![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Jun 19, 2020:
- 12:01 PM Ticket #3424 (Crash with trashed stack) created by
- […]
- 11:56 AM Ticket #3421 (view matrix camera: No module named 'chimerax.core.geometry') closed by
- fixed: Fixed. Missed a relative import of geometry module.
- 11:53 AM Ticket #3419 (Startup error with glGetFramebufferAttachmentParameteriv) closed by
- nonchimerax: ChimeraX does not run on Windows 7. As it says on the ChimeraX …
- 10:25 AM Ticket #3423 (Cannot save PIR) closed by
- fixed: Hi Andrea, Thanks for reporting this problem. It is fixed now and …
- 9:35 AM Ticket #3416 (Crash with trashed stack) closed by
- can't reproduce
- 1:37 AM Ticket #3423 (Cannot save PIR) created by
- […]
- 12:53 AM Ticket #3422 (XYZ files) created by
- […]
- 12:03 AM Ticket #3338 (Phenix mmCIF problems) closed by
- fixed: Changed ChimeraX to not try to give chains descriptions when mmcif_cid …
Jun 18, 2020:
- 11:54 PM Ticket #3421 (view matrix camera: No module named 'chimerax.core.geometry') created by
- […]
- 9:01 PM Ticket #3420 (Session restore error, 2d labels None) closed by
- fixed: Fixed. Session restore of state managers did not protect against …
- 8:56 PM Ticket #3420 (Session restore error, 2d labels None) created by
- […] prc.cxs
- 4:22 PM Ticket #3419 (Startup error with glGetFramebufferAttachmentParameteriv) created by
- […]
- 3:50 PM Ticket #3418 (RealSense camera freezes) created by
- […]
- 3:44 PM Ticket #3417 (labels don't work in headless mode) created by
- labels don't work because they're are using the GUI to get the font …
- 2:04 PM Ticket #3413 (Shorten Downloads web page) closed by
- fixed: done and svn-committed
- 10:33 AM Ticket #2828 (Rotamer dialog column sorting not numerical) closed by
- fixed: For now, just assume that items that look like numbers are numbers and …
- 10:32 AM Ticket #3416 (Crash with trashed stack) created by
- […]
Jun 17, 2020:
- 5:57 PM Ticket #3409 (Problem with locale when checking registration) closed by
- duplicate: I was under the misapprehension that there had already been a fix …
- 5:44 PM Ticket #3409 (Problem with locale when checking registration) reopened by
- 3:49 PM Ticket #2964 (Command-history change wipes command-entry text) closed by
- fixed
- 2:24 PM Ticket #3414 (Fails to start on Windows 10, corrupted ui preference file) created by
- ChimeraX fails to start on Windows 10 due to a corrupted ui …
- 2:10 PM Ticket #3168 (Support CHARMM/X-PLOR format PDB files) closed by
- fixed: "Fixed" in that segment IDs can be used instead of chain IDs if …
- 1:28 PM Ticket #3401 (Session save error after deleting a Structure) closed by
- fixed
- 12:20 PM Ticket #3411 (help command does not show browser for some abbreviated commands) closed by
- fixed: Fixed.
- 11:26 AM Ticket #3413 (Shorten Downloads web page) created by
- The ChimeraX Downloads web page does not show the table of downloads …
- 10:41 AM Ticket #3409 (Problem with locale when checking registration) closed by
- can't reproduce: I can't reproduce either of the problems you're having: blank graphics …
- 10:29 AM ChangeLog edited by
- (diff)
- 9:04 AM Ticket #3412 (Volume viewer: unexpected indentation) closed by
- duplicate
- 9:00 AM Ticket #3408 (Crash restoring session) closed by
- can't reproduce: Looks like a crash trying to draw the Qt interface (or maybe the main …
- 4:24 AM Ticket #3412 (Volume viewer: unexpected indentation) created by
- […]
Jun 16, 2020:
- 8:31 PM Ticket #3406 (Port IMOD model file reader) closed by
- fixed: Ported imod reader.
