![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Apr 24, 2020:
- 7:26 PM Ticket #1532 (Improve deferring of subcommand registration) closed by
- fixed
- 7:25 PM Ticket #2600 (Problem with "toolshed show") closed by
- fixed: Done.
- 7:18 PM Ticket #1771 ("devel install" cannot link OpenMM.lib) closed by
- fixed: Done.
- 4:33 PM Ticket #2250 (Simplify tool-author look up) closed by
- wontfix: For (2), until there is actually a high volume of new developers, just …
- 4:25 PM Ticket #3102 (volume subregion: 'NoneType' object has no attribute 'size') closed by
- fixed: Fixed. A clip cap of one map was colored by volume data value of …
- 4:23 PM Ticket #3022 (ISOLDE used with incompatible ChimeraX) closed by
- fixed: 0.93 is out. This problem should not crop up with future versions.
- 3:52 PM Ticket #2771 (_openmm fails to load) closed by
- fixed: Lastest numpy has the lastest MKL which has the fix. And is installed …
- 3:51 PM Ticket #2749 (ISOLDE installed into incompatible Ubuntu build of ChimeraX) closed by
- fixed: Fixed by common Linux ABI
- 3:41 PM Ticket #2710 (Somewhat mysterious warning when building bundles) closed by
- fixed: Testing has been removed from bundle builder.
- 3:34 PM Ticket #2694 (Autoscale ToolShed downloads graph widget) closed by
- wontfix: Lost this functionality in the Python3 version of the toolshed. A CSV …
- 3:28 PM Ticket #2672 (Toolshed down) closed by
- fixed
- 3:27 PM Ticket #2649 (Toolshed details does not display http link markup correctly.) closed by
- fixed: Conrad fixed regex in Markdown.Converter.js.
- 3:05 PM Ticket #2618 (Web page to release bundles on Tool Shed is broken) closed by
- fixed
- 2:01 PM Ticket #3025 (Installing bundle doesn't add its providers) closed by
- fixed
- 1:27 PM Ticket #1666 (bundle_info.xml DataFormat classifier needs allow_directory option) closed by
- fixed: The data-formats manager supports an "allow_directory" attribute.
- 1:14 PM Ticket #1976 ("is_default" does nothing in Open and Save ChimeraXClassifier) closed by
- fixed: I believe the issue is moot at this point, but with the new …
- 12:57 PM Ticket #2592 (Can't install ISOLDE for everyone) closed by
- duplicate: Work will be tracked in #2593.
- 12:39 PM Ticket #2444 (Weird import errors) closed by
- can't reproduce: Might be because user ran new version, resulting in new bundle cache, …
- 12:36 PM Ticket #2425 (ISOLDE cannot find symbol atomstruct::Residue::find_atom) closed by
- fixed: Fixed by common Linux ABI.
- 12:33 PM Ticket #2174 (Could not install ISOLDE/Clipper: EnvironmentError) closed by
- fixed: Can't install globally anymore.
- 12:30 PM Ticket #2087 (Problem with distutils-generated loader flags) closed by
- fixed
- 12:27 PM Ticket #1961 (Toolshed US download map not colored) closed by
- wontfix: GeoIP data costs real money now.
- 12:24 PM Ticket #1862 (Some funkiness installing wheels needing tilde expansion) closed by
- fixed: Use os.path.expanduser() to expand ~.
- 12:16 PM Ticket #1845 ("toolshed install" errors reporting to status bar rather than log) closed by
- duplicate: Work is happening in #3055.
- 12:14 PM Ticket #1819 (Problem with PyPI dependencies (or dependencies of dependencies?)) closed by
- duplicate: Work is happening in #3055.
- 12:12 PM Ticket #1546 ("Nightly build" system for Tool Shed) closed by
- duplicate: Duplicate of #1787.
- 12:09 PM Ticket #1786 (Naming of development bundles) closed by
- fixed: We now conform to PEP 440 version numbers.
- 12:00 PM Ticket #1766 (Permission denied installing Clipper) closed by
- fixed: No response.
- 11:58 AM Ticket #1686 ('ChimeraX -m pip install mdtraj' causes GUI to repeatedly flash up) closed by
- wontfix: Conrad says "I can live with that".
- 11:57 AM Ticket #1672 (Library linking failure after ISOLDE install) closed by
- fixed: Fixed by requiring all Linux binary bundles be built on the same …
- 11:55 AM Ticket #1650 (IncludeDir argument in bundle_info.xml no longer recognises $HOME) closed by
- wontfix: Conrad says don't use $HOME.
- 11:53 AM Ticket #1640 ('toolshed install isolde reinstall true' attempts to install wrong ...) closed by
- fixed: Workaround is use ~=VERSION in dependencies.
- 11:49 AM Ticket #1521 ('devel install' failing for RedHat rpm builds) closed by
- fixed: The include files are now in the CentOS 7 rpm.
- 11:45 AM Ticket #1402 (Bundle's own compiled libraries should be at top of symbol search path) closed by
- wontfix: Symbols from an already loaded library override subsequent loads.
- 11:35 AM Ticket #1278 (Option to only rebuild Python component of bundle) closed by
- wontfix: setup.py might be smart enough to limit the compile to just the Python …
- 11:34 AM Ticket #1106 (Dependencies on other bundle's include dirs) closed by
- duplicate: Dup of #1022.
