![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Nov 27, 2019:
- 4:26 PM Ticket #2621 (deleting scraggly parts of models from Modeller gives Error processing ...) closed by
- fixed: The association info was being updated on a piecemeal basis, so it …
- 2:42 PM Ticket #1228 (Run Modeller) closed by
- fixed
- 2:03 PM Ticket #2622 (Linux dynamic linking problem) created by
- […]
- 12:46 PM Ticket #2620 (Sequence viewer using deleted residues) closed by
- fixed: Was fixed in October, but the fix only helps new sessions, since …
- 12:05 PM Ticket #2621 (deleting scraggly parts of models from Modeller gives Error processing ...) created by
- open 3bp5 open uniprot:pdcd1_human sequence associate /A pdcd1_human …
- 11:52 AM Ticket #2620 (Sequence viewer using deleted residues) created by
- […] model-pdl-fig.cxs
- 9:53 AM Ticket #2619 (trying to open GLTF: ImportError: cannot import name 'surface' from ...) closed by
- fixed: Fixed. GLTF code was importing surface module which moved about a …
- 9:04 AM Ticket #2619 (trying to open GLTF: ImportError: cannot import name 'surface' from ...) created by
- I was trying to see if GLTF would save/restore colors of blobs colored …
Nov 26, 2019:
- 5:52 PM Ticket #2618 (Web page to release bundles on Tool Shed is broken) created by
- The web page to release bundles on the Tool Shed …
- 3:29 PM Ticket #2617 (Bundle builder cannot install PyPi dependency pyrealsense2) closed by
- fixed
- 11:01 AM Ticket #2617 (Bundle builder cannot install PyPi dependency pyrealsense2) created by
- How do I add a PyPi dependency to a Toolshed bundle? I have not been …
Nov 25, 2019:
- 7:04 PM Ticket #2613 (Sessions + Basic Actions + Objects == buggy) closed by
- fixed: restore_snapshot for MolecularSurface wasn't returning the restored …
- 5:45 PM Ticket #2615 (Save image: width/height and/or max_size is None) closed by
- fixed: Fixed. Forgot that the width/height of an image when not specified …
- 5:30 PM Ticket #2616 (Error in handling of multi-crystal MTZ files) created by
- […]
- 5:23 PM Ticket #2615 (Save image: width/height and/or max_size is None) created by
- […]
- 2:58 PM Ticket #2610 (Problem with .py files in file history) closed by
- not a bug: If you want to open a Python script more than once, it is convenient …
- 2:45 PM Ticket #2606 (Save image: Frame buffer invalid size) closed by
- not a bug: Issue simple error message when maximum image size is exceeded. save …
- 2:01 PM Ticket #2612 (Side view: self.view.render is None) closed by
- can't reproduce: Unable to reproduce with current code. OpenGL context management has …
- 1:36 PM Ticket #2614 (Segger not being installed on Linux) closed by
- fixed: Fixed in tonight's ChimeraX builds. The Makefile had some …
- 1:35 PM Ticket #2614 (Segger not being installed on Linux) created by
- Begin forwarded message: From: WERNERT Florian Subject: …
- 12:59 PM WikiStart edited by
- (diff)
- 12:01 PM Ticket #2613 (Sessions + Basic Actions + Objects == buggy) created by
- […] H1plusABchimerax.cxs
- 11:03 AM Ticket #2609 (Insufficient info when session save fails) closed by
- duplicate: Hopefully fixed by changes made in September. The reporting ChimeraX …
- 10:56 AM Ticket #2607 (Save image: Frame buffer invalid size) closed by
- duplicate: Duplicate of #2606
- 7:23 AM Ticket #2612 (Side view: self.view.render is None) created by
- […]
- 5:42 AM Ticket #2611 (mmCIF: local variable '_1to3' referenced before assignment) closed by
- fixed: Old bug from ChimeraX 0.9 release.
