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Timeline
Oct 10, 2017:
- 7:03 PM Ticket #876 (cartoon style "arrows" option gives traceback (undo-related)) closed by
- fixed: Fixed in af150d601. Typo.
- 12:02 PM Ticket #877 (TypeError: promote() missing 1 required positional argument: 'session') closed by
- fixed
- 11:42 AM 2017-09-28 edited by
- (diff)
- 11:41 AM 2017-09-28 edited by
- (diff)
- 11:09 AM Ticket #877 (TypeError: promote() missing 1 required positional argument: 'session') created by
- Traceback using "select up", e.g. open 1zik; display sel :tyr sel up …
Oct 9, 2017:
- 6:01 PM Ticket #875 (atomspec parsing problem with parentheses and zone) closed by
- fixed: Fixed in [changeset c5a2b6d8b]. Grammar did not allow zone atomspec …
- 4:29 PM Ticket #876 (cartoon style "arrows" option gives traceback (undo-related)) created by
- open 1bna car style arrows f Traceback (most recent call last): File …
- 3:58 PM 2017-09-28 edited by
- (diff)
- 3:52 PM Ticket #855 (RFE: put all selection changes on the undo stack (even non-command)) closed by
- fixed: After speaking with Elaine, we will keep the current behavior and …
- 3:38 PM ChangeLog edited by
- (diff)
- 11:50 AM Ticket #875 (atomspec parsing problem with parentheses and zone) created by
- The following does not work (example structure 2gbp) sel …
- 11:29 AM Ticket #874 (second "select" command of any session gives traceback) closed by
- duplicate: Same as #871
- 11:21 AM Ticket #874 (second "select" command of any session gives traceback) created by
- Seems like no matter what the details of the "select" command, the …
- 9:57 AM Ticket #871 ('Session' object has no attribute 'add') closed by
- fixed: Fixed in [changeset e0763663a]. Forgot to remove unneeded session …
- 3:19 AM Ticket #873 ("select ~protein" selects all atoms with pseudobonds) created by
- If I do "select ~protein" in the command line, all N and C atoms …
Oct 6, 2017:
- 12:26 PM Ticket #870 (attribute error opening sample OME-TIFF data) closed by
- fixed: Fixed. Bug in new code that assigns channel/time value effecting 2D …
- 12:26 PM Ticket #869 (keyError PhysicalSizeX opening sample OME-TIFF data) closed by
- fixed: Fixed. OME TIF file header value PhysicalSizeX is optional. If not …
- 1:23 AM Ticket #872 (Add chirality property to atoms) created by
- Apologies if this already exists, but I can't find anything in the …
Oct 5, 2017:
- 3:52 PM Ticket #871 ('Session' object has no attribute 'add') created by
- The following commands produce an undo-related traceback: open 1gcn …
- 2:41 PM Ticket #868 (Deleted atoms causes ribbon crash) closed by
- fixed: deleted atom wasn't being removed from the residue
- 2:33 PM Ticket #870 (attribute error opening sample OME-TIFF data) created by
- From the OME-TIFF sample data page …
- 2:16 PM Ticket #869 (keyError PhysicalSizeX opening sample OME-TIFF data) created by
- I tried opening some sample data downloaded from the OME-TIFF website …
- 1:32 PM 2017-09-28 edited by
- (diff)
- 10:30 AM Ticket #868 (Deleted atoms causes ribbon crash) created by
- open 1www addh hb f click the "hide ribbon" icon -> crash
Oct 4, 2017:
Oct 3, 2017:
- 4:57 PM Ticket #845 (cartoon style reporting needs improvement) closed by
- fixed: Fixed in 45bce4348 and 8a06421ed
- 4:11 PM Ticket #638 (Linux OpenBLAS library threading problems) closed by
- wontfix
- 4:09 PM Ticket #824 (New Edit menu interferes with text copy) closed by
- fixed: Undo/Redo now use the standard Qt key sequences which typically …
- 4:02 PM Ticket #865 (Redo shortcut works, undo does not) closed by
- fixed: See #824 for more information.
- 4:01 PM Ticket #857 (make "select up/down" commands work with "undo") closed by
- duplicate: Same as #855.
- 3:50 PM WikiStart edited by
- (diff)
- 3:33 PM Ticket #370 (cannot go Back after going to external web pages) closed by
- fixed: Implemented tabbed browser, so external web pages get a new tab.
