![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Oct 23, 2017:
- 6:24 PM Ticket #854 (status line text scaling incorrect on Linux and WIndows) closed by
- fixed: Fixed. Resize event handling was updating the status bar opengl …
- 5:42 PM Ticket #897 (matchmaker AttributeError: 'PseudobondGroup' object has no attribute ...) closed by
- fixed: Starting Structure change tracking wasn't also turning on the …
- 5:38 PM Ticket #898 (tried to save marker with label to file, got AttributeError: ...) closed by
- fixed: Fixed. Specifying model #3 also included the labels model #3.1. Made …
- 4:20 PM Ticket #899 (trying to save session with morph results nukes ChimeraX) created by
- I tried this twice. Nuked ChimeraX both times. open 2fvy open 2fw0 …
- 4:02 PM Ticket #898 (tried to save marker with label to file, got AttributeError: ...) created by
- I added a marker, labeled it, and tried to save it to a file to see …
- 3:55 PM Ticket #897 (matchmaker AttributeError: 'PseudobondGroup' object has no attribute ...) created by
- open 2mnr open 4enl mm #2 to #1 Error processing trigger "changes" …
- 3:48 PM Ticket #896 (hbonds "reveal true" after "hide" shows disconnected atoms) created by
- Something to do with "hide" hiding all bonds (now that they are …
- 3:06 PM Ticket #895 (Open file problem - NEVER MIND) closed by
- not a bug: Followup to #894
- 3:05 PM Ticket #894 (Open cxs file error) closed by
- not a bug: As per follow-on mail, should have been '.cxc', not '.cxs'
Oct 21, 2017:
- 3:54 PM Ticket #895 (Open file problem - NEVER MIND) created by
- […]
- 3:54 PM Ticket #894 (Open cxs file error) created by
- […]
Oct 20, 2017:
- 5:09 PM ChangeLog edited by
- (diff)
- 11:08 AM Ticket #889 (GUI not resizing) closed by
- fixed: Glad that worked! --Eric
Oct 19, 2017:
- 3:48 PM Ticket #893 (Make up/down arrow use "select up/down" command instead of direct code) closed by
- fixed: Done.
- 3:15 PM ChangeLog edited by
- (diff)
- 2:40 PM 2017-10-19 created by
- 2:26 PM Ticket #800 (Need undo manager) closed by
- fixed: Done and released in alpha 3
- 2:20 PM Ticket #893 (Make up/down arrow use "select up/down" command instead of direct code) created by
- 2:06 PM DeveloperMeetings edited by
- (diff)
- 2:02 PM Ticket #892 (can't show Marker Placement again after closing it) closed by
- fixed: Fixed.
- 1:45 PM Ticket #892 (can't show Marker Placement again after closing it) created by
- After I use the little "X" to close Marker Placement, I can't get it …
- 12:30 PM Ticket #891 (Make vseries show markers with frame attribute) created by
- Allow vseries playback to show markers for specific frames. In …
- 2:45 AM Ticket #890 (save image/supersample possible bug?) created by
- […] [[Image(...)]]
Oct 18, 2017:
- 6:37 PM ChangeLog edited by
- (diff)
- 3:06 PM Ticket #767 (image save from this session gives quadrant missing silhouette edges) closed by
- nonchimerax: Mac Intel graphics driver bug.
- 2:42 PM Ticket #810 (labels == slow) closed by
- fixed: Fixed. Individual drawings can now choose to not cast shadows. Made …
Oct 17, 2017:
- 3:40 PM Ticket #889 (GUI not resizing) created by
- […]
- 1:58 PM Ticket #887 (NameError: name 'PseudbondGroup' is not defined ("select intersect" ...) closed by
- fixed: Fixed. Typo in selected_pseudobonds() function that I guess was never …
- 1:03 PM Ticket #888 (element specifier "O" causes problems in "select" cmd, gets mixed up ...) created by
- command-line "select O" gives in Log: select objects Missing …
- 12:56 PM Ticket #887 (NameError: name 'PseudbondGroup' is not defined ("select intersect" ...) created by
- example: open 2gbp select ligand select intersect C ...whereas …
- 12:25 PM ChangeLog edited by
- (diff)
Oct 16, 2017:
- 6:02 PM Ticket #873 ("select ~protein" selects all atoms with pseudobonds) closed by
- fixed: The "protein", "nucleic", and "backbone" selectors now also select the …
- 3:47 PM Ticket #886 (color-command "halfbond" doesn't work for pseudobonds) closed by
- fixed: Fixed.
- 3:31 PM Ticket #423 (Shell error messages at startup) closed by
- fixed: No longer get these errors, probably due to new Qt version.