- 4:04 AM Ticket #2611 (mmCIF: local variable '_1to3' referenced before assignment) created by
- […]
- 1:20 AM Ticket #2610 (Problem with .py files in file history) created by
- […]
- 12:43 AM Ticket #2571 (No mail/feedback) reopened by
- If you bring up the Windows Event Viewer, do you see any events …
Nov 24, 2019:
Nov 23, 2019:
- 2:30 PM Ticket #2607 (Save image: Frame buffer invalid size) created by
- […]
- 2:29 PM Ticket #2606 (Save image: Frame buffer invalid size) created by
- […]
Nov 22, 2019:
- 4:34 PM ChangeLog edited by
- (diff)
- 4:14 PM Ticket #2604 (Make surface coloring undoable) closed by
- fixed: Done. Made the color command on models and surfaces, color …
- 4:11 PM Ticket #2604 (Make surface coloring undoable) created by
- Make the color command colorings of surface undoable.
- 12:32 PM Ticket #2603 (Fragmented surface after adding hydrogens) closed by
- fixed: Fixed. The show command didn't properly handle the case where adding …
- 11:28 AM Ticket #2603 (Fragmented surface after adding hydrogens) created by
- […] image1.png
- 7:35 AM Ticket #1972 (Structure factor .cif files: open command extension/disambiguation) closed by
- fixed: Seems all of this is working nicely now.
- 7:34 AM Ticket #1913 (Clipper: name '_f_sigf_chooser' is not defined) closed by
- fixed
- 7:12 AM Ticket #1874 (ISOLDE: isolde/libmolc.so: undefined symbol) closed by
- wontfix: Tidying up open tickets. While one could argue that the …
- 7:06 AM Ticket #1643 (FastVolumeSurface class not restorable) closed by
- fixed: Clipper and ISOLDE no longer break session saving (note - they don't …
- 7:05 AM Ticket #1637 (ISOLDE installation: UnicodeDecodeError) closed by
- fixed: Cleaning up old tickets - this issue is long since fixed.
- 7:04 AM Ticket #1439 (Ability to spawn secondary View instance(s)) closed by
- wontfix: Rob Oeffner in the lab here is working on a WebGL-based reflection …
- 7:01 AM Ticket #1270 (pbm running ISOLDE (OpenMM)) closed by
- fixed: Just cleaning up old tickets!
- 6:59 AM Ticket #2458 (Clipper not saving in sessions) closed by
- duplicate: Duplicate of #2539
- 6:58 AM Ticket #2538 (Clipper not saving in sessions) closed by
- duplicate
- 6:57 AM Ticket #2539 (Clipper prevents session saving) closed by
- fixed: The latest versions of Clipper and ISOLDE no longer cause crashes on …
Nov 21, 2019:
- 6:23 PM Ticket #2602 (View command includes vr room camera) created by
- […]
- 5:24 PM Ticket #2601 (KeyError in model chooser) closed by
- duplicate: Multiple fixes have occurred since this version of ChimeraX
- 5:18 PM Ticket #2594 (Crash opening model) closed by
- duplicate: Hi Lynette, Thanks for the info. From the behavior you describe and …
- 5:01 PM Ticket #2601 (KeyError in model chooser) created by
- […]
- 4:56 PM Ticket #2600 (Problem with "toolshed show") created by
- The first thing "toolshed show" does is to look for existing matching …
- 4:50 PM Ticket #2595 (problem with 'view' centering in ortho mode) closed by
- fixed: Fixed. In my test the behavior you observed was to be expected. …
- 4:43 PM ChangeLog edited by
- (diff)
- 4:23 PM Ticket #2571 (No mail/feedback) closed by
- worksforme: Still no response to last update of #2540. Sent email as myself …
- 4:12 PM Ticket #2599 ("select pyrimidine" doesn't select anything) created by
- Repeat by opening 1bna. "select purine" works, "select pyrimidine" …
- 3:49 PM Ticket #2590 (Make "view cofr true" use center-of-view) closed by
- fixed: Fixed. Made view command set "center of view" rotation method if …
- 12:39 PM Ticket #2596 (Problem with BlobOutlineBox in sessions) closed by
- fixed: Fixed. Pick blob outline box model did not have session saving support.