- 3:32 PM Ticket #609 (Session format decisions for alpha2) closed by
- fixed: msgpack is used for the current session file format.
- 3:31 PM Ticket #798 (Switch default session format (v3) to msgpack) closed by
- fixed: committed and currently used.
- 3:18 PM Ticket #612 (Session format: identify missing components in session files) closed by
- fixed: Link to bundle session-support status page is now on main wiki page.
- 3:14 PM Ticket #858 (traceback changing cartoon tube radius in separate command) closed by
- fixed: Fixed in 7f520101f.
- 2:24 PM Ticket #801 (Unpredictable keyword completion) closed by
- fixed: Checked in fix that takes into account the number of words in a keyword.
- 12:41 PM Ticket #805 (Help viewer no horizontal scroll if window made narrower than image) closed by
- wontfix: Out of our control :-). You could change the markup so the width of …
- 12:19 PM Ticket #867 ("hide pbonds target p" broken (undo-related)) closed by
- fixed: Fixed in 928a45660.
- 10:48 AM Ticket #866 (Re: [chimerax-users] mini info) closed by
- not a bug: Mistakenly sent to chimerax-bugs; redirected to chimerax-users
- 10:40 AM Ticket #867 ("hide pbonds target p" broken (undo-related)) created by
- hide pbonds target p Traceback (most recent call last): File …
- 12:00 AM Milestone Alpha 3 completed
- Bundle API change (command registration takes CommandInfo instead of …
Oct 2, 2017:
- 12:38 PM Ticket #866 (Re: [chimerax-users] mini info) created by
- […]
- 12:27 PM Ticket #864 (mini info) closed by
- not a bug: Redirected to chimerax-users
- 12:09 PM Ticket #865 (Redo shortcut works, undo does not) created by
- […]
Sep 29, 2017:
- 11:50 PM Ticket #864 (mini info) created by
- […]
- 4:01 PM Ticket #863 (collate message as HTML) created by
- Collated messages currently only handles plain text (designed for …
- 10:26 AM Ticket #860 (silhouettes partly blot out selection outlines) closed by
- fixed: Fixed. Silhouette edges were drawn on top of selection outlines. …
- 10:06 AM Ticket #862 (decide whether Side View is part of session or not) created by
- Currently "close session" (and restoring any session which apparently …
- 10:03 AM Ticket #861 (orthographic side view does not renormalize) created by
- orthographic side view does not renormalize if eye position dragged …
- 10:00 AM Ticket #860 (silhouettes partly blot out selection outlines) created by
- Selection highlights are hard to see if silhouettes are shown (black …
- 9:50 AM Ticket #859 (silhouettes on top of labels) created by
- Even though the labels are on top (default) the silhouettes are drawn …
Sep 28, 2017:
- 3:21 PM Ticket #858 (traceback changing cartoon tube radius in separate command) created by
- A single command setting both modeHelix and radius works, but I get a …
- 3:01 PM Ticket #857 (make "select up/down" commands work with "undo") created by
- If I understand correctly, the other "select" subcommands already work …
- 2:45 PM 2017-09-28 created by
- 2:14 PM Ticket #856 (Investigate replacing ctypes in atomic with Cython) created by
- Replace atomic/molc.cpp, molobject.py and molarray.py with molobject.pyx.
