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Timeline
Mar 2, 2017:
- 9:46 PM Ticket #571 (Save volume global settings in sessions) created by
- On Mar 2, 2017, at 2:27 PM, Elaine Meng <> wrote: Hi Tom, Are these …
- 5:15 PM Ticket #526 (Spurious extra quotes in logged command) closed by
- fixed: Fixed.
- 2:41 PM Ticket #570 (command "open formats" broken) closed by
- fixed: Fixed.
- 12:45 PM Ticket #570 (command "open formats" broken) created by
- open formats Traceback (most recent call last): File …
- 11:47 AM Ticket #569 (Show selected atoms under transparent surface) created by
- Current selection outline code does not associate a depth with the …
- 10:02 AM Ticket #568 (Exceptions crash console in Windows build) created by
- […]
Mar 1, 2017:
- 11:33 PM Ticket #567 (Add logger to bundle API for registering things) created by
- The bundle API prevents logging errors when registering commands, file …
- 11:29 PM Ticket #546 (generalize 'help http:....' to 'open http:...') closed by
- fixed: Done.
- 4:22 PM Ticket #541 ("help URL" doesn't work with https URL) closed by
- fixed: Works.
- 1:27 PM Ticket #378 (Atom spec parsing stops at non-whitespace) closed by
- fixed: The "save" command usage was already changed to put the filename …
- 11:52 AM Ticket #565 ("sym" copy new model changes cartoon from original) closed by
- fixed
- 11:28 AM Ticket #558 (opening session closes help viewer) closed by
- fixed: Fixed in a0010e9.
Feb 28, 2017:
- 4:50 PM Ticket #566 (drag select weirdness) closed by
- fixed: Fixed. Drag select was not taking account of positions of moved models.
- 3:40 PM Ticket #566 (drag select weirdness) created by
- In the attached session, the selected strand has an unselected strand …
- 11:13 AM Ticket #565 ("sym" copy new model changes cartoon from original) created by
- Basically 2 helices that are adjacent but shown as separate helices in …
Feb 27, 2017:
- 6:01 PM Ticket #529 (ChimeraX runs out of memory opening 2a06) closed by
- fixed: Missing backbone nitrogen between residues 20 and 21 on chains B and O …
- 1:55 PM 2017-02-27 edited by
- (diff)
- 1:51 PM 2017-02-27 edited by
- (diff)
- 11:54 AM 2017-02-27 created by
- 11:21 AM DeveloperMeetings edited by
- (diff)
- 10:26 AM Ticket #417 (Help viewer suggestions) closed by
- fixed: Yay! So much nicer, thanks. I'll close this as fixed since the …
Feb 23, 2017:
- 6:54 PM Ticket #563 (opening and closing sideview on Windows causes crash) closed by
- fixed: Duplicate of #491. Fixed.
- 6:52 PM Ticket #491 (Crash closing side view and opening shell) closed by
- fixed: Fixed. Side view Drawing for eye and field of view lines and clip …
- 4:34 PM Ticket #507 (Make "help movie" show docs instead of list of subcommands) closed by
- fixed: Fix by looking for local help file even for commands without a …
- 4:33 PM Ticket #564 ("Help... Contact Us" link broken) closed by
- fixed
- 3:51 PM Ticket #564 ("Help... Contact Us" link broken) created by
- I am pretty sure this used to work, but menu: Help... Contact Us gives …
- 3:19 PM 2017-02-23 created by
- 2:57 PM Ticket #235 (Compressed session files should have suffix .cxs instead of .cxs.gz) closed by
- fixed: .cxs file are gzip files now.
- 2:53 PM Ticket #563 (opening and closing sideview on Windows causes crash) created by
- With no model opened, starting SideView and then closing it causes a …
- 2:42 PM Ticket #283 (Curved helix tubes) closed by
- fixed: Many other ribbon tickets still open.