- 12:13 PM Ticket #2598 (New Model classes often break session saving) created by
- […]
- 11:12 AM Ticket #2585 (Excessive Windows compiler output for atomic) closed by
- fixed: Did what I felt I could. If there are further specific suggestions …
- 8:10 AM Ticket #2597 (Toolshed unwanted version downgrade on Windows) created by
- […]
- 7:02 AM Ticket #2596 (Problem with BlobOutlineBox in sessions) created by
- […]
- 1:22 AM Ticket #2587 (6pkv connectivity) closed by
- nonchimerax: It's a bug in the mmCIF file. The file says that those two residues …
- 12:59 AM Ticket #2595 (problem with 'view' centering in ortho mode) created by
- […]
Nov 20, 2019:
- 4:47 PM Ticket #2594 (Crash opening model) created by
- […]
- 2:20 PM Ticket #2593 (Various graphics/install/toolshed problems) created by
- […]
- 1:52 PM Ticket #2592 (Can't install ISOLDE for everyone) created by
- […] install_error.txt
- 11:29 AM Ticket #2591 ("view sel" fails when only bonds are selected) closed by
- fixed: Fixed. Objects.bounds() was not including bonds since usually atoms …
- 4:33 AM Ticket #2591 ("view sel" fails when only bonds are selected) created by
- […]
- 4:31 AM Ticket #2574 ('usage' on an alias fails) closed by
-
not a bug: My bad. Forgot I needed to add the alias to
register_command()in … - 3:54 AM Ticket #2590 (Make "view cofr true" use center-of-view) created by
- […]
- 3:26 AM Ticket #2588 (Wrong version of Clipper (duplicate of #2214)) closed by
- duplicate: Duplicate of #2214.
- 3:18 AM Ticket #2589 (Basic Clipper session restore) created by
- […]
Nov 19, 2019:
- 5:34 PM Ticket #2588 (Wrong version of Clipper (duplicate of #2214)) created by
- […]
- 3:33 PM Ticket #2488 (AddH: treat UNK as truncated amino acid) closed by
- fixed: Okay, implemented.
- 2:38 PM Ticket #2587 (6pkv connectivity) created by
- In entry 6pkv, the mmCIF makes some missing structure into covalent …
- 1:35 PM Ticket #2297 (Showing all tools suppressed during global tool hide) closed by
- fixed: Okay, AFAICT all the concerns in this ticket and #2404 are addressed.
- 11:32 AM Ticket #2478 (CCD templates should us different XYZ fields) closed by
- fixed: Didn't read the ideal PDB coordinates into the separate variables that …
- 11:26 AM Ticket #2478 (CCD templates should us different XYZ fields) reopened by
- The code is designed to fallback to the experimental coordinates if …
- 5:18 AM Ticket #2586 (fmt.category is a set) created by
- […]
Nov 18, 2019:
- 4:39 PM Ticket #2585 (Excessive Windows compiler output for atomic) created by
- […] make_atomic.txt
- 3:58 PM Ticket #2584 (bounds determination: zero-size array to reduction operation minimum ...) closed by
- fixed: Fixed. I couldn't reproduce the error. But I can see how it could …
- 12:30 PM Ticket #2584 (bounds determination: zero-size array to reduction operation minimum ...) created by
- […]
- 11:59 AM Ticket #2583 ("surface zone" maxComponents broken?) closed by
- fixed: Fixed. Sharp edge surface triangulation was not being handled …
- 11:18 AM Ticket #2583 ("surface zone" maxComponents broken?) created by
- From the following: open 2gbp surf surf zone #1 near ligand dist 6 …
- 10:39 AM Ticket #2582 (Non-ASCII to log produces error) closed by
- fixed: I believe this was fixed on August 13th by …
- 10:34 AM MSC2019Deliverables edited by
- (diff)
- 10:32 AM Ticket #2581 (color comparison: numpy stupidity) closed by
