![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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
- […]
Mar 23, 2020:
- 6:10 PM Ticket #2973 (Numpy type problem reading .cmap file) closed by
- fixed: Fixed. Chimera map files containing symmetries as float32 (as written …
- 4:10 PM Ticket #2971 (Crash drawing Qt interface) closed by
- can't reproduce
- 4:08 PM Ticket #2973 (Numpy type problem reading .cmap file) created by
- […]
- 3:16 PM Ticket #2972 (Weird problem reading Amber CMAP terms) created by
- […]
- 2:15 PM Ticket #2971 (Crash drawing Qt interface) created by
- […]
- 11:07 AM Ticket #2969 (addh: metal-clash proton stripping) closed by
- fixed: The added-hydrogen-to-metal distance of 2.955 for Cys B77 is beginning …
- 9:04 AM Ticket #2970 (opening mmCIF but saving PDB loses "seqres" info) created by
- Example structure 6vxx. This information is preserved after opening …
- 8:49 AM Ticket #2968 (Crash drawing Qt interface) closed by
- duplicate: Same as #2966
- 8:48 AM Ticket #2967 (Crash drawing Qt interface) closed by
- duplicate: Same as #2966
- 1:15 AM Ticket #2969 (addh: metal-clash proton stripping) created by
- […]
Mar 21, 2020:
- 7:02 PM Ticket #2968 (Crash drawing Qt interface) created by
- […]
- 6:32 PM Ticket #2967 (Crash drawing Qt interface) created by
- […]
- 6:23 PM Ticket #2966 (Crash drawing Qt interface) created by
- […]
Mar 20, 2020:
- 8:50 AM Ticket #2962 (Crash drawing Qt interface) closed by
- can't reproduce
- 3:17 AM Ticket #2965 (Clipper: 'XmapHandler_Live' object has no attribute 'set_display_style') created by
- […]
Mar 19, 2020:
- 4:30 PM Ticket #2964 (Command-history change wipes command-entry text) created by
- […]
- 4:04 PM Ticket #2963 (Open dialog mishandles symbolic links) created by
- […]
- 2:23 PM Ticket #2962 (Crash drawing Qt interface) created by
- […]
- 8:48 AM Ticket #2960 (CrashReporter can't access ~/Library/Logs/DiagnosticReports) closed by
- duplicate: Duplicate of #2959
Mar 18, 2020:
- 2:24 PM Ticket #2961 (Tips for remote use) created by
- With the current rapidly-evolving situation, there's suddenly a whole …
- 11:27 AM Ticket #2959 (CrashReporter can't access ~/Library/Logs/DiagnosticReports) closed by
- can't reproduce: This is on macOS Catalina where you have to allow access to Downloads, …
- 10:37 AM Ticket #2960 (CrashReporter can't access ~/Library/Logs/DiagnosticReports) created by
- […]
- 8:55 AM Ticket #2957 (have Blast Protein report resolution) closed by
- fixed: it's documented, at least: …
- 8:37 AM Ticket #2958 (Crash in Qt on exit) closed by
- can't reproduce
- 7:12 AM Ticket #2959 (CrashReporter can't access ~/Library/Logs/DiagnosticReports) created by
- […]
- 4:47 AM Ticket #2958 (Crash in Qt on exit) created by
- […]
- 1:43 AM Ticket #2957 (have Blast Protein report resolution) created by
- […]
Mar 17, 2020:
Mar 16, 2020:
- 5:22 PM Ticket #2955 (Nucleotides trying to save closed structure) created by
- […]
- 12:21 PM Ticket #2926 (Adding coord sets) closed by
- not a bug: Ok, so it was just a misunderstanding how ChimeraX handles coordinate …
- 9:53 AM Ticket #2953 (Unwriteable settings) closed by
- can't reproduce
Mar 14, 2020:
- 6:39 PM Ticket #2954 (Crash drawing Qt interface) created by
- […]
- 2:10 AM Ticket #2953 (Unwriteable settings) created by
- […]
Mar 13, 2020:
- 2:14 PM Ticket #2919 ("sequence chain" fails after chain lengthened) closed by