- 2:07 PM Ticket #562 (Update to Python 3.6 and PyQt 5.8) created by
- Update to latest releases of standard packages
- 2:03 PM DeveloperMeetings edited by
- (diff)
- 10:35 AM Ticket #561 (cartoon should show abutting helices as separate instead of continuous) created by
- I.e. should show a short coil-type connector from the last CA of the …
Feb 22, 2017:
- 11:42 AM Ticket #557 (session windowsize doesn't work) closed by
- can't reproduce
Feb 21, 2017:
- 11:24 PM Ticket #560 (Warning opening any standard mmCIF file) closed by
- fixed: Fixed. Simplified code interface, so this bug is less likely to occur …
- 2:52 PM Ticket #560 (Warning opening any standard mmCIF file) created by
- Every mmCIF file I open now produces this warning: skipping …
- 1:38 PM Ticket #559 (cartoon cross section applied to whole model) closed by
- not a bug: Elaine: Not a bug. Cartoon style settings apply to the whole model, …
- 1:32 PM Ticket #559 (cartoon cross section applied to whole model) created by
- When I open 1gcn and use the following command: cart style :12-17 xs …
Feb 20, 2017:
- 8:59 AM Ticket #558 (opening session closes help viewer) created by
- Currently opening a session closes everything that was open. I …
- 8:43 AM Ticket #557 (session windowsize doesn't work) created by
- When I opened a session file, it detected that my current windowsize …
Feb 18, 2017:
Feb 17, 2017:
- 6:44 PM Ticket #495 (Toolshed cannot install tool, write permission error) closed by
- fixed: The toolshed code now asks the user whether to install for "Just me", …
- 6:41 PM Ticket #439 (Signing windows ChimeraX fails) closed by
- fixed: Fixed. First, the signing certificate is imported into the "Personal" …
- 6:33 PM Ticket #532 (Saving and restoring sessions) closed by
- fixed: After discussion, with Greg doing all the coding, we changed the API …
- 6:27 PM Ticket #198 (finish session molecular data save/restore) closed by
- fixed: I made a first pass using Python-level code to save ribbon attributes. …
Feb 16, 2017:
- 9:09 AM Ticket #556 (Re: Unable to save figure) closed by
- duplicate: Yes, that is indeed the problem, so you could fix it yourself. I …
- 9:04 AM Ticket #556 (Re: Unable to save figure) created by
- […]
- 8:50 AM Ticket #555 (Unable to save figure) closed by
- fixed: Sorry, that was an oversight on my part. It will be fixed in …
- 8:22 AM Ticket #555 (Unable to save figure) created by
- […]
Feb 15, 2017:
- 6:28 PM Ticket #554 (Ribbon: RuntimeWarning: invalid value encountered in less d[d < ...) created by
- open 3bfu issues this warning to the log …
- 4:24 PM Ticket #553 (tube helix with stripes 5cbf) created by
- Another possibly weird case is 5cbf. One of the helix tubes has …
- 2:16 PM Ticket #552 (cartoon 4y7j crashes ChimeraX) created by
- I guess the summary says it all. It's initially displayed as spheres. …
- 2:04 PM Ticket #551 (cartoon tube "armadillos" in 3jac) created by
- In general cartoon tubes seem to work well, but I did find one …
- 12:38 PM Ticket #550 (Toolshed install of Clipper bundle does nothing) created by
- Clicking the Download button on the Clipper bundle using the Toolshed …
- 12:21 PM Ticket #549 (Mac middle mouse drag: QNSView mouseDragged: Internal mouse button ...) created by
- Dragging with middle mouse on Mac with Qt 5.7.1 gives log warnings …
Feb 14, 2017:
- 12:28 PM Ticket #548 (ChimeraX does not quit on Mac) closed by
- fixed: Fixed. Seems to be a Qt 5.7.1 bug. Worked around it by adding an …
Feb 13, 2017:
- 4:10 PM Ticket #548 (ChimeraX does not quit on Mac) created by
- After using menu ChimeraX / Quit or Cmd-Q on Mac ChimeraX windows …
- 2:23 PM WikiStart edited by
- (diff)
- 2:18 PM Ticket #547 ("mlp" command gives ImportError: No module named 'chimerax.mlp._mlp') closed by
- fixed: Fixed. Was broken 3 months ago when Greg converted bundle makefiles.
- 1:39 PM 2017-02-13 edited by
- (diff)
- 1:33 PM 2017-02-13 created by
- 12:01 PM DeveloperMeetings edited by
- (diff)
- 10:03 AM Ticket #547 ("mlp" command gives ImportError: No module named 'chimerax.mlp._mlp') created by
- open 5u71 Summary of feedback from opening 5u71 fetched from pdb …
Feb 9, 2017:
- 3:40 PM Ticket #546 (generalize 'help http:....' to 'open http:...') created by
- The idea is to simplify the help command by having the open command …
- 11:20 AM Ticket #545 (Volume API for setting surface colors is not intuitive) created by
- Hi all, I have something strange going on when I try to create …
- 11:16 AM Ticket #537 (Re: application does not work) closed by
- duplicate: Answered on chimerax-users mailing list.
