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7:45 AM Ticket #653 (Odd library problem installing OpenMM 7.1.0) created by Tristan Croll: As per Tom's suggestion a while back, I've installed OpenMM 7.1.0 into …

1:00 PM Ticket #652 (infinite loop in PDB reader) created by Greg Couch: The PDB reader goes into an infinite loop when trying to open 5a8l. …

9:18 AM Ticket #651 (Toolshed failing) created by Tristan Croll: I received errors on submitting a new bundle release (although it does …

4:12 AM Ticket #650 (Add shutdown to session.triggers) created by Tristan Croll: At the moment I can't find any way for a Python process to know when …

5:15 PM Ticket #649 (bundle specification of open/save arg UI) created by pett: Our current scheme of registering keywords needs to be expanded …
4:40 PM Ticket #648 (consider pop-up text explaining Log click-to-execute links) closed by pett: fixed: I implemented the request, though I capitalized the first letter of …
3:11 PM Ticket #648 (consider pop-up text explaining Log click-to-execute links) created by Elaine Meng: This is an idea rather than a demand.... maybe the click-to-execute …
2:23 PM Ticket #647 (save-restore session compressed two models into one) created by Elaine Meng: open 1zik open 1zik.pb open 1zik move y 10 mod #3 open 1zik2.pb ... …
1:52 PM Ticket #646 (consider whether file-history should remember coordset status) created by Elaine Meng: If I open something as a trajectory, this status is not retained in …
1:44 PM Ticket #645 (mouse over crosslinks histogram of closed structure causes traceback) created by Elaine Meng: More along the lines of idiot-proofing. Need to close histogram when …
1:33 PM Ticket #644 (mouse over crosslink ensemble histogram gives IndexError) created by Elaine Meng: Example: open 5ml1 format pdb coord t (select one pseudobond) crossl …

3:55 PM Ticket #603 (Add support for display chain sequences) closed by pett: fixed

2:37 PM Ticket #623 (Move selected core bundles to toolshed) closed by pett: duplicate: Duplicate of #621
2:35 PM Ticket #624 (Session format: test msgpack as an alternative to pickle) closed by pett: duplicate: Duplicate of #611

3:27 PM Ticket #643 (chimerax not starting) created by behrouzi@…: […]
3:13 PM Ticket #642 (OpenMM bug) created by tic20@…: […]
2:00 PM Ticket #641 (Restoring session with atomic model fails) closed by pett: fixed

7:36 PM Ticket #640 (Rapid access file history can slow startup checking if files exist) closed by Tom Goddard: fixed: I made file history not check for deleted files at start-up. …
7:05 PM Ticket #641 (Restoring session with atomic model fails) created by Tom Goddard: open 1a0m save test.cxs close open test.cxs Unable to restore …
6:00 PM Ticket #640 (Rapid access file history can slow startup checking if files exist) created by Tom Goddard: The current file history code checks all the files in the history to …
1:30 PM Ticket #639 (atomspec model ordering not used in matrixcopy between multiple models) closed by Tom Goddard: fixed: Fixed. Model argument parsing was not preserving order with TopModelsArg.
10:57 AM Ticket #637 (Toolshed: missing 'logger' arg) closed by Conrad Huang: fixed: Fixed in 89f6694. Pass in logger to …
9:20 AM Ticket #639 (atomspec model ordering not used in matrixcopy between multiple models) created by Elaine Meng: This may be the same problem as an atomspec ordering ticket, but I was …
4:26 AM Ticket #638 (Linux OpenBLAS library threading problems) created by Tristan Croll: This came up a while back, and I have the below workaround defined in …

3:39 PM Ticket #637 (Toolshed: missing 'logger' arg) created by pett: In toolshed/info.py on line 653, the call to _get_api() is missing the …

12:22 PM Ticket #635 (silhouettes don't work right in orthographic) closed by Tom Goddard: fixed: Fixed. The silhouette edge depth jump test was assuming perspective …
11:25 AM Ticket #636 (Side View does not renormalize) created by Elaine Meng: Maybe "renormalize" is not the right word, but what I mean is that it …
10:30 AM Ticket #635 (silhouettes don't work right in orthographic) created by Elaine Meng: With silhouettes + camera ortho, the outlines for depth jumps …

2:15 PM Ticket #384 (problem dealing with microheterogeneity) closed by Greg Couch: fixed: Changed code to delete the "microheterogeneity" residues instead of …
11:28 AM Ticket #634 ("windowsize" as first command after starting ChimeraX does not work) created by Elaine Meng: Apparently resizes the whole window to that size, instead of the …

1:07 PM Ticket #631 (Crossfade wrong on retina MacBook Pro 2012, 2x scaling problem) closed by Tom Goddard: fixed: Fixed.

5:37 PM Ticket #619 (Bug reporting lite) closed by pett: fixed
5:14 PM Ticket #633 (Status messages cause havoc by running event loop) created by Tom Goddard: To get status messages to appear we run the Qt event loop when the …
12:50 PM Ticket #632 (2d label improvements) created by meng@…: 1) Most important feature to make 2d labels more usable is a mouse …
9:22 AM Ticket #631 (Crossfade wrong on retina MacBook Pro 2012, 2x scaling problem) created by Tom Goddard: When crossfading to hide one of two superposed models crossfade 100 …

2:52 PM Ticket #627 (Atom deleted during atoms.radii lookup) closed by pett: fixed: Fixed. Needed to clear destruction-batcher variables earlier to clear …
12:04 PM Ticket #629 (Drawing.display not saved/restored in session) closed by Tom Goddard: fixed: Fixed. Whether models are displayed was not being saved in sessions.
11:48 AM Ticket #630 (Add "position" command) created by Tom Goddard: The "view initial", "view matrix" and "view position" subcommands are …

7:37 PM Ticket #629 (Drawing.display not saved/restored in session) created by Elaine Meng: As per summary. Open 1mtx; turn off 'shown' for first three models in …
2:47 PM Ticket #606 ("close" in this session quits ChimeraX) closed by pett: fixed
2:32 PM Ticket #628 (Graphical selection not working; other usage problems) closed by Tom Goddard: not a bug: I guess you mean you want to display the rest of the atoms. You can …

1:47 PM Ticket #552 (cartoon 4y7j crashes ChimeraX) closed by Conrad Huang: fixed: Fixed in 2b58710. The last fragment in chain D are …

6:15 PM Ticket #628 (Graphical selection not working; other usage problems) created by jamestorecaldwell@…: […]
2:47 PM Ticket #627 (Atom deleted during atoms.radii lookup) created by Tom Goddard: Loading exosome.ihm (attached) loads several mmCIF files and generates …
5:50 AM Ticket #626 (If a volume is selected in the Models panel, Density Map Toolbar ...) created by Tristan Croll: At present, restricting the display buttons to act on one volume …

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