- 2:05 PM DeveloperMeetings edited by
- (diff)
- 2:00 PM ChangeLog edited by
- (diff)
- 1:59 PM Ticket #855 (RFE: put all selection changes on the undo stack (even non-command)) created by
- Since there is a selection-changed trigger, maybe it would be possible …
- 1:44 PM Ticket #850 (ChimeraX fails on macOS El Capitan) closed by
- fixed: The next builds will work on El Capitan, except for movie recording …
- 1:32 PM ChangeLog edited by
- (diff)
- 1:30 PM ChangeLog edited by
- (diff)
Sep 27, 2017:
- 5:27 PM ChangeLog edited by
- (diff)
- 1:46 PM Ticket #854 (status line text scaling incorrect on Linux and WIndows) created by
- On Linux and Windows, status line text is incorrectly scaled after …
- 1:43 PM Ticket #853 (Bug restoring model panel from session) closed by
- fixed: Fix: don't fire "model name changed" trigger if model not open
- 12:59 PM Ticket #853 (Bug restoring model panel from session) created by
- Open an NMR structure, e.g., 176d. Save a session with it. Then open …
Sep 26, 2017:
- 11:09 AM Ticket #852 (Log chain lengths when opening structure) created by
- Would be useful to include chain lengths (residue count) in the chain …
- 11:05 AM Ticket #851 (List ligands in log when opening structure) created by
- Would be very handy to list ligands in addition to chains in the log …
Sep 25, 2017:
- 3:31 PM Ticket #850 (ChimeraX fails on macOS El Capitan) created by
- […]
- 10:57 AM Ticket #845 (cartoon style reporting needs improvement) reopened by
- Decrease priority as much as you want, but the style reporting really …
Sep 22, 2017:
- 2:30 PM ChangeLog edited by
- (diff)
- 2:23 PM Ticket #849 (Polymer type not always assigned correctly) closed by
- fixed: Was looking at last residue of chain to determine polymer type. On …
- 1:59 PM ChangeLog edited by
- (diff)
- 1:06 PM Ticket #813 (prolines initially shown as "hooks" (open rings)) closed by
- fixed: Fixed in 1f8da340e. Need to update ribbon visibility of …
- 12:19 PM Ticket #589 (cartoon short-strand orientations unstable over trajectory) closed by
- fixed: Fixed in 0a1121f6. Strands shorter than 4 residues are …
- 11:59 AM Ticket #849 (Polymer type not always assigned correctly) created by
- Opening 1gcn works (helix has a wide cross section) but opening 1a0m …
- 11:54 AM Ticket #784 (Revise BundleAPI for registering commands) closed by
- fixed: Implemented. Classes derived from BundleAPI that have attribute …
- 11:33 AM Ticket #837 (Allow lower detail ribbons for VR export) closed by
- wontfix: Cartoon code REALLY REALLY wants to have both a front and back end to …
- 11:23 AM Ticket #847 (RFE: add "cartoon style" option "divisions" (per residue)) closed by
- fixed: Fixed in 525b86376. Did not remove "graphics …
Sep 21, 2017:
- 3:05 PM 2017-09-21 edited by
- (diff)
- 3:03 PM 2017-09-21 created by
- 2:02 PM DeveloperMeetings edited by
- (diff)
- 1:26 PM Ticket #848 (Session restore fails: Can't form pseudobond to itself) closed by
- fixed: Okay, all fixed not AFAICT
- 11:59 AM Ticket #848 (Session restore fails: Can't form pseudobond to itself) reopened by
- Hmm, well *one* problem was fixed. Not all apparently.
- 11:57 AM Ticket #848 (Session restore fails: Can't form pseudobond to itself) closed by
- fixed
- 9:36 AM Ticket #848 (Session restore fails: Can't form pseudobond to itself) created by
- open 5ftj save test.cxs # Restart ChimeraX open test.cxs Unable to …
Sep 19, 2017:
- 3:30 PM Ticket #847 (RFE: add "cartoon style" option "divisions" (per residue)) created by
- Not urgent, but it seems weird that one must use the "graphics" …
Sep 18, 2017:
- 5:14 PM Ticket #842 (surface cap doesn't match corresponding surface) closed by
- fixed: Fixed. The cap will only get the set surface color if the whole …
- 3:46 PM Ticket #843 (3D labeling broken (traceback)) closed by
- fixed: Fixed. Broke label code when fixing status line which was using label …
- 3:10 PM Ticket #846 (cartoon style splineNormals causes undo-manager error) closed by
- fixed: Fixed in 540987893. Typo.
- 3:05 PM Ticket #845 (cartoon style reporting needs improvement) closed by
- fixed: Fixed in 57a526628. Cut-and-paste error.