- 5:44 PM Ticket #3348 (Filled rings unusably slow on large structures) closed by
- fixed: So splitting ring-finding into sibling routines based on whether …
- 4:04 PM Ticket #3410 (segmentation surfaces: no attribute 'find_attribute') closed by
- fixed: Fixed. Code was trying to use find_attribute() method that is only …
- 4:02 PM Ticket #3411 (help command does not show browser for some abbreviated commands) created by
- […]
- 3:55 PM ChangeLog edited by
- (diff)
- 3:47 PM Ticket #3410 (segmentation surfaces: no attribute 'find_attribute') created by
- […]
- 3:22 PM Ticket #1891 (RFE: Blast Protein query sequence from text) closed by
- fixed: I'm interpreting this one as another case of "launch blast from …
- 3:18 PM Ticket #1930 (RFE: Blast Protein ability to use sequence from Sequence Viewer as query) closed by
- fixed: Sequence viewer's context menu now has an Info category from which the …
- 3:13 PM Ticket #2736 (all-same-value attribute coloring yields black instead of 'mid' color) closed by
- fixed: Fixed. Color byattribute uses a red/white/blue colormap with all 3 …
- 1:12 PM Ticket #2984 (AddH: N-linked glycans) closed by
- fixed: Fixed. Works in one pass now.
- 12:56 PM Ticket #3409 (Problem with locale when checking registration) created by
- […] full screen.zip
- 11:47 AM Ticket #3408 (Crash restoring session) created by
- […]
- 11:22 AM Ticket #3407 (Maximum common substructure) created by
- […]
- 11:08 AM Ticket #3404 (ChimeraX bug report submission) closed by
- fixed: Fixed in 04ec502b1. Only models that are displayed (have …
- 10:44 AM Ticket #2640 (Preference GUI not refreshed) closed by
- fixed: This seems to have "fixed itself" as of the 1.0 release.
- 10:32 AM Ticket #3405 (Orderable TmplAtom) closed by
- fixed: TmplAtom now sorts on name. In the next daily build.
- 9:57 AM Ticket #3406 (Port IMOD model file reader) created by
- Should be easy to port IMOD model file reader to ChimeraX. Might also …
- 9:19 AM Ticket #3402 (Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been ...) closed by
- fixed: Hi Daniel, This problem was fixed the day after the version you have, …
- 7:22 AM Ticket #3405 (Orderable TmplAtom) created by
- […]
Jun 15, 2020:
- 5:42 PM Ticket #3404 (ChimeraX bug report submission) created by
- […] tiling fails.cxs
- 5:12 PM Ticket #3403 (Submit patch/bug report to Python/pip about problematic version number ...) created by
- According to pip/PEP docs, a requirement of 1.1 should be satisfied by …
- 5:08 PM Ticket #3393 (DICOM icon: 'MainWindow' object has no attribute 'folder_open_cb') closed by
- fixed: Fix will be in the next daily build
- 4:26 PM Ticket #3402 (Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been ...) created by
- […]
- 4:10 PM Ticket #3367 (Save position matrices for subtomogram boxes) closed by
- fixed: Added "positions" file format. The positions file gives positions of …
- 3:35 PM Ticket #3399 (Session save error caused by deleted Structure) closed by
- duplicate: Simpler case reported in #3401. Just "delete #1" to close a structure …
- 3:34 PM Ticket #3401 (Session save error after deleting a Structure) created by
- […]
- 3:02 PM Ticket #3400 (Volume crop mouse mode moves in wrong direction) closed by
- fixed: Fixed. Face normal vector was transformed incorrectly as a point …
- 1:39 PM Ticket #3400 (Volume crop mouse mode moves in wrong direction) created by
- […]
- 1:04 PM Ticket #3399 (Session save error caused by deleted Structure) created by
- […]
- 11:22 AM Ticket #3361 (Clip in VR further from face) closed by
- fixed: I added vr command options nearClipDistance and farClipDistance …
- 10:42 AM Ticket #3394 (CUDA problem: Error initializing CUDA: CUDA_ERROR_UNKNOWN (999)) closed by