- 3:31 PM Ticket #886 (color-command "halfbond" doesn't work for pseudobonds) created by
- It was documented as working for pseudobonds if coloring"target" …
- 3:30 PM Ticket #438 (PDBFixer doesn't add correct atoms) closed by
- wontfix: PDBFixer has many problems. Have taken it out of distributions. Eric …
- 3:26 PM Ticket #510 (Mac graphics driver crash, virus capsid full lighting) closed by
- fixed: Works in macOS 10.12.6 on same machine.
- 3:24 PM Ticket #509 (Status message slow rendering frame rate on Linux) closed by
- fixed: Changed status message display code to use OpenGL (a horrendous hack) …
- 3:23 PM Ticket #885 (AttributeError: 'Residues' object has no attribute 'ribbon_adjust') closed by
- fixed: Fixed in 094db110c. Another typo.
- 3:13 PM Ticket #539 (Corrupted log window) closed by
- can't reproduce: No longer observe this bug. Some changes have occurred to reduce …
- 3:10 PM Ticket #582 (Log panel does not scroll, Mac) closed by
- fixed: Fixed in Qt 5.9 which ChimeraX now uses.
- 3:06 PM Ticket #596 (sometimes silhouettes still shown after structures closed) closed by
- can't reproduce: Very likely a graphics driver bug. Also seems harmless except for …
- 3:04 PM Ticket #597 (sometimes windowsize doesn't work and contents go gray) closed by
- can't reproduce: We have updated to newer Qt versions since this Qt bug was observed. …
- 3:02 PM Ticket #625 (Status messages during draw causes OpenGL error) closed by
- fixed: Added OpenGL context caching. Then I replaced the status line to use …
- 2:59 PM Ticket #778 (changing coordinates very slow for large structures) closed by
- fixed: As described in the previous 46 comments, some changes allowed faster …
- 2:52 PM Ticket #790 (error saving session with crosslinks histogram) closed by
- fixed: Forgot to close this 2 months ago.
- 2:50 PM Ticket #806 (Chimera X QT bug?) closed by
- nonchimerax: This problem only appears with Intel graphics, not with Nvidia …
- 2:44 PM Ticket #825 (Incorrect planes read from OME TIFF file) closed by
- fixed: I put in code to always reopen the TIFF file instead of seeking to an …
- 12:03 PM Ticket #885 (AttributeError: 'Residues' object has no attribute 'ribbon_adjust') created by
-
Opened 1gcn, did
cartoon smooth 1, got: […] - 11:43 AM Ticket #884 (need more tether positions on ribbon) created by
- When drawing nucleotides representations, ladders and sugar tubes, …
Oct 13, 2017:
- 5:36 PM Ticket #882 (AddH not working with metal coordination) closed by
- fixed: Mostly used your changes; with one addition in the …
- 11:49 AM Ticket #883 (command "select clear" gives traceback (undo-related)) closed by
- fixed: Fixed in fd7ca83a2.
Oct 12, 2017:
- 6:53 PM Ticket #879 (Make bonds and pseudobonds selectable) closed by
- fixed: Eric has added session saving of bond and pseudobond selection. I …
- 5:40 PM Ticket #881 (mmCIF writer writing uninitialised values into _atom_site.label_alt_ID) closed by
- fixed: Alt locs changed from bytes to strings when I implemented the …
- 2:12 PM Ticket #883 (command "select clear" gives traceback (undo-related)) created by
- Problem does not occur when selection is cleared by Ctrl-click in …
- 12:04 PM Ticket #880 (mmCIF writer writing uninitialised values into _atom_site.label_alt_ID) closed by
- duplicate: Duplicate of #881.
- 11:59 AM Ticket #878 (Command keyword error) closed by
-
not a bug: Try
style #1 ba 1and you'll see that the ba is expanded to … - 9:34 AM Ticket #882 (AddH not working with metal coordination) created by
- The following edits to add_h/simple.py seem to get things working …
- 3:43 AM Ticket #881 (mmCIF writer writing uninitialised values into _atom_site.label_alt_ID) created by
- open 2r4O save 2r4O_test.cif #1 open 2r4O_test.cif […] (in Bash …
- 3:43 AM Ticket #880 (mmCIF writer writing uninitialised values into _atom_site.label_alt_ID) created by
- open 2r4O save 2r4O_test.cif #1 open 2r4O_test.cif […] (in Bash …
Oct 11, 2017:
- 7:47 PM Ticket #879 (Make bonds and pseudobonds selectable) created by
- Currently bonds and pseudobonds are not selectable although they do …
- 6:53 PM Ticket #878 (Command keyword error) created by
- Command keyword argument abbreviated to the first word, for example, …
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 …
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