- fixed: atom.color until recently returned a tinyarray. Those don't support …
- 10:11 AM Ticket #2569 (Scroll ViewDockX table to show active row) closed by
- fixed
- 9:03 AM Ticket #2582 (Non-ASCII to log produces error) created by
- […]
Nov 16, 2019:
Nov 15, 2019:
- 4:25 PM Ticket #2578 (Crash in (PyOpenGL-invoked?) shader code) closed by
- nonchimerax: This is a typical Mac graphics driver crash due to buggy Apple …
- 3:08 PM Ticket #2564 (atom.color[:3] NotImplementedError: Slices are not implemented.) closed by
- fixed: Returning a tinyarray had the upside of being able to be compared to a …
- 8:12 AM Ticket #2580 (Volume bounding box should contract with background) created by
- […]
- 8:11 AM Ticket #2579 (Shell broken if created while Volume Viewer context menu is posted) created by
- […]
Nov 14, 2019:
- 10:50 PM Ticket #2578 (Crash in (PyOpenGL-invoked?) shader code) created by
- […]
- 10:09 PM Ticket #2563 (ViewdockX clashes button broken, needs to be updated for new syntax) closed by
- fixed: Fixed in b94b4e6be.
- 5:55 PM Ticket #2577 (Model whose ID is None being sorted by ID during model removal) closed by
- fixed: Fixed. Closing map eraser tool window after the eraser sphere model …
- 4:49 PM Ticket #2576 (Volume Eraser: output array is read-only) closed by
- duplicate: This ChimeraX bug using Volume Eraser was fixed 3 months ago. Update …
- 4:41 PM Ticket #2577 (Model whose ID is None being sorted by ID during model removal) created by
- […]
- 4:29 PM Ticket #2576 (Volume Eraser: output array is read-only) created by
- […]
- 1:15 PM 2019-11-14 edited by
- (diff)
- 1:09 PM 2019-11-14 created by
- 12:14 PM DeveloperMeetings edited by
- (diff)
- 11:14 AM Ticket #2568 (Too many tools in General category) closed by
- not a bug: The plan is to pull tools into non-General categories once there is …
- 10:57 AM Ticket #2575 (incorrect error message from "open" command) created by
- I was testing whether the structurefactors option from Clipper works …
- 9:39 AM Ticket #2574 ('usage' on an alias fails) created by
- […]
- 7:55 AM Ticket #2573 (safe-save permission denied writing temp file) created by
- […]
- 6:15 AM Ticket #2572 (Atom matching occurring in input order rather than name order) created by
- […] glu.zip
- 4:57 AM Ticket #2571 (No mail/feedback) created by
- […]
- 4:49 AM Ticket #2570 (Some help files crash ChimeraX) created by
- […]
Nov 13, 2019:
- 6:28 PM Ticket #2569 (Scroll ViewDockX table to show active row) created by
- Phil wants the ViewDockX table to scroll to show the active row when …
- 6:16 PM Ticket #2568 (Too many tools in General category) created by
- […]
- 6:08 PM Ticket #2567 (Command History window shown when it shouldn't be) created by
- […]
- 9:42 AM Ticket #2566 (Can't start ChimeraX) created by
- […]
Nov 12, 2019:
- 4:14 PM Ticket #2565 (Problems using previously fetched files) created by
- […]
- 1:35 PM Ticket #2564 (atom.color[:3] NotImplementedError: Slices are not implemented.) created by
- Atom.color returns a tinyarray which does not allow slicing. ChimeraX …
- 1:29 PM Ticket #2561 (Saving marker sets: Slices are not implemented) closed by
- fixed: Fixed. Atom.color is returning a tinyarray which does not allow …
- 12:55 PM Ticket #2560 (Unexpected lighting change when volume morphing) closed by
- fixed: Fixed. Color interpolation was incorrectly using scale factors. Also …