- nonchimerax: Great to hear it! Will go ahead and close this, since it seems most …
- 10:39 AM Ticket #3398 (debugging output logged) closed by
- fixed
- 10:31 AM Ticket #3398 (debugging output logged) created by
- […]
- 8:46 AM Ticket #3397 (ChimeraX: mmcif connectivity lost in some chains; OK in Coot  + PDB ...) created by
- […] [[Image(...)]] OK_in_coot.mmcif …
- 6:42 AM Ticket #3396 (Saving mmCIF: 'software' is None) created by
- […]
- 1:03 AM Ticket #3395 (Crash showing tooltip text) created by
- […]
Jun 14, 2020:
- 5:22 PM Ticket #3394 (CUDA problem: Error initializing CUDA: CUDA_ERROR_UNKNOWN (999)) created by
- […]
Jun 13, 2020:
- 7:33 AM Ticket #3393 (DICOM icon: 'MainWindow' object has no attribute 'folder_open_cb') created by
- […]
Jun 12, 2020:
- 4:57 PM Ticket #3371 (Make "usage open" report some option info) closed by
- fixed: Since 1.1 is going to be "sooner rather than later", I decided to put …
- 4:31 PM Ticket #3285 (Slow graphics updates) closed by
- fixed: Well, fixed with the crudest trigger-blocking solution (and made that …
- 3:46 PM Ticket #3225 (Failure reading DCD: unexpected end of data) closed by
- fixed: In the remarks section of the DCD, the parts past the null in the …
- 10:09 AM Ticket #3389 (MRC file: file size too small for grid size) closed by
- nonchimerax: This user has no luck. There graphics provides only OpenGL 2.1 so …
- 8:52 AM Ticket #3392 (defattr command) created by
- as per summary
- 8:47 AM Ticket #3391 ("defattr" format for 'save' command) created by
- Some of the options analogous to "color byattr"
Jun 11, 2020:
- 11:29 PM Ticket #3390 (Session save: cycle detected) created by
- […]
- 8:16 PM Ticket #3389 (MRC file: file size too small for grid size) created by
- […]
- 6:10 PM Ticket #3388 (MatchMaker tool) created by
- as per summary
- 6:08 PM Ticket #3387 (Render By Attribute tool) created by
- As per summary
- 6:03 PM Ticket #3386 (Make header values available as residue attributes) created by
- As per summary
- 10:31 AM Ticket #3385 (Don't spam log with volume color change commands) created by
- […]
- 10:28 AM Ticket #3384 (Preserve volume per-vertex colors in sessions) created by
- […]
- 10:24 AM Ticket #3382 (Map replacement results in session-save failure: self.positions is None) closed by
- fixed: Fixed in ChimeraX 1.1, not in 1.0. We plan to make a ChimeraX 1.0 …
- 2:28 AM Ticket #3383 (Redirect Python logging to the ChimeraX log) created by
- […]
- 2:06 AM Ticket #3382 (Map replacement results in session-save failure: self.positions is None) created by
- […]
Jun 10, 2020:
- 6:05 PM Ticket #3381 (RFE: fatter lines in Side View on hi-res displays) created by
- The Side View lines (small square, diverging lines, clip-plane lines) …
- 11:27 AM Ticket #3379 (Volume tilted slab to plane: glClear invalid framebuffer operation) closed by
- fixed: Fixed. Problem was that 3D texture for single-plane region in tilted …
- 11:04 AM Ticket #3380 (Read compressed cif files) created by
- I was wondering if it would be possible to add option for chimerax to …
Jun 9, 2020:
- 10:41 PM Ticket #3378 (Closing multichannel volume, TypeError: object of type 'NoneType' has ...) closed by
- fixed: Fixed. Change to Models class caused it to try to remove and already …
- 10:37 PM Ticket #3379 (Volume tilted slab to plane: glClear invalid framebuffer operation) created by
- […]
- 10:37 PM Ticket #3378 (Closing multichannel volume, TypeError: object of type 'NoneType' has ...) created by
- […]
- 10:37 PM Ticket #3377 (Template mismatch errors) created by
- […]
- 10:19 AM Ticket #3374 (Touch event key modifiers) closed by
- fixed: All seems to be working now.
