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Timeline
Jun 30, 2017:
- 5:20 PM BundleReformatting edited by
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- 4:45 PM BundleReformatting edited by
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- 1:19 PM Ticket #749 (Session ids for different pseudobonds are identical) closed by
- fixed: Needed to set up the pseudobond session IDs earlier in the save …
Jun 29, 2017:
- 12:23 PM Ticket #750 (could not save dcd, at least for PDB entries opened with "coord true") closed by
- fixed: Fixed. I made specifying models in the save dcd command optional -- …
- 11:20 AM Ticket #750 (could not save dcd, at least for PDB entries opened with "coord true") created by
- I tried both NMR ensembles 1g1p and 1plx. Example open 1g1p coord t …
Jun 28, 2017:
- 6:55 PM Ticket #749 (Session ids for different pseudobonds are identical) created by
- When I try to save a session with 3d labels on pseudobonds the label …
- 1:35 PM Ticket #634 ("windowsize" as first command after starting ChimeraX does not work) closed by
- fixed: Need to force Rapid Access off for accurate window size
- 1:22 PM Ticket #748 (trying to color single selected pseudobond colors the whole pseudobond ...) closed by
- fixed: Fixed. Problem was that the selection includes the pseudobond group …
- 12:16 PM Ticket #747 (Model panel close of submodel closes everything) closed by
- fixed
- 12:12 PM Ticket #748 (trying to color single selected pseudobond colors the whole pseudobond ...) created by
- Example: open 2gbp view ions zoom .8 (Ctrl-click to select one of the …
- 11:43 AM Ticket #747 (Model panel close of submodel closes everything) created by
- open 5igy Click model #1.1 hydrogen bonds in Model Panel and press …
- 8:10 AM Ticket #746 (Global pseudobonds not hidden if model hidden) closed by
- fixed: Fixed
Jun 27, 2017:
- 5:23 PM Ticket #742 (hbonds selrestrict "both" or atomspec gives traceback) closed by
- fixed: Testing a Collection for equality against a string wasn't returning …
- 5:16 PM Ticket #743 (hbonds intramol f gives traceback) closed by
- fixed: Fixed typo
- 5:10 PM Ticket #744 (hbonds retain true makes retained H-bonds into tater tots) closed by
- fixed: Radius setting was badly messed up.
- 2:53 PM Ticket #745 ("hbonds" doesn't like ensembles, I guess) closed by
- fixed
- 2:51 PM Ticket #746 (Global pseudobonds not hidden if model hidden) created by
- Whereas pseudobonds in per-structure groups (e.g. metal-coordination …
- 2:22 PM Ticket #745 ("hbonds" doesn't like ensembles, I guess) created by
- I tried 2 different ensembles, seemingly unrelated: 1g1p and 2nbk …
- 1:39 PM Ticket #614 (Add support for zones and attributes in atom spec) closed by
- fixed: First implemention has been committed bb266f8. Probably …
- 11:54 AM Ticket #744 (hbonds retain true makes retained H-bonds into tater tots) created by
- If I use "hb retain t" the pre-existing H-bonds become really fat and …
- 11:41 AM Ticket #743 (hbonds intramol f gives traceback) created by
- Example: open 1zik hb intramol f hbonds intraMol false Traceback …
- 11:36 AM Ticket #742 (hbonds selrestrict "both" or atomspec gives traceback) created by
- However, selrestrict "cross" or "any" seem to be working fine. …
Jun 26, 2017:
- 3:47 PM Ticket #533 (Hydrogen bond finder) closed by
- fixed: For the purposes of this ticket, this is completed. For final …
- 3:15 PM Ticket #726 (opening CFTR structure and multiple sequence alignment in either order ...) reopened by
- The problem is that a temporary StructureSeq in the C++ layer gets …
- 10:14 AM Ticket #741 (style command "dashes" but not "pseudobondRadius" works with pb model spec) closed by
- fixed: Fixed. Just forgot to make this work when I added support for …
- 9:54 AM Ticket #741 (style command "dashes" but not "pseudobondRadius" works with pb model spec) created by
- The style command "dashes" option works with pb model specified …
Jun 23, 2017:
- 4:51 PM Ticket #726 (opening CFTR structure and multiple sequence alignment in either order ...) closed by
- fixed: Was calling .front() (and more importantly, .pop_front()) on an empty …