- 11:33 AM Ticket #1104 (Installing ISOLDE gives traceback, needs user-friendly error message) closed by
- fixed: ChimeraX no longer tries to install incompatible packages.
- 11:30 AM Ticket #1099 (PyPI dependency fail on 'make app-install') closed by
- fixed: Using newer OpenSSL now.
- 11:28 AM Ticket #1089 (Option to recursively include contents of directory in bundle) closed by
- fixed: Added <DataDir> option to <DataFiles> section in bundle_info.xml
- 11:25 AM Ticket #1022 (Allow Toolshed bundles to provide access to their C++ API) closed by
- fixed: If bundle is dependent on another bundle, bundle_builder will add the …
- 11:23 AM Ticket #958 (Toolshed offers to install Linux bundle on Mac) closed by
- fixed
- 11:05 AM Ticket #1646 (Clip broken + depth cueing question) closed by
- fixed: This problem was mostly solved by having the clip command warn when …
- 11:03 AM Ticket #3108 (Allow clip command to specify positions relative to center of rotation) created by
- Would like the "fromCenter true" option that Chimera has for setting …
- 10:59 AM Ticket #3107 (Enable depth cue with mesh lighting off) created by
- Currently depth cue is considered part of lighting and the setting …
- 10:59 AM Ticket #2805 (Update toolshed to Python3 and more recent django) closed by
- fixed
- 10:57 AM Ticket #3106 (Side view shows wrong clip positions when near plane is behind far plane) created by
- Oliver Clarke accidentally put the near clip plane behind the far clip …
- 10:43 AM Ticket #2571 (No mail/feedback) closed by
- can't reproduce: No response.
- 10:04 AM Ticket #3104 (Adjusting cage-builder edge length: 'NoneType' object has no attribute ...) closed by
- fixed: Fixed in tonight's ChimeraX build. The problem was not with edge …
- 9:33 AM Ticket #3103 (Strudel Score can't write its own config file) closed by
- can't reproduce
- 9:22 AM Ticket #3105 (addh wrong hydrogen name on glycosylated Asn residues) created by
- When the asparagine is glycosylated, since there is only one hydrogen …
- 5:34 AM Ticket #3104 (Adjusting cage-builder edge length: 'NoneType' object has no attribute ...) created by
- […]
- 5:08 AM Ticket #3103 (Strudel Score can't write its own config file) created by
- […]
- 12:19 AM Ticket #2520 (ISOLDE synopsis in User Guide Index should link to ISOLDE website) closed by
- fixed: Fixed getting generated user manual index with accessing via a href. …
Apr 23, 2020:
- 5:42 PM RestAPI edited by
- (diff)
- 5:39 PM RestAPI edited by
- (diff)
- 5:34 PM RestAPI edited by
- (diff)
- 5:31 PM RestAPI edited by
- (diff)
- 5:24 PM RestAPI created by
- 5:14 PM Features edited by
- (diff)
- 2:20 PM Ticket #3102 (volume subregion: 'NoneType' object has no attribute 'size') created by
- […]
- 1:46 PM Ticket #3101 (save mmCIF after opening PDB gives AttributeError: 'NoneType' object ...) closed by
- duplicate: Duplicate of #3047. Fixed earlier today.
- 1:41 PM Ticket #2825 (Residue::find_atom() being looked for in isolde/libmolc.so) closed by
- fixed: Now have common Linux ABI.
- 1:38 PM Ticket #3101 (save mmCIF after opening PDB gives AttributeError: 'NoneType' object ...) created by
- […]
- 11:14 AM Ticket #3047 (Problem writing 'software' info to mmCIF) closed by
- fixed
- 9:56 AM Ticket #3100 (IndexError during ribbon pick) closed by
- duplicate: Hi Karim, Thanks for reporting this problem. It was fixed just a …
- 9:28 AM Ticket #3099 (auto-wipe some commands?) reopened by
- Yeah, we're not fans of this particular paternalistic behavior. I …
- 9:12 AM Ticket #3099 (auto-wipe some commands?) closed by
- wontfix: Yeah, actually neither the Actions menu nor the toolbar icons use the …
- 7:04 AM Ticket #3100 (IndexError during ribbon pick) created by
- […]
- 3:32 AM Ticket #3099 (auto-wipe some commands?) created by
- […]
Apr 22, 2020:
- 5:00 PM Ticket #2634 (Crash clicking help-browser link) closed by
- fixed: Does not crash on macOS 10.13 with current daily build that has Qt 5.12.8.
- 4:51 PM Ticket #2782 (Some help files crash ChimeraX) closed by
- fixed: Unable to reproduce with daily build (Qt 5.12.8).
- 11:46 AM Ticket #3097 (Undeposited structure: 'NoneType' object has no attribute 'isupper') closed by
- fixed: Fixed in the next build. The issue was with the HETNAM record for …
- 11:22 AM Ticket #3096 (Session restore failure: ValueError: int is not allowed for map key) closed by
- duplicate: Hi Ondrej, This bug was fixed just yesterday, so if you get today's …
- 11:08 AM Covid19Grant edited by
- (diff)
- 11:07 AM Covid19Grant created by
- 11:05 AM WikiStart edited by
- (diff)
- 11:03 AM WikiStart edited by
- (diff)
- 11:01 AM WikiStart edited by
- (diff)
- 10:33 AM Ticket #3098 (Add fitmap option to low pass filter before fitting) created by
- Would be convenient to have a fitmap command option to low pass filter …
- 7:39 AM Ticket #3097 (Undeposited structure: 'NoneType' object has no attribute 'isupper') created by
- […]
- 12:10 AM Ticket #3096 (Session restore failure: ValueError: int is not allowed for map key) created by
- […]
Apr 21, 2020:
- 9:52 PM Ticket #2570 (Some help files crash ChimeraX) closed by
- fixed: Just revised the daily build to use PyQt 5.12.3 with Qt 5.12.8. And I …
- 5:11 PM PhenixTools created by
- 5:05 PM WikiStart edited by
- (diff)
- 4:11 PM Ticket #3084 (Inserted fragments should update missing-structure pseudobonds) closed by
- fixed: The insertion now automatically updates the missing-structure …
- 3:14 PM Ticket #3059 (Toolshed bundle release page does not work) closed by
- fixed: Works well enough for now.