Jun 8, 2020:
- 5:25 PM Ticket #3266 (RFE: have matchmaker maintain original SS assignments) closed by
- fixed: Fixed. Fix available in next daily build as 'keepComputedSs' keyword, …
- 5:11 PM Ticket #3376 (Error closing submodel and parent model in same close command.) closed by
- fixed: Fixed. A deleted model was not being deleted from parent. This bug …
- 4:24 PM Ticket #3376 (Error closing submodel and parent model in same close command.) created by
- […]
- 2:23 PM Ticket #2435 (Select menu protein, nucleic acid, ribose should be under Chemistry ...) closed by
- fixed: Fixed. Only available in the daily build (until 1.1 release)
- 1:16 PM Ticket #3375 (Toolshed uninstall failure) created by
- […]
- 4:14 AM Ticket #3374 (Touch event key modifiers) created by
- […]
Jun 5, 2020:
- 7:03 PM ChangeLog edited by
- (diff)
- 6:50 PM ChangeLog edited by
- (diff)
- 6:26 PM ChangeLog edited by
- (diff)
- 6:14 PM Ticket #3373 (Opening large RNA takes 90 seconds instead of 2 seconds due to ...) created by
- […]
- 6:01 PM Ticket #3105 (addh wrong hydrogen name on glycosylated Asn residues) closed by
- fixed: Fixed in the next daily build. Might put an AddH 1.0.1 bundle on the …
- 5:50 PM Ticket #3372 (Writing mmCIF file takes 35 minutes) created by
- […] sarscov2_rna.cif
- 5:45 PM Ticket #3371 (Make "usage open" report some option info) created by
- […]
- 4:36 PM Ticket #3358 (Remove deprecated chimerax.core.geometry imports) closed by
- fixed: Fixed in ChimeraX 1.1 (not 1.0).
- 4:10 PM Ticket #3359 (map/surface color is None) closed by
- fixed: Fixed. Made volume viewer handle situation where surface is closed. …
- 3:35 PM Ticket #3162 (Incorrect commands easily lost) closed by
- fixed: Failed commands no longer get auto-selected, so it is not easy to …
- 3:07 PM Ticket #3370 (split command ValueError: Tried to add model with incompatible id) closed by
- fixed: Fixed. Split command was adding child models to a new grouping model. …
- 2:58 PM Ticket #3370 (split command ValueError: Tried to add model with incompatible id) created by
- […]
Jun 4, 2020:
- 8:33 PM Ticket #3360 (Ribbon index error) closed by
- duplicate: Fixed 1.5 months ago.
