needed Command Functionality edited by Elaine Meng
(diff)
12:34 PM Needed Command Functionality edited by Elaine Meng
(diff)
12:32 PM Needed Command Functionality edited by Elaine Meng
(diff)
12:32 PM Needed Command Functionality edited by Elaine Meng
(diff)
12:24 PM Needed Command Functionality edited by Elaine Meng
(diff)
11:53 AM Needed Command Functionality edited by Elaine Meng
(diff)
11:24 AM Needed Command Functionality edited by Elaine Meng
(diff)
10:56 AM Needed Command Functionality edited by Elaine Meng
(diff)
10:36 AM Needed Command Functionality edited by Elaine Meng
(diff)
10:29 AM Needed Command Functionality edited by Elaine Meng
(diff)
9:57 AM Needed Command Functionality edited by Elaine Meng
(diff)
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