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Timeline
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- wontfix: Since this demo version of findclash has been withdrawn, this bug …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
- (diff)
- 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 …
May 30, 2017:
- 2:09 PM Ticket #694 (Add C-alpha trace depictions) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 12:56 PM Ticket #693 (Add next / previous map buttons) created by
- Begin forwarded message: From: Oliver Clarke <> Subject: …
- 12:54 PM Ticket #692 (Add a scale bar tool) created by
- Begin forwarded message: From: Oliver Clarke Subject: …
- 10:53 AM Ticket #691 ("atomic" keyword to "open" for structures) created by
- Controls whether the result is a Structure or an AtomicStructure
May 29, 2017:
- 8:39 AM Ticket #690 (Custom atom/residue properties?) created by
- There are various situations where one might want to associate custom …
May 26, 2017:
- 9:52 AM Ticket #683 (atomspec_has_atoms() is inconsistently applied.) closed by
- fixed: Using atom.hide = True did the trick.
May 25, 2017:
- 5:45 PM Ticket #688 (Toolshed 'author' link: TemplateSyntaxError) closed by
- fixed
- 4:40 PM Ticket #689 (Non-canonical H-bonds) created by
- Extend the H-bond detection functionality to include non-canonical …
- 4:24 PM BundleReformatting created by
- 4:05 PM 2017-05-25 edited by
- (diff)
- 3:44 PM Ticket #517 (toolshed hide "Model Panel" does not hide model panel) closed by
- fixed: Fixed in 49ca5ec52. The way the "toolshed show/hide" …
- 3:10 PM 2017-05-25 edited by
- (diff)
- 2:10 PM 2017-05-25 created by
- 2:09 PM DeveloperMeetings edited by
- (diff)
- 1:44 PM Ticket #688 (Toolshed 'author' link: TemplateSyntaxError) created by
- On cxtoolshed.rbvi.ucsf.edu, clicking on ISOLDE and then on the author …
- 1:05 PM Ticket #687 (Pick atoms beneath density map surfaces) created by
- On May 25, 2017, at 6:24 AM, Oliver Clarke wrote: Hi, Often I want …
- 12:40 PM Ticket #684 (Bugs in changes.py) closed by
- fixed: Ok, I fixed these 3 problems in atomic/changes.py
- 6:18 AM Ticket #684 (Bugs in changes.py) reopened by
- I see now why I couldn't find it - I was unaware that more than one …
May 24, 2017:
- 4:46 PM Ticket #686 (Provide vector graphics output of silhouette edges) created by
- On May 23, 2017, at 9:50 AM, Oliver Clarke wrote: Hi, Probably low …
- 4:44 PM Ticket #685 (Add wire display style for molecules) created by
- On May 23, 2017, at 9:47 AM, Oliver Clarke wrote: Hi, would it be …
- 10:29 AM Ticket #684 (Bugs in changes.py) closed by
- not a bug: There is a trigger to detect Atom display state changes and many other …
- 3:49 AM Ticket #684 (Bugs in changes.py) created by
- At the moment, the 'model display changed' trigger only fires when an …
May 23, 2017:
- 12:16 PM Ticket #682 (cone geometry) closed by
- fixed
- 12:16 PM Ticket #682 (cone geometry) reopened by
- Fixed. The problem was that the cone base triangles had the wrong …
May 22, 2017:
- 1:53 PM Ticket #682 (cone geometry) closed by
- not a bug: The original code looks correct to me. It is setting the normal …
- 10:06 AM Ticket #681 (Error with partial display of tubes) closed by
- fixed
- 6:54 AM Ticket #683 (atomspec_has_atoms() is inconsistently applied.) created by
- Context: I'm sub-classing AtomicStructure to provide a visualisation …
- 4:17 AM Ticket #682 (cone geometry) created by
- Trivial thing really. In chimerax.core.surface.shapes, line 190, the …
May 19, 2017:
- 5:18 PM Ticket #681 (Error with partial display of tubes) created by
- Error from: open 3jac ~car ~/a:2105-2150 car style model tube …
- 4:09 PM Ticket #678 (Multimodel PDB file crash) closed by
- fixed: Changed PDBio to assign unique model numbers in such cases
- 4:00 PM Ticket #680 (Make deleting Model or Drawing notify parent.) created by
- Want to be able to use m.delete() instead of …
- 3:20 PM Ticket #679 (Crash tab completing pseudobonds collection methods in Python shell) closed by
- fixed: That particular attr is for internal use during session saving and …
May 18, 2017:
- 3:50 PM Ticket #679 (Crash tab completing pseudobonds collection methods in Python shell) created by
- open 3loh # In shell p = session.models.list()[1] # Pseudobond group …
May 17, 2017:
- 7:25 PM Ticket #678 (Multimodel PDB file crash) created by
- Opening the attached multimodel PDB file and then closing all models …
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