- 8:20 PM Ticket #3369 (Make bug reporter to check if bug already fixed) created by
- Users often report the same fixed bug many times. It would save the …
- 8:05 PM Ticket #3368 (API needed for saving non-State classes) created by
- Currently geometry.Place and graphics.Drawing, graphics.View, ... do …
- 7:56 PM Ticket #3364 (Surface dust restored from session not saved in session) closed by
- fixed: Fixed. There were two bugs. When a session with hide dust was …
- 7:07 PM Ticket #3367 (Save position matrices for subtomogram boxes) created by
- Would like to be able to write out the position matrices for …
- 7:01 PM Ticket #3366 (Report color by height settings) created by
- Want a command to report current color by height settings, useful when …
- 6:59 PM Ticket #3365 (Report surface dust settings) created by
- Would like a command to report the current surface dust settings, …
- 6:57 PM Ticket #3364 (Surface dust restored from session not saved in session) created by
- […]
- 6:47 PM Ticket #3363 (Visually distinguish old log output from new) created by
- […]
- 6:42 PM Ticket #3362 (Run command from VR wand button press) created by
- Would like to be able to click a VR button to run a command such as …
- 6:31 PM Ticket #3361 (Clip in VR further from face) created by
- When moving around inside tomograms with surface display it would help …
- 5:56 PM Ticket #3360 (Ribbon index error) created by
- […]
- 5:10 PM Ticket #3359 (map/surface color is None) created by
- […]
- 5:01 PM Ticket #3358 (Remove deprecated chimerax.core.geometry imports) created by
- After geometry was moved out of core, temporary code was put in …
- 4:01 PM Ticket #3356 (Test clean startup with updated bundle) closed by
- fixed: A fake 1.1 version of the Help bundle is on the preview website. …
- 3:49 PM Ticket #3352 (Disable toolshed bundle update notification mechanism) closed by
- fixed
- 1:45 PM Ticket #3357 (Add installed version numbers to the bug reporter) created by
- 1:40 PM Ticket #3356 (Test clean startup with updated bundle) created by
- Greg will put a new version of help viewer on preview site
- 1:37 PM Ticket #3355 (Open ticket with UCSF IT to open up pre-release toolshed to outside ...) created by
- 1:37 PM Milestone 1.0 completed
- == Overview * Useful subset of Chimera features * Focus on …
- 1:35 PM Ticket #3354 (Test update of bundles with binary (e.g. C++) components) created by
- Atomic is a good example
- 1:34 PM Ticket #3353 (Flatten bundle hierarchy) created by
- Atomic and Volume are good examples of this.
- 1:32 PM Ticket #3352 (Disable toolshed bundle update notification mechanism) created by
- 9:44 AM Ticket #3351 (ribbon pick: index is out of bounds for axis) closed by
- duplicate: Fixed a month and a half ago.
- 12:16 AM Ticket #3351 (ribbon pick: index is out of bounds for axis) created by
- […]
Jun 3, 2020:
- 5:41 PM Ticket #3348 (Filled rings unusably slow on large structures) reopened by
- 5:32 PM Ticket #3327 (mmCIF output problem for inserted residues) closed by
- fixed: Okay, fixed AFAICT. My test case with a peptide stitched into a …
- 4:40 PM Ticket #3233 (Remove bogus 1-star reviews) closed by
- fixed: No response from Tempy contact. Went ahead and deleted the ratings …
- 4:36 PM Ticket #3348 (Filled rings unusably slow on large structures) closed by
- fixed: Adding a add_shapes API, to add multiple shapes at one time, changed …
- 12:33 PM Ticket #3350 (Better information for bundle requirement problems) created by
- […]
- 8:56 AM Ticket #3349 (Problem handling bad template) closed by
- fixed: While this particular error has been fixed for a while, I'd like to …
- 12:43 AM Ticket #3349 (Problem handling bad template) created by
- […]
Jun 2, 2020:
- 4:29 PM Ticket #3348 (Filled rings unusably slow on large structures) created by
- […]
- 12:17 PM Ticket #3347 (Session saving creating arbitrary class instances) closed by
- fixed: isinstance is used throughout the session saving and serialization …
- 10:19 AM Ticket #3346 (config file is all nulls) closed by
- can't reproduce: Not sure why this happened. But you recover by deleting …