- 2:38 PM Ticket #3095 (Crash in WebEngine trying to access Qt) closed by
- can't reproduce: Hi Amedee, It looks like this crash occurred with the 0.8 version of …
- 2:28 PM Ticket #3093 (Error forming missing-structure pseudobonds to internally disconnected ...) closed by
- fixed: Just pushed a fix.
- 2:18 PM Ticket #2625 (Problems with dependency version specifiers when uploading to Tool Shed) closed by
- fixed: All of those version specifiers are now accepted.
- 12:19 PM Ticket #3095 (Crash in WebEngine trying to access Qt) created by
- […]
- 11:45 AM Ticket #3088 (Crash initializing OpenGL) closed by
- can't reproduce: Qt crashing trying to initialize some OpenGL on a window resize. …
- 11:21 AM Ticket #3086 (IndexError during ribbon pick) closed by
- fixed: Fixed. Sorted triangle ranges was not reset so had value from first …
- 10:41 AM Ticket #3094 (Ribbon error after deleting atoms) closed by
- fixed: Fixed. An empty ribbon residue range caused this error due to a bug …
- 10:29 AM Ticket #3089 (Session restore failure: ValueError: int is not allowed for map key) closed by
- fixed: Fixed in the next daily build. Bug was due to change in msgpack 1.0 …
- 10:25 AM Ticket #3094 (Ribbon error after deleting atoms) created by
- […]
- 10:04 AM Ticket #3090 (open2 not handling TIFF stack correctly) closed by
- fixed: format-name checking also needed to check against prefixes
- 9:55 AM Ticket #3093 (Error forming missing-structure pseudobonds to internally disconnected ...) created by
- […]
- 9:26 AM Ticket #3080 (ImportError: cannot import name 'RibbonDrawing' from ...) closed by
- duplicate: This was fixed 10 days ago. Get a current daily build. Problem is …
- 9:18 AM Ticket #3092 (pb_scene_coord returning None) closed by
- duplicate: Hi Kasey, Thanks for reporting this problem. It has been fixed in …
- 9:04 AM Ticket #3087 (Sequence-association problem upon 'split') closed by
- duplicate: Hi, I believe this problem is fixed in newer releases of ChimeraX. …
- 8:09 AM Ticket #3092 (pb_scene_coord returning None) created by
- […]
- 7:58 AM Ticket #3091 (ToolInstance.delete(self) during session reset produces KeyError) created by
- […]
Apr 20, 2020:
- 9:57 PM Ticket #3090 (open2 not handling TIFF stack correctly) created by
- […]
- 5:51 PM Ticket #3089 (Session restore failure: ValueError: int is not allowed for map key) created by
- […]
- 5:47 PM Ticket #3088 (Crash initializing OpenGL) created by
- […]
- 4:58 PM Ticket #3087 (Sequence-association problem upon 'split') created by
- […] split model.html split model-1.html
- 4:41 PM Ticket #3044 (document pseudobond group create_type arg) closed by
- fixed: Okay, that argument is documented now.
- 4:15 PM Ticket #3086 (IndexError during ribbon pick) created by
- […]
- 2:44 PM Ticket #3078 (ribbon cross section: unsupported operand type(s) for *: 'float' and ...) closed by
- fixed: Fixed. The helix tube radius is normally calculated for each helix. …
- 2:15 PM Ticket #3085 (sequence viewer messed up when fragment inserted into missing-structure gap) created by
- Doesn't crash it, but the deleted residues appear as missing and their …
- 2:12 PM Ticket #3084 (Inserted fragments should update missing-structure pseudobonds) created by
- summary pretty much covers it
- 11:53 AM Ticket #3083 (partially numeric residue name not handled by atom spec) closed by
- fixed: Fixed in 6f9e798ad. "92D" looks like "residue 92 insert …
- 11:42 AM Ticket #3074 (Mac Catalina prevent toolbar image save to desktop) closed by
- can't reproduce: macOS Catalina asks permission to access Downloads, Desktop and …
- 10:24 AM Ticket #3083 (partially numeric residue name not handled by atom spec) created by
- in structure 5val, "sel :92D" does not select the ligand.
