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Timeline
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 …
Sep 9, 2017:
- 4:14 PM Ticket #826 (Make ribbons use uint8 colors instead of float32) closed by
- fixed: Fixed in 3dc2ea602. Correctly treat ribbon colors as …
Sep 8, 2017:
- 1:17 PM Ticket #826 (Make ribbons use uint8 colors instead of float32) created by
- Ribbon code is currently calculating the vertex colors as float32 …
- 11:45 AM Ticket #825 (Incorrect planes read from OME TIFF file) created by
- Reading an 8-channel OME TIFF file from the Allen Institute …
Sep 7, 2017:
- 6:43 PM ChangeLog edited by
- (diff)
- 3:36 PM Ticket #824 (New Edit menu interferes with text copy) created by
- I don't know if this is fixable, but Mac clover-c after highlighting …
- 2:39 PM 2017-09-07 created by
- 2:08 PM DeveloperMeetings edited by
- (diff)
- 11:14 AM Ticket #823 (changing number of dashes resets pseudobond color) closed by
- fixed: Fixed. Was a color updating bug -- color of bond didn't change but …
- 10:37 AM Ticket #823 (changing number of dashes resets pseudobond color) created by
- Example: open 1zik hb sidechain restrict both reveal t color yellow …
Sep 5, 2017:
- 1:34 PM Ticket #822 (Improved drawing of symmetry equivalents) created by
- At present in the Clipper plugin I handle crystallographic symmetry by …
- 12:34 PM Ticket #633 (Status messages cause havoc by running event loop) closed by
- fixed: Made status bar render with OpenGL with no Qt event processing.
- 12:34 PM msgpack-testing created by
- 12:19 PM DeveloperMeetings edited by
- (diff)
- 11:37 AM 2017-08-24 edited by
- (diff)
- 4:07 AM Ticket #821 (Have pseudobonds respect user hide flags) created by
- I understand why it makes sense to have pseudobonds remain visible …
Sep 1, 2017:
- 5:26 PM Ticket #820 ('Session' object has no attribute 'undo') closed by
- not a bug: I don't think my development install was completely up to date.
- 5:14 PM Ticket #820 ('Session' object has no attribute 'undo') created by
- Open 5uak and click the 'hide ribbon' toolbar icon. Traceback (most …
- 11:39 AM Ticket #819 (Add option to make surfaces have thickness) created by
- Begin forwarded message: From: Elaine Meng Subject: interesting …
Aug 31, 2017:
- 7:10 PM Ticket #818 (core dump deleting atoms) closed by
- fixed: Fixed, I think. Could not reproduce the crash (working on Mac), but …
- 5:17 PM Ticket #818 (core dump deleting atoms) created by
- On Linux and Windows, but not always on Macs, deleting a chain will …
- 4:16 PM Ticket #817 (traceback trying to use texture command) closed by
- fixed: Fixed. Problem was image was not found because command didn't handle …
- 3:43 PM Ticket #817 (traceback trying to use texture command) created by
- Maybe I misunderstood the usage information, but when I had mol surf …
- 1:04 PM Ticket #691 ("atomic" keyword to "open" for structures) closed by
- fixed
Aug 30, 2017:
- 12:59 PM Ticket #816 (Save dialog should add file suffix if none typed in) closed by
- fixed
- 10:58 AM ChangeLog edited by
- (diff)
- 10:53 AM ChangeLog edited by
- (diff)
- 8:58 AM Ticket #815 (chain-level zone atomspec not yet implemented) reopened by
- As Eric hinted at, this approach only includes polymers. My 1zik …
Aug 29, 2017:
- 4:44 PM Ticket #815 (chain-level zone atomspec not yet implemented) closed by
- fixed: Using Eric's two-level conversion for chains<->atoms, the chain zone …
- 4:33 PM Ticket #816 (Save dialog should add file suffix if none typed in) created by
- The File / Save... dialog currently does not add the file suffix if a …
- 4:30 PM Ticket #814 (Save .obj error) closed by
- fixed: Fixed. The File / Save... menu dialog was broken due to some recent …
- 3:49 PM Ticket #815 (chain-level zone atomspec not yet implemented) created by
- “/<“ doesn’t promote to chain… gives the same set of atoms as “@<“ …
Aug 28, 2017:
- 6:03 PM Ticket #814 (Save .obj error) created by
- […]
- 4:38 PM Ticket #801 (Unpredictable keyword completion) reopened by
- Sorry to reopen this when the problem is that we didn't specify the …
- 4:22 PM Ticket #812 (Adding pseudobonds causes graphics error) closed by
- fixed: Fixed. Pseudobond deletion was not being detected by graphics and …
- 3:08 PM Ticket #813 (prolines initially shown as "hooks" (open rings)) created by
- However, simply recoloring them shows the closed ring. Example: open …
Aug 26, 2017:
- 5:58 PM Ticket #776 (Right-click on Side View produces traceback) closed by
- fixed: Fixed a while ago.
- 5:46 PM Ticket #812 (Adding pseudobonds causes graphics error) created by
- Finding hydrogen bonds for 1eyg produces: 414 hydrogen bonds found …
- 5:43 PM Ticket #801 (Unpredictable keyword completion) closed by
- fixed: Done.
Aug 25, 2017:
- 3:42 PM Ticket #811 (Optimize cmap hdf5 format read speed for light microscopy data) created by
- The Chimera map format (*.cmap) HDF5 seems to be slow reading …
Aug 24, 2017:
- 3:04 PM 2017-08-24 edited by
- (diff)
- 3:00 PM 2017-08-24 edited by
- (diff)
- 2:51 PM 2017-08-24 created by
- 2:06 PM DeveloperMeetings edited by
- (diff)
- 2:05 PM Ticket #809 (mmCIF CA trace not quite correct) closed by
- fixed: Changed missing structure test for adjacent residues from gap or (not …
- 1:55 PM Ticket #810 (labels == slow) created by
- In the attached session I have roughly 10 labels shown, but the …
- 1:44 PM Ticket #809 (mmCIF CA trace not quite correct) created by
- For structures that change from full-atomic to chain-trace at some …
- 12:59 PM Ticket #808 (attempt to cartoon P-only nucleic in 1gsg gives indexError traceback) created by
- open 1gsg cartoon ...gives the following traceback (can be blamed on …
- 12:05 PM Ticket #807 (Atoms are wrong color after some are deleted) closed by
- fixed: Fixed. Recent graphics update code changes were not updating colors …
- 11:46 AM Ticket #807 (Atoms are wrong color after some are deleted) created by
- open 3fx2 hide ribbon ; show atoms delete solvent Atoms end up all …
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