Jun 22, 2017:
- 6:53 PM BundleReformatting edited by
- (diff)
- 6:06 PM Ticket #740 (inter-model pbonds selection highlighting not shown initially) closed by
- fixed: Fixed. Global pseudobond groups didn't know when the atoms connected …
- 5:55 PM Ticket #739 (Opening files from shell command line opens them twice) closed by
- fixed: Fixed. Mac OS generates QFileOpenEvents for command-line arguments …
- 5:24 PM Ticket #740 (inter-model pbonds selection highlighting not shown initially) created by
- Example: open 1zik struts @ca sel pbonds (or: sel @ca) ...the …
- 3:51 PM Ticket #728 (previous (closed) model displays briefly when new model is opened) closed by
- fixed: Fixed by Tom G, who said (via email): I fixed the ghost molecule …
- 3:27 PM 2017-06-22 created by
- 2:08 PM DeveloperMeetings edited by
- (diff)
- 1:12 PM Ticket #739 (Opening files from shell command line opens them twice) created by
- If I start ChimeraX from mac command line also specifying the input …
- 12:02 PM Ticket #737 (cannot turn off sharp boundaries in pre-existing molecular surface) closed by
- fixed: Fixed.
- 11:38 AM Ticket #738 (RFE: some way of smoothing molecular surface cusps) created by
- Sometimes I get cusps on the molecular surface which I assume may be …
- 10:58 AM Ticket #737 (cannot turn off sharp boundaries in pre-existing molecular surface) created by
- Users are unlikely to try this, so you may want to lower priority. If …
- 10:37 AM Ticket #720 (Make space navigator work on Windows) closed by
- fixed: Buttons working on Windows now.
Jun 21, 2017:
- 4:18 PM Ticket #543 (Help viewer right-click "save link" doesn't work) closed by
- fixed: Should be fixed by 7e6e00a56.
- 11:44 AM Ticket #534 (Full toolshed semantics) closed by
- fixed: Alpha 2 functionality is done. Tickets #735 and #736 were created for …
- 11:42 AM Ticket #736 (Need tool for managing active tools) created by
- The toolshed used to have functionality for listing active tools. …
- 11:37 AM Ticket #735 (Need access to Python from Javascript in HTML pages) created by
- Using HTML pages as UI for tools may sometimes require access to …
Jun 20, 2017:
- 7:00 PM Ticket #320 (opening ChimeraX file from system command line doesn't actually open file) closed by
- fixed: Fixed. Added drag and drop support a few days ago which involved …
- 4:53 PM Ticket #734 (surface near caps keep disappearing as I move near clipping plane) closed by
- fixed: Fixed. Now that caps are models I let the user control their hiding …
- 4:34 PM Ticket #733 (errors related to surface-cap model) closed by
- fixed: Fixed. Code that delete clipping caps had not been updated to handle …
- 11:38 AM Ticket #734 (surface near caps keep disappearing as I move near clipping plane) created by
- If you move the clipping plane so that the surface isn't clipped, but …
- 10:45 AM Ticket #733 (errors related to surface-cap model) created by
- I don't understand the underlying reason, but after turning off …
Jun 19, 2017:
- 7:15 PM Ticket #729 (ChimearX exits immediately after opening main window (Windows 7)) closed by
- nonchimerax
- 7:15 PM Ticket #729 (ChimearX exits immediately after opening main window (Windows 7)) reopened by
- 7:12 PM Ticket #729 (ChimearX exits immediately after opening main window (Windows 7)) closed by
- fixed: I put in code to report and ignore this OpenGL error on startup. On …
- 6:49 PM BundleReformatting edited by
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- 6:46 PM BundleReformatting edited by
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- 5:50 PM Ticket #732 (ChimeraX dies on startup -- need better diagnostics) closed by
- fixed: Added code that shows an error dialog when an OpenGL error occurs at …
- 12:56 PM Ticket #732 (ChimeraX dies on startup -- need better diagnostics) created by
- Often some window flashes up briefly and then disappears. Usually …
- 11:41 AM Ticket #731 (Side View starts too small (can only see checkboxes)) created by
- Is there a way to assign startup window dimensions or a minimum …
- 11:29 AM Ticket #730 (unhelpful links in Log from "open formats" command) created by