- 11:54 AM Ticket #2563 (ViewdockX clashes button broken, needs to be updated for new syntax) created by
- The "clash" command syntax changed to be the same as "hbonds" (keyword …
- 11:53 AM Ticket #2562 (ViewdockX Hbonds/clashes needs to be smarter about which sets of atoms ...) created by
- For induced-fit results, each ligand has its own receptor …
- 11:12 AM Ticket #2559 (Session restore: 'Ring' object has no attribute '_c_pointer_ref') closed by
- fixed: Hi Valentyn, Thanks for reporting this problem. I believe it was …
Nov 11, 2019:
- 12:31 PM Ticket #2561 (Saving marker sets: Slices are not implemented) created by
- […]
- 9:08 AM Ticket #2560 (Unexpected lighting change when volume morphing) created by
- […] Annotation 2019-11-11 120741.png
- 5:24 AM Ticket #2559 (Session restore: 'Ring' object has no attribute '_c_pointer_ref') created by
- […]
- 1:09 AM Ticket #2558 (Wrong version of Clipper in ChimeraX 0.9) closed by
- duplicate
Nov 10, 2019:
Nov 8, 2019:
- 3:42 PM Ticket #2556 (DICOM reader: broken data stream when reading image file) closed by
- nonchimerax: The error message "OSError: broken data stream when reading image …
- 3:35 PM Ticket #2557 (Graphics hardware error) closed by
- nonchimerax: Crash in Apple graphics driver. Unfortunately macOS graphics drivers …
- 3:24 PM Ticket #2555 (Memory leak fitting volume in volume) closed by
- fixed: Fixed in tonight's ChimeraX builds. There were two memory leaks. …
- 2:16 PM Ticket #2557 (Graphics hardware error) created by
- […]
- 1:02 PM Ticket #2556 (DICOM reader: broken data stream when reading image file) created by
- […]
- 12:29 PM Ticket #2555 (Memory leak fitting volume in volume) created by
- Begin forwarded message: From: Andrei Istrate Subject: ChimeraX …
- 12:00 PM Ticket #2554 (Command History window appears randomly) created by
- […] test3.py
- 3:48 AM Ticket #2553 (Spurious dependencies with "reinstall true") created by
- […]
- 2:02 AM Ticket #2552 (Enhancement: mousemode to Z-shift CofR) created by
- I've just added this to Clipper, but it might make sense as part of …
Nov 7, 2019:
- 2:44 PM Ticket #2551 (camera sbs opengl errors) closed by
- fixed: Fixed bug using camera option pixelEyeSeparation. That option only …
- 2:25 PM Ticket #2551 (camera sbs opengl errors) created by
- […]
- 1:06 PM Ticket #2549 (Inadequate OpenGL) closed by
- not a bug: ChimeraX could not get OpenGL context. Save image error reporting was …
- 12:53 PM Ticket #2550 ('OptionalRGBAOption' object has no attribute 'get') closed by
- duplicate: Hi, Thanks for reporting this problem. It has been fixed for a few …
- 12:43 PM Ticket #2550 ('OptionalRGBAOption' object has no attribute 'get') created by
- […]
- 12:09 PM Ticket #2549 (Inadequate OpenGL) created by
- […]
- 10:55 AM Ticket #1990 (model-list widgets need to respond to name changes) closed by
- fixed: Update menu button if model name (only) changes
Nov 6, 2019:
- 5:11 PM Ticket #2492 (Error closing RealSense camera) closed by
- fixed: Fixed. RealSense Model had two delete() methods defined.
- 12:58 PM Ticket #2545 (Bad HTML anchors in help for multi-word commands) closed by
- fixed: If Sphinx doesn't use anchors with spaces and uses hyphens, then …
- 12:51 PM Ticket #2548 (surface dust command hides clip caps) closed by
- fixed: Fixed. Now surface dust does not apply to clip caps.