- 9:58 AM Ticket #3082 (Molecular Docking problem) closed by
- not a bug: Redirected to chimera-users
- 9:56 AM Ticket #3081 (ISOLDE cannot link Residue::find_atom) closed by
- duplicate
- 9:29 AM Ticket #3077 (pb_scene_coord: Cannot multiply Place times "None") closed by
- duplicate
- 9:21 AM Ticket #3076 (run .cxc file) closed by
- not a bug: Hi, The 'runscript' command is for executing Python scripts, not …
- 8:37 AM Ticket #3082 (Molecular Docking problem) created by
- […]
- 8:25 AM Ticket #3081 (ISOLDE cannot link Residue::find_atom) created by
- […]
- 4:09 AM Ticket #3080 (ImportError: cannot import name 'RibbonDrawing' from ...) created by
- […]
Apr 19, 2020:
- 10:04 PM Ticket #3079 (Registration failure (while plato was down)) created by
- […]
- 6:41 AM Ticket #3078 (ribbon cross section: unsupported operand type(s) for *: 'float' and ...) created by
- […]
Apr 18, 2020:
- 2:09 PM Ticket #3075 (Slow coloring of large molecular surfaces) closed by
- fixed: Fixed. 100x faster now on 6owg test case (0.3 seconds instead of 30 …
- 7:17 AM Ticket #3077 (pb_scene_coord: Cannot multiply Place times "None") created by
- […]
- 3:07 AM Ticket #3076 (run .cxc file) created by
- […]
Apr 17, 2020:
- 8:55 PM Ticket #3067 (Bug reporter losing log text) closed by
- fixed: Fixed.
- 7:18 PM Ticket #3075 (Slow coloring of large molecular surfaces) created by
- […]
- 6:12 PM ChangeLog edited by
- (diff)
- 3:50 PM Ticket #3073 (empty surfaces slow things down) closed by
- not a bug: ~surface is an alias for "surface hide". (The command "alias …
- 2:54 PM Ticket #3069 (Delete backbone atom while ribbon displayed: Cylinder end-point and ...) closed by
- fixed: Fixed. Deleting a CA atom for a residue showing a ribbon caused this …
- 12:49 PM Ticket #3074 (Mac Catalina prevent toolbar image save to desktop) created by
- […]
- 11:43 AM Ticket #3072 ("chains" that are not polymers) closed by
- not a bug: Well, obviously a chain is a series of connected polymeric residues, …
- 11:31 AM Ticket #3073 (empty surfaces slow things down) created by
- […]
- 11:18 AM Ticket #3070 (Inter-residue bonds should not select residues) closed by
- fixed
- 10:35 AM Ticket #3066 (Actions menu: no visible models produces error) closed by
- fixed
- 9:56 AM Ticket #3072 ("chains" that are not polymers) created by
- […]
- 9:34 AM Ticket #3071 (Crash in ~Structure) closed by
- can't reproduce: old version of ChimeraX
- 9:22 AM Ticket #3071 (Crash in ~Structure) created by
- […]
- 8:19 AM Ticket #3070 (Inter-residue bonds should not select residues) created by
- […]
- 12:29 AM Ticket #3069 (Delete backbone atom while ribbon displayed: Cylinder end-point and ...) created by
- […]
Apr 16, 2020:
- 8:40 PM Ticket #3068 (Crash starting ISOLDE) created by
- […]
- 8:26 PM Ticket #3067 (Bug reporter losing log text) created by
- […] Screen Shot 2020-04-16 at 8.23.06 PM.png
- 8:20 PM Ticket #3066 (Actions menu: no visible models produces error) created by
- […]
- 7:05 PM ChangeLog edited by
- (diff)
- 7:02 PM ChangeLog edited by
- (diff)
- 7:00 PM ChangeLog edited by
- (diff)
- 5:14 PM Ticket #3051 (Error building core related to version number changing) closed by
- fixed: Fixed core to always regenerate the setup.py and buildinfo.py files …
- 4:36 PM ChangeLog edited by
- (diff)
- 3:59 PM Ticket #3065 (ISOLDE simulation stopped: 'OpenMM_Thread_Handler' object has no ...) created by
- […]
- 3:26 PM Ticket #3057 (pseudobond's atoms pb_scene_coord is None(?)) closed by
- fixed: Fixed. I changed Atom.ribbon_coord to return None instead of throwing …
- 12:56 PM Ticket #3064 (Adding images and descriptions to RBVI bundles) created by
- Conrad's subset from #3060 master list of bundles. After bundles have …
- 12:54 PM Ticket #3063 (Adding images and descriptions to RBVI bundles) created by
- Greg's subset from #3060 master list of bundles. After bundles have …
- 12:53 PM Ticket #3062 (Adding images and descriptions to RBVI bundles) created by
- Eric's subset from #3060 master list of bundles. After bundles have …
- 12:49 PM Ticket #3061 (Adding images and descriptions to RBVI bundles) created by
- TomG's subset from #3060 master list of bundles. After bundles have …
- 12:34 PM PhenixChimeraX edited by
- (diff)
- 11:56 AM Ticket #3060 (Adding images and descriptions to RBVI bundles) created by
- After bundles have been added to the toolshed, they need to be edited …
- 11:16 AM Ticket #3059 (Toolshed bundle release page does not work) reopened by