- If in the daily build you use command “open formats” and then try to …
Jun 16, 2017:
- 4:50 PM Ticket #578 (Toolshed "download stats" links do nothing in ChimeraX browser) closed by
- fixed: Download link is replaced with explanation of why stats are not …
- 4:35 PM Ticket #518 (findclash gives traceback unless "test self" specified) closed by
- wontfix: Since this demo version of findclash has been withdrawn, this bug …
- 4:08 PM BundleReformatting edited by
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- 3:41 PM Ticket #506 (pip install overrides LD_LIBRARY_PATH) closed by
- fixed: The ChimeraX distribution now includes include files and link …
- 3:27 PM Ticket #445 (Traceback when executing a long select command) closed by
- wontfix: The atom specifier parser uses tail recursion for the | and & …
- 1:48 PM Ticket #729 (ChimearX exits immediately after opening main window (Windows 7)) created by
- […]
- 12:05 PM Ticket #728 (previous (closed) model displays briefly when new model is opened) created by
- If I have models in ChimeraX and close them all with "close", then …
- 10:53 AM Ticket #727 (Recently used colors?) created by
- […]
- 10:49 AM Ticket #599 ("Transplanting" a model loses track of children) closed by
- not a bug
Jun 15, 2017:
- 5:30 PM Ticket #724 (recoloring surface does not recolor surface cap) closed by
- fixed: I think a nice solution to allow caps to be given their own color and …
- 4:31 PM Ticket #723 (accidentally trying to save image in dir w/o permission gives traceback) closed by
- fixed: Fixed. Made all export IO errors omit the traceback.
- 3:08 PM Ticket #726 (opening CFTR structure and multiple sequence alignment in either order ...) created by
- I can open 5uak and I can open the attached sequence alignment. …
- 1:55 PM Ticket #725 (RFE: allow models to be immune to clipping) created by
- Mainly of interest for clipping a surface without clipping ribbons or …
- 1:44 PM Ticket #724 (recoloring surface does not recolor surface cap) created by
- I added a "front" (rotatable) clip plane but then later decided to …
- 12:31 PM Ticket #723 (accidentally trying to save image in dir w/o permission gives traceback) created by
- This is obviously user error, failure to specify a pathname where I …
- 11:51 AM Ticket #722 (if "windowsize" is first command in script, makes the whole window ...) closed by
- duplicate: Duplicate of #634
- 11:04 AM Ticket #722 (if "windowsize" is first command in script, makes the whole window ...) created by
- If I run this command script, the whole window (including log etc.) is …
Jun 14, 2017:
- 5:38 PM Ticket #721 (Hang at splash screen on start-up on Windows) closed by
- fixed: Fixed. Toolshed was trying to acquire a lock on the toolshed cache …
- 5:37 PM Ticket #721 (Hang at splash screen on start-up on Windows) created by
- ChimeraX hangs the first time it is run on Windows (7 and 10). Begin …
- 3:42 PM Ticket #643 (chimerax not starting) closed by
- wontfix: Unfortunately, remote display is not a high priority at this point of …
- 3:27 PM Ticket #342 (Convert from cxhelp/cxcmd schemes to http scheme) closed by
- fixed: "Fixed" in 35e6c7a. Added Javascript to make cxcmd links …
- 3:17 PM Ticket #672 (unable to connect to toolshed?) closed by
- fixed: Fixed in ccbb226f5.
- 11:50 AM Ticket #695 (Ribbon should not affect Atom.hide for structures with no ribbons) closed by
- fixed
- 11:45 AM Ticket #651 (Toolshed failing) closed by
- can't reproduce: Bundle submission and approval seems to be working now. We can reopen …
Jun 13, 2017:
- 7:28 PM Ticket #716 (Error reading TIFF volume with I;16S image mode) closed by
- fixed: Added compilation of patched Pillow code to read 16-bit signed data. …
- 5:29 PM Ticket #720 (Make space navigator work on Windows) created by
- Currently space navigator does not work on Windows because the …
- 5:09 PM Ticket #719 (SSL error fetching from PDB on Windows) created by
- Fetching any PDB (1a0m) fails on Windows 7 (vizvault boxx machine) …
- 4:14 PM Ticket #718 (selection cascade hysteresis (volume model stays selected)) closed by
- fixed: Fixed.