- 2:46 PM Ticket #846 (cartoon style splineNormals causes undo-manager error) created by
- UCSF ChimeraX version: 0.1 (2017-09-15) OpenGL version: 4.1 …
- 11:55 AM WikiStart edited by
- (diff)
- 11:53 AM Ticket #845 (cartoon style reporting needs improvement) created by
- UCSF ChimeraX version: 0.1 (2017-09-15) OpenGL version: 4.1 …
- 11:52 AM BetaRelease created by
- 10:44 AM Ticket #844 (can show multiple Side View windows with command) created by
- Choosing from the Tools menu repeatedly does not show multiple copies, …
- 10:31 AM Ticket #843 (3D labeling broken (traceback)) created by
- UCSF ChimeraX version: 0.1 (2017-09-15) OpenGL version: 4.1 …
- 10:05 AM Ticket #842 (surface cap doesn't match corresponding surface) created by
- If you adjust color/transparency of a surface before starting to clip …
- 3:28 AM Ticket #841 (ctrl-right-click interpreted as ctrl-left-click on Mac) closed by
- not a bug: Never mind. Found the real reason in mousemodes.py. Will re-map to a …
Sep 17, 2017:
- 3:08 AM Ticket #841 (ctrl-right-click interpreted as ctrl-left-click on Mac) created by
- A little bit of MouseMode weirdness. In ISOLDE during simulations I …
Sep 15, 2017:
- 12:50 PM Ticket #815 (chain-level zone atomspec not yet implemented) closed by
- fixed: Fixed in 332a29749. Chain zone atomspecs now use chain …
- 11:39 AM Ticket #829 (Ribbon normal vectors do not have length 1) closed by
- fixed
Sep 14, 2017:
- 6:33 PM Ticket #840 (Make 2d labels a model shown in Model Panel) created by
- Make 2d labels a top-level model. Currently 3d labels are a model but …
- 6:28 PM Ticket #839 ("close session" doesn't get rid of 2D labels) closed by
- fixed: Fixed. I think 2d labels should also close when you simply close all …
- 6:14 PM Ticket #830 (Non-main status text a little too large) closed by
- fixed: Vertical positioning of statusbar text was wrong. Fixed that. …
- 5:14 PM Ticket #839 ("close session" doesn't get rid of 2D labels) created by
- Example: start ChimeraX, click lightning bolt to show graphics …
- 5:01 PM Ticket #838 (Name selection command/GUI) created by
- From chimerax-users: One thing that is missing is a similar list of …
- 3:56 PM Ticket #837 (Allow lower detail ribbons for VR export) created by
- The ribbon divisions along the length of the ribbon currently can be …
- 3:41 PM 2017-09-14 created by
- 2:07 PM DeveloperMeetings edited by
- (diff)
- 1:26 PM msgpack-testing edited by
- (diff)
- 11:21 AM Ticket #836 (Allow fit sequential to work on partial molecules) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 11:15 AM Ticket #832 (Bonds.visibles raises an error) closed by
- fixed: Fixed (both code and comment) in 320c40e12.
- 11:12 AM Ticket #834 (Status bar ugly font in Linux) closed by
- duplicate: Unfortunately we are not able to use Qt font rendering for status …
- 6:07 AM Ticket #835 (Order of events on ToolInstance deletion) closed by
- invalid: Actually, never mind. Just double-checked and I only get the traceback …
- 6:04 AM Ticket #835 (Order of events on ToolInstance deletion) created by
- From the ChimeraX programming guide under ToolInstance: delete() …
- 2:54 AM Ticket #834 (Status bar ugly font in Linux) created by
- Possibly just something to do with the new PyQt version? Sometime in …
- 2:34 AM Ticket #833 (Allow Drawing.position (or positions) = None) created by
- Just because this seems a very Pythonic/intuitive way of handling the …
- 1:35 AM Ticket #832 (Bonds.visibles raises an error) created by
- […] I get the impression that this is simply an old and unused …
- 1:28 AM Ticket #831 (Allow methods to access current changes to a specific Structure) created by
- At the moment in ISOLDE I have four different types of annotations to …
Sep 13, 2017:
- 5:23 PM Ticket #821 (Have pseudobonds respect user hide flags) closed by
- not a bug: Okay, the design intent of atom 'hide' flags are that when a hide bit …
- 2:46 PM Ticket #830 (Non-main status text a little too large) created by
- For non-main-window status lines, the text is slightly too large and …
- 2:05 PM Ticket #829 (Ribbon normal vectors do not have length 1) created by
- Ribbon normal vectors do not have length 1. Observed this with pdb …
- 10:08 AM ChangeLog edited by
- (diff)
Sep 12, 2017:
Sep 11, 2017:
Sep 10, 2017:
- 1:05 PM Ticket #828 (Typo in core/commands/cartoon.py) created by
-
Line 86:
residues.ribbon_hide_backbones, suppress_backbond_display) - 11:14 AM Ticket #827 (Structure file I/O issues) created by
- Simple-but-important one first: mmcif_write.py currently crashes due …
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