- It looks like my request gets into an authentication loop: GET …
- 11:01 AM Ticket #3059 (Toolshed bundle release page does not work) closed by
- worksforme: Works for me. Maybe you tried it when I briefly broke it while …
- 10:51 AM Ticket #3059 (Toolshed bundle release page does not work) created by
- The bundle release page …
- 10:47 AM Ticket #3058 (Automate putting release (and daily) wheels on toolshed) created by
- When a release is made, all wheels other than core should be placed on …
- 10:42 AM Ticket #3057 (pseudobond's atoms pb_scene_coord is None(?)) created by
- […]
- 10:32 AM Ticket #3054 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') closed by
- duplicate: duplicate of #3024
- 10:18 AM Ticket #3050 (OpenMM: User-supplied template does not match the residue) closed by
- fixed: The traceback is suppressed in more recent ISOLDE builds, so closing …
- 10:14 AM Ticket #3052 (Toolbar icon image save → can't access Desktop) closed by
- nonchimerax
- 9:02 AM Ticket #3056 (ISOLDE's ToolShed entry broken) closed by
- fixed: The 1.0b5.1 has been removed. Will change bundle submission code to …
- 8:12 AM Ticket #3056 (ISOLDE's ToolShed entry broken) created by
- I'm afraid I just broke ISOLDE's ToolShed entry by uploading a bundle …
- 6:57 AM Ticket #3055 (Add ParmEd to ChimeraX's standard bundles) created by
- I think I brought this up once before, but can't find an existing …
- 3:02 AM Ticket #3054 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') created by
- […]
Apr 15, 2020:
- 10:22 PM Ticket #3053 (Click logged command → crash) created by
- […]
- 7:37 PM Ticket #3052 (Toolbar icon image save → can't access Desktop) created by
- […]
- 6:50 PM Ticket #3051 (Error building core related to version number changing) created by
- […]
- 2:28 PM Ticket #3050 (OpenMM: User-supplied template does not match the residue) created by
- […]
- 2:22 PM Ticket #3049 (OpenMM coordinate update: RuntimeError: Release Object) created by
- […]
- 2:13 PM Ticket #3046 (bundles missing in the Linux build?) closed by
- fixed: Confirmed that there are no chimerax.atomic.rotamers.libs in the Linux …
- 9:35 AM Ticket #3048 (Graphics error drawing selection) closed by
- nonchimerax: Duplicate. Graphics driver problem with VMWare / Mesa 19.2.8 drawing …
- 8:56 AM Ticket #3045 (Merging models/fragments) closed by
- not a bug: Information relevant to ticket #2236; referred to this ticket there
- 6:45 AM Ticket #3048 (Graphics error drawing selection) created by
- […]
- 3:43 AM Ticket #3047 (Problem writing 'software' info to mmCIF) created by
- […]
Apr 14, 2020:
- 2:47 PM Ticket #3046 (bundles missing in the Linux build?) created by
- […]
- 10:56 AM Ticket #3041 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') closed by
- duplicate
- 10:56 AM Ticket #3041 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') reopened by
- 10:56 AM Ticket #3041 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') closed by
- fixed: Duplicate, fixed a few days ago.
- 8:52 AM Ticket #3045 (Merging models/fragments) created by
- I understand adding a "merge models" command has been on the to-do …
- 8:45 AM Ticket #3042 (Using wrong Linux distro?) closed by
- duplicate: Yep - duplicate of #2214. Should go away once people update to 0.93 …
- 7:50 AM Ticket #3044 (document pseudobond group create_type arg) created by
- […]
- 6:29 AM Ticket #3043 (Save a residue as mmCIF template) created by
- Would be great to have the ability to save a given residue as a mmCIF …
- 3:30 AM Ticket #3038 (Restoring session: 'SymmetryManager' object has no attribute '_unit_cell') closed by
- fixed: Fixed. I'd like to get a couple of other things done before pushing a …
- 12:58 AM Ticket #3042 (Using wrong Linux distro?) created by
- […]
- 12:05 AM Ticket #3009 (add ability to add software citations to mmCIF files) closed by
- fixed: Was already working on this. Added …
Apr 13, 2020:
- 12:15 PM Ticket #3040 (Error with close session) closed by
- fixed: Guard against state_containers changing during reset.
- 11:41 AM Ticket #3041 (cannot import name 'RibbonDrawing' from 'chimerax.atomic.ribbon') created by
- […]
- 11:38 AM Ticket #3039 (crash in glDeleteBuffers) closed by
- can't reproduce: Probable graphics driver bug. "Graphics hardware encountered an error …
- 11:32 AM Ticket #3040 (Error with close session) created by
- […] orig.cxs
- 9:23 AM Ticket #3033 (OpenMM: 'coords' is None) closed by
- duplicate: Duplicate of #2990. Fixed in the latest build.