- 4:02 PM Ticket #718 (selection cascade hysteresis (volume model stays selected)) created by
- If I select one atom in an atomic model in the presence of volume …
- 3:30 PM Ticket #713 (Drag and drop closes Open Dialog when dragging over Log panel) closed by
- fixed: Fixed. Made log panel and other HTML panels not accept file drops.
- 3:28 PM Ticket #717 (Center of rotation changes during spin movie with volumetric data displayed) closed by
- fixed: Fixed. Made switching volume planes during rendering not cause a …
- 3:28 PM Ticket #717 (Center of rotation changes during spin movie with volumetric data displayed) created by
- Center of rotation changes during spin movie with volumetric data …
- 3:20 PM Ticket #714 (Allow drag and drop of data files on Mac dock icon or ChimeraX window) closed by
- fixed: Added file open by drag and drop on app window or Mac Dock icon.
- 12:23 PM 2017-06-01 edited by
- (diff)
Jun 12, 2017:
- 4:13 PM Ticket #460 (mmCIF reader does not have "explode" option to make coordinate sets) closed by
- fixed: Added coordsets support.
- 2:09 PM Ticket #600 (Model.metadata does not contain cell information for model from an ...) closed by
- fixed: Next successful build will have "cell" and "symmetry" metadata.
Jun 9, 2017:
- 8:20 PM Ticket #611 (Session format: compare performance of msgpack vs. pickle) closed by
- fixed: After putting FinalizedState object output, only 1.2% of time was …
- 5:47 PM Ticket #716 (Error reading TIFF volume with I;16S image mode) created by
- Reading a light microscopy map in 3D TIFF format with I;16S image …
- 5:38 PM Ticket #715 (Center of rotation changes in spin move of map in volumetric style) closed by
- fixed: Fixed. Problem was that the volumetric rendering shows a stack of …
- 5:36 PM Ticket #715 (Center of rotation changes in spin move of map in volumetric style) created by
- Spin movie center of rotation jumps in the middle of a spin movie when …
- 4:16 PM Ticket #611 (Session format: compare performance of msgpack vs. pickle) reopened by
- For 4v8r, 85% of the restore time is in …
- 4:05 PM Ticket #714 (Allow drag and drop of data files on Mac dock icon or ChimeraX window) created by
- From Slack conversation: graham [3:57 PM] Agreed. Even better- I …
- 4:03 PM Ticket #713 (Drag and drop closes Open Dialog when dragging over Log panel) created by
- Trying to drag a data file onto the open dialog works unless the drag …
Jun 8, 2017:
- 11:07 PM Ticket #712 (mmCIF won't extrude chem_comp table to metadata) closed by
- fixed: The name field will always be in the metadata even if it isn't in the …
- 11:05 PM Ticket #669 (mmCIF 1grl needs to put missing structure between :302-303) closed by
- fixed: Added code to suppress warning about missing linking atom when …
- 10:36 PM Ticket #611 (Session format: compare performance of msgpack vs. pickle) closed by
- fixed: Here are some preliminary results using a session file that only has …
- 5:04 PM Ticket #712 (mmCIF won't extrude chem_comp table to metadata) created by
- As per summary, probably because the code parses the table itself …
Jun 7, 2017:
Jun 6, 2017:
- 4:22 PM Ticket #711 (mis-association (misalignment) between structure 1ml1 and its own sequence) created by
- If I open 1ml1 and then click the “monotim” to show all the chains …
Jun 5, 2017:
- 6:14 PM Ticket #710 (Allow switching into sequential stereo after startup) created by
- Currently a command-line flag --stereo is needed to use sequential …
- 6:13 PM Ticket #709 (Better sequential stereo rendering parameters) created by
- The current sequential stereo camera parameters are a bit weird, …
- 2:59 PM Ticket #702 (fmt referenced before assignment) closed by
- fixed: This was a one-day-special bug and is fixed now.