- 12:45 PM Ticket #2548 (surface dust command hides clip caps) created by
- […]
- 10:57 AM Ticket #2547 (Have toolshed say "reinstall" for already installed bundles) created by
- It would be great if the toolshed knew which bundles were already …
- 10:46 AM Ticket #2546 (Wrong OpenCL driver used on machine with Nvidia and Intel GPUs) created by
- Bug report from Joel Mackay in Sydney. On his Windows machine …
- 5:29 AM Ticket #2545 (Bad HTML anchors in help for multi-word commands) created by
- Adding command documentation for ISOLDE to work with the new …
- 2:16 AM Ticket #2543 (Clipper: No module named 'chimerax.core.graphics.clipping') closed by
- duplicate: Discussed with Joel off-list.
- 2:15 AM Ticket #2544 (Wrong version of Clipper installed) closed by
- duplicate
Nov 5, 2019:
- 7:19 PM Ticket #2544 (Wrong version of Clipper installed) created by
- […]
- 6:25 PM Ticket #2537 (User interface blank Windows 10 with new Intel driver 26.x.x.x) closed by
- fixed: Worked around bug as described in previous comment. Some black …
- 5:17 PM Ticket #2542 (Re: [chimerax-users] Catalina woes) closed by
- not a bug
- 5:16 PM Ticket #2543 (Clipper: No module named 'chimerax.core.graphics.clipping') created by
- […]
- 3:16 PM Ticket #2542 (Re: [chimerax-users] Catalina woes) created by
- […]
- 11:01 AM Ticket #2541 (Catalina woes) closed by
- not a bug
- 10:47 AM Ticket #2541 (Catalina woes) created by
- […] [[Image(...)]]
Nov 4, 2019:
- 11:26 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) closed by
- fixed: No problem -- we all have things to do. Committed a fix for the …
- 1:09 AM Ticket #2540 (chimerax don't start on windows 10) created by
- […]
Nov 3, 2019:
- 12:02 PM Ticket #2539 (Clipper prevents session saving) created by
- […]
- 11:59 AM Ticket #2538 (Clipper not saving in sessions) created by
- […]
Oct 31, 2019:
- 12:52 PM Ticket #2535 (Crash on structure with non-unique atom names) closed by
- fixed: The non-unique naming of the atoms in this large residue caused addh …
- 12:31 PM Ticket #2537 (User interface blank Windows 10 with new Intel driver 26.x.x.x) created by
- […]
Oct 30, 2019:
- 7:59 PM Ticket #2536 (Tug mouse mode bad allocation error) created by
- […]
- 4:29 PM Ticket #2535 (Crash on structure with non-unique atom names) created by
- […] DB13038_triolein.pdb
- 1:27 PM Ticket #2534 (Inconsistent ribbon selection behavior) created by
- If I control-click on a ribbon section, it selects the corresponding …
Oct 29, 2019:
- 10:54 PM Ticket #2523 (Better session debugging info) closed by
- fixed: I think it must, or else the "RuntimeError: Residue already deleted" …
- 10:10 PM Ticket #2526 (help links in Log for internal aliases (e.g. ribbon, blastpdb, mm, ...) closed by
- fixed: Help links for aliases need to be done by hand. I've added links for: …
- 2:37 PM Ticket #2533 ("tape measure" mouse mode: cannot unpack non-iterable NoneType object) closed by
- fixed: Fixed. Yes tape measure does support DICOM and all volume formats. …
- 2:23 PM Ticket #2533 ("tape measure" mouse mode: cannot unpack non-iterable NoneType object) created by
- […]
- 10:37 AM Ticket #2532 (SwissDock .chimerax file) closed by
- nonchimerax: Hi Angelo, I know it's confusing, but .chimerax files are used in …
Oct 28, 2019:
- 9:00 PM Ticket #2532 (SwissDock .chimerax file) created by
- […] open.chimerax
- 1:54 PM Ticket #2531 ("spotlight moved" trigger handler using dead Structure) created by
- […]
- 11:37 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) reopened by
- Needs to be smarter about more than a single atom/bond being added in …
- 10:29 AM Ticket #2530 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 9:24 AM Ticket #2530 (Crash in free_keys_object/subtype_dealloc) created by
- […]
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