- 9:13 AM Ticket #3035 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') closed by
- duplicate: duplicate of #3024
Apr 12, 2020:
- 10:25 AM Ticket #3039 (crash in glDeleteBuffers) created by
- […]
- 6:48 AM Ticket #3038 (Restoring session: 'SymmetryManager' object has no attribute '_unit_cell') created by
- […]
Apr 11, 2020:
- 1:47 PM Ticket #3037 (Selection problems) created by
- […]
- 11:09 AM Ticket #3036 (Mouse hover over atoms gives error) closed by
- fixed: Fixed. Hover was trying to check for ribbon pick. Even though no …
- 11:00 AM Ticket #3036 (Mouse hover over atoms gives error) created by
- […]
- 4:48 AM Ticket #3035 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') created by
- […]
- 3:27 AM Ticket #3034 (Infrequent ISOLDE crash) created by
- […]
Apr 10, 2020:
- 11:22 PM LinuxBuildSetup edited by
- (diff)
- 11:21 PM LinuxBuildSetup created by
- 11:18 PM WikiStart edited by
- (diff)
- 10:55 AM PhenixChimeraX edited by
- (diff)
- 10:54 AM PhenixChimeraX created by
- 10:50 AM WikiStart edited by
- (diff)
- 9:40 AM Ticket #3033 (OpenMM: 'coords' is None) created by
- […]
- 8:50 AM Ticket #3032 (Crash during close) closed by
- duplicate: Duplicate of #2895, fixed on 2/28/20
- 8:30 AM Ticket #3032 (Crash during close) created by
- […]
- 12:41 AM linuxbundles edited by
- (diff)
- 12:39 AM linuxbundles edited by
- (diff)
- 12:37 AM linuxbundles created by
- 12:21 AM WikiStart edited by
- (diff)
- 12:17 AM SourceCode edited by
- (diff)
- 12:05 AM nightlydocker edited by
- (diff)
Apr 9, 2020:
- 4:01 PM Ticket #3024 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') closed by
- fixed: We will start using version numbers like 0.94.dev202004031434 for …
- 3:58 PM Ticket #3031 (No partial dot surfaces) closed by
- fixed: Fixed. Got it, the whole surface was shown as dots even if it had a …
- 2:35 PM Ticket #3031 (No partial dot surfaces) created by
- Once I added surface styles to the Actions menu, it became obvious …
- 1:12 PM Ticket #3030 (Add Label to Actions Menu) created by
- 1:10 PM Ticket #3029 (Add Color to Actions Menu) created by
- Done except for Actions→Color→All Options... which is a stretch goal.
- 12:12 PM Ticket #2804 (Update ChimeraX dependencies) closed by
- fixed: Done.
- 11:21 AM Ticket #3027 (Peptide builder should remove whitespace and catch non-peptide characters) closed by
- fixed
- 10:06 AM Ticket #3028 (Crash during close) closed by
- duplicate: duplicate of #2895
- 9:59 AM Ticket #3026 (Peptide builder should remove whitespace and catch non-peptide characters) closed by
- duplicate: Duplicate of #3027
- 5:00 AM Ticket #3028 (Crash during close) created by
- […]
- 1:03 AM Ticket #3027 (Peptide builder should remove whitespace and catch non-peptide characters) created by
- […]
Apr 8, 2020:
- 11:05 PM Ticket #3026 (Peptide builder should remove whitespace and catch non-peptide characters) created by
- […]
- 6:00 PM Ticket #3025 (Installing bundle doesn't add its providers) created by
- So when checking my updates to the developer tutorials, I noted that …
- 11:54 AM Ticket #2295 (Crash in OpenGL) closed by
- fixed: Some changes went into the daily build which we hope will either fix …
- 11:51 AM Ticket #2976 (Crash closing dialog) closed by
- fixed: I made use of the WA_DeleteOnClose flag where possible with these …
- 2:06 AM Ticket #3024 ('cartoon' command: 'Atoms' object has no attribute 'evaluate') created by
- […]
Apr 7, 2020:
- 9:17 PM Ticket #3023 (Crash showing menu) created by
- […]
- 6:01 PM Ticket #2085 (Crash in Qt in Mac graphics driver) closed by
- duplicate: I intend to try to rework window closing as per ticket #2976 and …
- 5:50 PM Ticket #2995 (threading crash) closed by
- can't reproduce: Yes, please copy the ChimeraX app onto your machine rather than …
- 5:16 PM ChangeLog edited by
- (diff)
Apr 6, 2020:
- 11:12 PM Ticket #3018 (Toolshed release history bug) closed by
- fixed: Had accidentally switched to a lexical comparison.
- 1:55 PM ChangeLog edited by
- (diff)
- 1:13 PM Ticket #3020 (SMILES conversion failure if string contains filesystem-relevant characters) closed by
- fixed: It was indeed the '/' character that was the problem. Fixed now, and …
- 12:32 PM Ticket #3022 (ISOLDE used with incompatible ChimeraX) created by
- […]
- 12:05 PM Ticket #1857 (RFE: Blast Protein ability to show alignment for any subset of hits in ...) closed by
- fixed: I believe this is done. Tried it just now in case I was remembering wrong.
- 10:39 AM Ticket #3021 (ISOLDE: various errors) created by
- […]
- 9:50 AM Ticket #3019 (FitMap's map button updating after tool closed) closed by
- can't reproduce: Tried a few simple things, but couldn't reproduce.
- 9:41 AM Ticket #3017 (cellPACK: Collada scheme failure) closed by
- duplicate: Duplicate of #3016
- 9:21 AM Ticket #3013 (Crash during close) closed by
- duplicate: Hi Peter, This problem was fixed about 5 weeks ago, so if you get a …
- 8:20 AM Ticket #3020 (SMILES conversion failure if string contains filesystem-relevant characters) created by
- […]
- 3:41 AM Ticket #3019 (FitMap's map button updating after tool closed) created by
- […]
- 2:23 AM Ticket #3018 (Toolshed release history bug) created by
- […]
Apr 5, 2020:
- 8:13 PM Ticket #3017 (cellPACK: Collada scheme failure) created by
- […]
- 7:22 PM Ticket #3016 (cellPACK: Collada scheme failure) created by
- […]
Apr 4, 2020:
- 4:17 PM Ticket #3015 (Crash in Finder(?)) created by
- […]
- 8:29 AM Ticket #3014 (Blast Protein tool: threading) created by
- […]
- 2:34 AM Ticket #3013 (Crash during close) created by
- […]
Apr 3, 2020:
- 9:44 PM ChangeLog edited by
- (diff)
- 8:09 PM Ticket #3000 (Show / hide slow on very large structures due to change tracking) closed by
- fixed: Fixed. I've exclude atoms from the modified list on display and color …
- 6:39 PM Ticket #477 (cartoon: some tube-coil joins not so hot) closed by
- fixed: Fixed. Coil junctions with tube helix look much better with the …
- 6:22 PM Ticket #3012 (Tube helices have wrong curve) created by
- […]
- 3:52 PM Ticket #2809 (make ChimeraX website documentation URL point to vdocs) closed by
- fixed: Done.