- fixed
- 12:03 PM Ticket #2952 (Eventual failure in glDrawBuffer) closed by
- duplicate
- 11:14 AM Ticket #2951 (Adding coord sets) closed by
- duplicate: FYI. replying to a mail generated from the original ticket should get …
- 7:33 AM Ticket #2952 (Eventual failure in glDrawBuffer) created by
- […]
Mar 12, 2020:
- 11:16 AM Ticket #2951 (Adding coord sets) created by
- […]
- 11:09 AM Ticket #2941 (Chromium backend crash?) closed by
- can't reproduce: Hi Arun, Thanks for getting back to us with the info. It seems like …
- 10:52 AM Ticket #2949 ("sequence chain" fails after chain lengthened) closed by
- duplicate
- 10:51 AM Ticket #2948 ("sequence chain" fails after chain lengthened) closed by
- duplicate: Hi Yaikhomba, I see this is essentially the same problem you reported …
- 10:42 AM Ticket #2947 (Crash drawing Qt interface) closed by
- duplicate
- 10:26 AM Ticket #2950 (Could not create pixmap from [icon] png) created by
- […]
- 9:15 AM Ticket #2949 ("sequence chain" fails after chain lengthened) created by
- […] Screenshot from 2020-03-12 14-49-03.png
- 9:13 AM Ticket #2948 ("sequence chain" fails after chain lengthened) created by
- […] Screenshot from 2020-03-12 16-07-20.png
- 8:22 AM Ticket #2947 (Crash drawing Qt interface) created by
- […]
Mar 11, 2020:
- 7:31 PM Ticket #2945 (Crash opening 6bb5 on Windows) closed by
- fixed: Fixed. New code that produce a numpy array from a C++ vector<int64_t> …
- 6:32 PM Ticket #2946 (Debug option --debug not working on Windows.) created by
- […]
- 6:27 PM Ticket #2945 (Crash opening 6bb5 on Windows) created by
- […]
- 11:05 AM Ticket #2942 (Problem with Molecular Dynamics Viewer) closed by
- nonchimerax: Probably opened a PDB file without MODEL/ENDMDL records or other problems
- 10:49 AM Ticket #2944 (Include build_tools into chimerax git repository) created by
- The separate build_tools git repository that makes our daily builds …
- 10:42 AM Ticket #2943 (Put daily build test output in a separate file) created by
- Would like the daily build test output to go to a separate file with a …
- 2:42 AM Ticket #2942 (Problem with Molecular Dynamics Viewer) created by
- […]
- 2:34 AM Ticket #2941 (Chromium backend crash?) created by
- […]
Mar 10, 2020:
- 6:51 PM Ticket #2937 (Segmentation fault in Point_List::bounding_box() for large models (?)) closed by
- fixed: Fixed. I made find_close_points() handle large map sizes using 64-bit …
- 3:05 PM Ticket #2940 (subclassable AtomicStructure) closed by
- fixed: Hi Ben, I have added the set_state_from_snapshot support to …
- 11:40 AM Ticket #2845 (VR hand controllers swapped, Oculus Rift S) closed by
- fixed: Fixed. The controller role is not assigned correctly when waking. I …
- 8:41 AM Ticket #2850 (_openmm could not be found) closed by
- duplicate: Duplicate of #2771.
- 8:40 AM Ticket #2879 (openmm/swig: type object 'object' has no attribute '__getattr__') closed by
- fixed: Bug is fixed in more recent builds. Just for reference: the traceback …
- 8:36 AM Ticket #2884 (OpenMM: Error initializing context: clGetDeviceIDs) closed by
- fixed: I'll close this as fixed - it won't truly be until OpenMM 7.5 is …
- 4:42 AM Ticket #2875 (ISOLDE imports obsolete MainToolWindow from core.ui) closed by
- fixed: Fixed. Will be in the next build (an "official" ISOLDE release to go …
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