- 2:46 PM Ticket #703 (Traverse command history with up/down arrows) closed by
- fixed: If any keys get forwarded to the command line, it takes over focus and …
- 2:31 PM Ticket #708 (RFE: context menu to delete specific File History (Rapid Access) icons) closed by
- duplicate: I guess this is already part of #665. Sorry about that.
- 2:30 PM Ticket #708 (RFE: context menu to delete specific File History (Rapid Access) icons) created by
- Would be great if there were a context menu from clicking a specific …
- 2:26 PM Ticket #707 (trying to open incorrect http URL creates file history entry) created by
- I don't know if this is fixable, since although this generates a "not …
- 2:20 PM Ticket #706 (using File History to open http URL echoes command with "http" as database) created by
- If I use command open …
- 2:09 PM Ticket #705 (File history icons for html and sequence alignment files) created by
- Make file history use generic icons for sequence alignment and html …
- 1:49 PM BundleReformatting edited by
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Jun 2, 2017:
- 3:04 PM BundleReformatting edited by
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- 2:39 PM BundleReformatting edited by
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- 2:30 PM BundleReformatting edited by
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- 1:47 PM Ticket #704 (Set fetched EDS map initial contour levels to +/- N sigma) created by
- Begin forwarded message: From: Tristan Croll Subject: Re: New …
- 1:24 PM BundleReformatting edited by
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- 1:17 PM Ticket #703 (Traverse command history with up/down arrows) created by
- Oliver points out that in Chimera if you click into the graphics …
- 1:13 PM BundleReformatting edited by
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- 12:50 PM BundleReformatting edited by
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- 12:03 PM BundleReformatting edited by
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- 11:45 AM BundleReformatting edited by
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- 11:41 AM BundleReformatting edited by
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- 11:19 AM BundleReformatting edited by
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- 10:33 AM BundleReformatting edited by
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- 10:25 AM BundleReformatting edited by
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- 12:20 AM Ticket #702 (fmt referenced before assignment) created by
- […] [[Image(...)]] [[Image(...)]]
Jun 1, 2017:
- 11:44 PM BundleReformatting edited by
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- 3:08 PM 2017-06-01 edited by
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- 2:00 PM 2017-06-01 created by
- 1:57 PM DeveloperMeetings edited by
- (diff)
- 12:04 PM Ticket #701 (Add buttons to toggle map or atomic structure display) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 6:33 AM Ticket #700 (Toolshed dependency issue) created by
- My ISOLDE plugin is dependent upon my Clipper plugin. In the ISOLDE …
- 12:54 AM Ticket #699 (core.commands.rename issues) created by
- If I create an empty model first: […] ... then load a structure …
May 31, 2017:
- 11:49 PM Ticket #697 (cif file saved from model with children causes segmentation fault on load) closed by
- fixed: There was a bug in the code that faked the missing entity_poly_seq …
- 9:08 PM BundleReformatting edited by
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- 9:05 PM BundleReformatting edited by
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- 2:57 PM BundleReformatting edited by
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- 2:39 PM Ticket #274 (Select through transparent surface or mesh) closed by
- fixed: Fixed. The default behavior is now to select through transparent …
- 2:33 PM Ticket #569 (Show selected atoms under transparent surface) closed by
- fixed: Fixed. The selection outlines for objects behind transparent surfaces …
- 2:01 PM BundleReformatting edited by
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- 2:00 PM BundleReformatting edited by
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- 1:58 PM BundleReformatting edited by
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- 12:10 PM Ticket #698 (Make slider record button bring up movie option panel) created by
- The coordinate set slider, map series slider, model series slider, and …
- 10:02 AM Ticket #697 (cif file saved from model with children causes segmentation fault on load) created by
- Two-parter here: 1. If I have an AtomicStructure with child models …
- 9:54 AM Ticket #696 (File/save causing segmentation fault in Linux) created by
- Doesn't appear related to anything I've done (crashes even in a …
- 3:23 AM Ticket #695 (Ribbon should not affect Atom.hide for structures with no ribbons) created by
- I have a class (subclassed from Structure) used to draw position …
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