- 3:14 PM Ticket #1673 (Linux flavor ABI incompatibility) closed by
- fixed: Currently using CentOS 7 binary bundles on all Linux variants, so …
- 3:11 PM Ticket #2693 (Problem importing surface module due to missing libstdc++.so.6) closed by
- fixed: This should have been fixed by switching to use CentOS 7 binary …
- 3:10 PM Ticket #2956 (KeyError reading mmCIF) closed by
- can't reproduce: No response to request for problematic mmCIF file.
- 12:14 PM Milestone 0.93 completed
- Refactor bundleinfo.xml: * I/O section tags Update toolshed: * …
- 10:40 AM Ticket #477 (cartoon: some tube-coil joins not so hot) reopened by
- I've attached an image 1a0s_407_ mesh.png that shows the exact way …
- 10:00 AM Ticket #3011 (Disconnected hydrogens in 6rhz) created by
- In entry 6rhz, the following hydrogens have no bonds: /B CLA 1238 …
- 8:37 AM Ticket #2919 ("sequence chain" fails after chain lengthened) reopened by
- Well, you did say "the bug arises specifically when you add a residue …
- 6:02 AM Ticket #2965 (Clipper: 'XmapHandler_Live' object has no attribute 'set_display_style') closed by
- fixed
- 6:01 AM Ticket #2972 (Weird problem reading Amber CMAP terms) closed by
- can't reproduce: Don't think this has anything to do with ISOLDE per se. Just looks …
- 5:01 AM Ticket #2998 (Clipper symmetry: self.structure is None) closed by
- fixed: Fixed. The Clipper data layout originally wasn't really designed to …
Apr 2, 2020:
- 5:46 PM Ticket #3008 (Residues not organized correctly) closed by
- fixed: Sorry about that. Should be fixed now.
- 4:04 PM Ticket #477 (cartoon: some tube-coil joins not so hot) closed by
- not a bug: I'm not sure what "pretty poor" tube helix coil junctions means. It …
- 3:22 PM Ticket #3010 (Speed up ribbon helix tubes) created by
- Ribbon helix tube display is much slower than normal ribbons. For PDB …
- 3:06 PM Ticket #3007 (Cartoon tube helix error) closed by
- fixed: Fixed. Helix tube radius was uninitialized. Set initial value to 2.0.
- 2:11 PM Ticket #3006 (File→Open crash) closed by
- duplicate: Duplicate of #3005
- 12:39 PM Ticket #2496 (macOS Catalina can't verify daily build, signing problem) closed by
- fixed: MacOS code signing has been replaced by notarization.
- 12:37 PM Ticket #3009 (add ability to add software citations to mmCIF files) created by
- Make it so tools can add citations to model metadata so it will be …
- 12:29 PM Ticket #2983 (Want support for PEP 440 ~= dependencies) closed by
- fixed: Done
- 12:17 PM Ticket #3008 (Residues not organized correctly) created by
- […]
- 11:57 AM Ticket #3007 (Cartoon tube helix error) created by
- […]
- 10:59 AM Ticket #3006 (File→Open crash) created by
- […]
- 10:37 AM Ticket #3005 (File→Open crash) created by
- […]
- 10:06 AM Ticket #3004 (Save dialog → PNG image → several errors) closed by
- fixed: Fix(es) available in next build.
- 6:52 AM Ticket #2990 (isolde.openmm.openmm_interface: 'coords' is None) closed by
- fixed
- 3:33 AM Ticket #3004 (Save dialog → PNG image → several errors) created by
- […]
Apr 1, 2020:
- 4:59 PM Ticket #3001 (Session save slow with molecular surfaces) closed by
- fixed: I made session save not compress. This gives 20x faster write, 3x …
- 1:31 PM Ticket #3002 (open2 'dataFormat' should accept/expect nicknames) closed by
- fixed: 'dataFormat' now the same as 'format': only accepts nicknames (more …
- 1:29 PM Ticket #3003 (open2 'dataFormat' with full format name not working with sequences ...) closed by
- fixed: 'format' was the same -- it was a problem in the alignments bundle
- 12:11 PM Ticket #3003 (open2 'dataFormat' with full format name not working with sequences ...) created by
- chimerax/seqalign/parse.py tries to use a parser based on the full …
- 12:09 PM Ticket #3002 (open2 'dataFormat' should accept/expect nicknames) created by
- Currently only accepts full format names
- 10:43 AM Ticket #3001 (Session save slow with molecular surfaces) created by
- […]
- 10:33 AM Ticket #300 (Control over tool (and data ownership) used when data opened) closed by
- wontfix: I think the bundle that registers the "opener" function for the data …
- 10:29 AM Ticket #1519 (Restrict open/save keyword handling to those relevant for that format) closed by
- fixed
- 10:26 AM Ticket #2806 (Refactor bundleinfo.xml) closed by
- fixed
Mar 31, 2020:
- 7:26 PM Ticket #3000 (Show / hide slow on very large structures due to change tracking) created by
- Show and hide commands for atoms on large structure such as 6q3g (1 …
- 10:43 AM Ticket #2987 (Random crashes) closed by