Feb 8, 2017:
- 5:17 PM Ticket #62 (Register file fetch using database name) closed by
- fixed: Tom did this. Changed to not be contained within a session so …
- 5:04 PM Ticket #284 (handle mmCIF with missing sequence information) closed by
- fixed: All of the example cif files now open. Files without the …
Feb 7, 2017:
- 11:51 PM Ticket #469 (HTML link to open local file should be interpreted relative to HTML ...) closed by
- fixed: Worked around by having a separate profile for each widget whose …
- 3:50 PM Ticket #488 (Model panel view button should not enable clip planes) closed by
- fixed: Okay, "View" no longer turns on clipping. Also, model panel buttons …
- 3:10 PM Ticket #544 ("set bgcolor" seems to have died) closed by
- fixed: Fixed. Bug introduced yesterday when standard named colors were made …
- 2:13 PM Ticket #544 ("set bgcolor" seems to have died) created by
- Now I get a traceback from "set bgcolor" including by clicking the …
- 2:08 PM Ticket #543 (Help viewer right-click "save link" doesn't work) created by
- As far as I can tell, nothing happens when you try to save a linked …
Feb 6, 2017:
- 10:00 PM Ticket #140 (Provide common database fetching routines) closed by
- fixed: Tom did most of this work. We settled on data being cached in …
- 5:35 PM Ticket #542 (Test ticket) closed by
- invalid
- 5:34 PM Ticket #542 (Test ticket) created by
- Testing to see if I can attach files
- 2:52 PM 2017-02-06 edited by
- (diff)
- 2:13 PM 2017-02-06 edited by
- (diff)
- 2:05 PM Ticket #374 (Help viewer in Qt version does not show movie) reopened by
- 1:59 PM 2017-02-06 edited by
- (diff)
- 1:52 PM Ticket #541 ("help URL" doesn't work with https URL) created by
- if the URL is https, there is a file not found message, e.g. help …
- 1:33 PM 2017-02-06 created by
- 12:11 PM DeveloperMeetings edited by
- (diff)
Feb 4, 2017:
- 9:50 PM Ticket #513 (2dlabels "all" specifier stopped working) closed by
- fixed: Fixed. 'all' can not be abbreviated.
- 9:00 PM Ticket #418 (problems with help command new-viewer option) closed by
- fixed: Removed new_viewer
- 5:48 PM Ticket #374 (Help viewer in Qt version does not show movie) closed by
- fixed: The problem is that the Qt viewer does not support h264 videos due to …
Feb 3, 2017:
- 4:25 PM Ticket #504 (Changing the .selected attribute of Drawing objects doesn't propagate ...) closed by
- not a bug: A few of the selection APIs are hard to find. …
- 4:19 PM Ticket #540 (Make file fetch give progress messages in status bar) closed by
- fixed: Done.
- 4:19 PM Ticket #511 (Report mmCIF assemblies in log when mmCIF opened) closed by
- fixed: Done.
Feb 2, 2017:
- 6:32 PM Ticket #540 (Make file fetch give progress messages in status bar) created by
- Currently fetching files (all types) gives no progress messages. It …
- 5:55 PM Ticket #407 (Update status line during long computations) closed by
- fixed: I put in code to work around the Qt bug described in the previous …
- 3:41 PM FAI edited by
- (diff)
- 3:39 PM 2017-01-09 edited by
- (diff)
- 2:31 PM Ticket #175 (2x slower opening 3j3q) closed by
- fixed: Current times to open 3j3q on my iMac (Mac OS 10.12.2) are 9.9 seconds …
- 2:14 PM Ticket #175 (2x slower opening 3j3q) reopened by
- Been 6 months since our last timings done. Need to re-run "time open …
- 1:51 PM Ticket #539 (Corrupted log window) created by
- After running the following commands by hand in the command-line the …
- 1:09 PM Ticket #494 (Dropping one floating window into another and then tearing it away ...) closed by
- fixed: This bug appears to be fixed with Qt 5.7.1.
- 12:27 PM Ticket #538 ("split ligands" doesn't work) closed by
- fixed: Fixed. The split command was added long ago before there was ligand …
- 10:19 AM Ticket #538 ("split ligands" doesn't work) created by
- I tried "split ligands" on 2gbp (1 glucose ligand) and 4hhb (4 heme …
Feb 1, 2017:
- 9:17 PM Ticket #537 (Re: application does not work) created by
- […]
- 6:24 PM Ticket #536 ("split atoms atomspec" gives traceback) closed by
- fixed: Fixed. Also made split accept multiple atoms options.
- 4:47 PM Ticket #536 ("split atoms atomspec" gives traceback) created by
- I was originally testing whether the "atoms" keyword could be given …
- 10:24 AM Ticket #69 (Atom spec parsing does not preserve model or chain order) closed by
- fixed: Fixed in dd03a06c8.
Jan 31, 2017:
- 4:02 PM GraphicsAPI edited by
- (diff)
- 3:21 PM Ticket #535 (Mouse hover balloons don't show if ribbon selected) closed by
- fixed: Fixed. After selecting a ribbon residue the scene was redrawn every …
- 11:08 AM Ticket #535 (Mouse hover balloons don't show if ribbon selected) created by
- If any part of a ribbon is selected, the hovering mouse over atoms or …
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