- can't reproduce: Justin has ISOLDE working on Linux. The crashes using ISOLDE on …
- 10:40 AM Ticket #2999 (Session support missing for Map Eraser) closed by
- fixed: Fixed. The error saving a session with the map eraser sphere showing …
- 10:04 AM Ticket #2997 (settings error-reporting using non-existent attribute) closed by
- duplicate: Hi Fengwei, I have fixed the main error in this report, which was a …
- 9:57 AM Ticket #2996 (settings error-reporting using non-existent attribute) closed by
- fixed
- 3:09 AM Ticket #2999 (Session support missing for Map Eraser) created by
- […]
Mar 30, 2020:
- 6:33 PM Ticket #2998 (Clipper symmetry: self.structure is None) created by
- […]
- 12:41 PM Ticket #2997 (settings error-reporting using non-existent attribute) created by
- […]
- 12:21 PM Ticket #2996 (settings error-reporting using non-existent attribute) created by
- […]
- 10:17 AM Ticket #2991 (Graphics error drawing selection) closed by
- duplicate: This has been reported several times, glBlitFramebuffer error, I …
- 10:10 AM Ticket #2989 (ISOLDE referencing a Structure that's been deleted) closed by
- duplicate: Seems like a duplicate of #2992 (although that one's Mac) and #2992 …
- 10:02 AM Ticket #2995 (threading crash) created by
- […]
- 8:55 AM Ticket #2994 (Nucleotides trying to save closed structure) created by
- […]
- 8:04 AM Ticket #2993 (KeyError picking ribbon) created by
- […]
- 12:02 AM Ticket #2992 (ISOLDE referencing a Structure that's been deleted) created by
- […]
Mar 29, 2020:
- 11:32 PM Ticket #2991 (Graphics error drawing selection) created by
- […]
- 7:43 PM Ticket #2990 (isolde.openmm.openmm_interface: 'coords' is None) created by
- […]
- 11:14 AM Ticket #2989 (ISOLDE referencing a Structure that's been deleted) created by
- […]
Mar 28, 2020:
- 10:00 AM Ticket #2988 (Session save: 'NoneType' object has no attribute 'array') closed by
- duplicate: Hi, This problem was fixed awhile ago. Please upgrade to the 0.92 …
- 9:53 AM Ticket #2988 (Session save: 'NoneType' object has no attribute 'array') created by
- […]
- 8:06 AM Ticket #2987 (Random crashes) created by
- […]
Mar 27, 2020:
- 1:35 PM Ticket #2986 (Problem restoring session) closed by
- duplicate: Hi Lynette, This problem was fixed a few weeks back, so if you …
- 1:01 PM Ticket #2986 (Problem restoring session) created by
- […] 1RTD_PuglisiLabColoring.cxs
- 11:18 AM Ticket #2985 (Crash drawing Qt interface) closed by
- duplicate
- 10:51 AM Ticket #2985 (Crash drawing Qt interface) created by
- […]
- 9:09 AM Ticket #2982 (tool instance already removed from dict) closed by
- can't reproduce: Intend to rework the way windows get destroyed anyway
- 9:02 AM Ticket #2981 (ChimeraX bug report submission) closed by
- duplicate
- 9:01 AM Ticket #2980 (Crash drawing Qt interface) closed by
- duplicate
- 6:59 AM Ticket #2984 (AddH: N-linked glycans) created by
- […]
Mar 26, 2020:
- 7:19 PM Ticket #2983 (Want support for PEP 440 ~= dependencies) created by
- PEP 440 ~= compatible release operator limits dependencies to the …
- 3:49 PM Ticket #2982 (tool instance already removed from dict) created by
- […]
- 1:31 PM Ticket #2979 (Every residue is 48) closed by
- fixed: Bug was with how a missing optional auth_seq_id was handled. Fixed now.
- 12:57 PM Ticket #2981 (ChimeraX bug report submission) created by
- […]
- 12:41 PM Ticket #2980 (Crash drawing Qt interface) created by
- […]
- 11:13 AM Ticket #2979 (Every residue is 48) created by
- […] PDBDEV_00000018.cif
- 10:56 AM Ticket #2978 (Side view affects image saving) closed by
- fixed: Fixed. Your poor quality image was at half resolution, ie half the …
- 9:00 AM Ticket #2978 (Side view affects image saving) created by
- […] example_ChimeraX.png
- 8:45 AM Ticket #2977 (Crash closing dialog) closed by
- duplicate: duplicate of #2976
Mar 25, 2020:
- 11:42 PM Ticket #2977 (Crash closing dialog) created by
- […]
- 11:22 PM Ticket #2976 (Crash closing dialog) created by
- […]
- 11:05 AM Ticket #2974 (Selection outline error? (glBlitFramebuffer: invalid operation)) closed by
- can't reproduce: This has been reported several times, always with Linux and VMWare …
- 9:42 AM Ticket #2975 (ChimeraX documentation down) closed by
- fixed: Thanks for the bug report. It is fixed now.
- 9:32 AM Ticket #2975 (ChimeraX documentation down) created by
- […]
- 4:59 AM Ticket #2974 (Selection outline error? (glBlitFramebuffer: invalid operation)) created by
- […]
Note:
See TracTimeline
for information about the timeline view.