- 8:18 AM Ticket #3347 (Session saving creating arbitrary class instances) created by
- […]
- 2:50 AM Ticket #3346 (config file is all nulls) created by
- […]
Jun 1, 2020:
- 6:24 PM Ticket #2567 (Command History window shown when it shouldn't be) closed by
- fixed: I *believe* I fixed this on 2/21/2020 with commit …
- 3:42 PM Ticket #3345 (Model closed twice) closed by
- fixed: Fixed. Code change a few hours ago that made Models.remove() not …
- 3:26 PM Ticket #3345 (Model closed twice) created by
- […]
- 11:36 AM Ticket #3339 (Easy to get surface cap deletion wrong) closed by
- fixed: Ok, I changed Models.remove() so it does not disassemble the tree of …
- 10:46 AM Ticket #3340 (Permission denied saving image to C:\Users\Public\Desktop) closed by
- not a bug: The save snapshot button tries to save the image file on the desktop. …
- 9:56 AM Ticket #3344 (Opening structure-factor cif) closed by
- not a bug: No, you've got that backwards, given a format/suffix the open command …
- 9:52 AM Ticket #3343 (OpenMM: gbforce.addParticles: AttributeError) closed by
- fixed: Long since fixed - the user has an old, mid-development build of …
- 9:28 AM Ticket #3344 (Opening structure-factor cif) created by
- […]
May 31, 2020:
May 30, 2020:
- 1:04 PM Ticket #3342 (Segger: crash selecting segments) created by
- […]
- 4:27 AM Ticket #3341 (Memory error in libqsvg.so on exit) created by
- I've been seeing occasional segmentation faults (maybe 1 time in 20) …
- 4:12 AM Ticket #3340 (Permission denied saving image to C:\Users\Public\Desktop) created by
- […]
- 3:03 AM Ticket #3339 (Easy to get surface cap deletion wrong) created by
- […]
May 29, 2020:
- 11:43 PM Ticket #3295 (Help Viewer back-button bug) closed by
- fixed: Not updating the status of the back and forward buttons also happened …
- 11:41 PM Ticket #3317 (CCD fetch failures need to be cached) closed by
- fixed: Also reduce the warnings due to a missing CCD entry to one line …
- 10:32 AM Ticket #3337 (Error assigning non-contiguous array to atom.bfactors) closed by
- fixed: Fixed in ChimeraX 1.1. Assigning a molecular collection attribute …
- 9:58 AM Ticket #3336 (Many graphics errors) closed by
- nonchimerax: Your graphics driver is defective and ChimeraX does not support Windows 7.
- 9:52 AM Ticket #3338 (Phenix mmCIF problems) created by
- We should work with the Phenix group to get them to output conforming …
- 8:14 AM Ticket #3337 (Error assigning non-contiguous array to atom.bfactors) created by
- […]
May 28, 2020:
- 9:48 PM Ticket #3336 (Many graphics errors) created by
- […]
- 6:06 PM Ticket #3334 (20.04 install fail) closed by
- fixed: Thank you for reporting this. It will be fixed in the next release …
- 2:20 PM Ticket #3333 (Probable HTML crash (help viewer?)) closed by
- can't reproduce: I thought Greg/Conrad did do something about that. Created a Schema …
- 2:18 PM Ticket #3333 (Probable HTML crash (help viewer?)) reopened by
- 2:01 PM Ticket #3330 (Sequence window unreadable in Dark Mode) closed by
- fixed: Hi Loc, Thanks for reporting this problem. I have fixed it and the …
- 1:56 PM Ticket #3335 (open command: UnboundLocalError: local variable 'data_format' ...) closed by
- duplicate: Fixed on 4/30
- 1:28 PM Ticket #3333 (Probable HTML crash (help viewer?)) closed by
- can't reproduce
- 11:29 AM Ticket #3335 (open command: UnboundLocalError: local variable 'data_format' ...) created by
- […]
- 10:43 AM Ticket #3319 (cartoon style modeHelix wrap: 'NoneType' object does not support item ...) closed by
- fixed: Fixed in ChimeraX 1.1. Cartoon helix mode wrap assumed guide atoms (O …
- 10:27 AM Ticket #3334 (20.04 install fail) created by
- […] 20200528_Chimerax_ubuntu_20_04_install_fail_log
- 9:55 AM Ticket #3333 (Probable HTML crash (help viewer?)) created by
- […]
- 9:51 AM Ticket #3332 (Get sample code from relevant branch) created by
- Original mail: The CGI script that generates the sample-code zip file …
- 1:23 AM Ticket #3331 (Installation error) created by
- […] chimerax_error2.png [attachment:"Screenshot …
May 27, 2020:
- 11:58 PM Ticket #3330 (Sequence window unreadable in Dark Mode) created by
- […] Screen Shot 2020-05-28 at 2.55.31 AM.png
- 10:47 PM Ticket #3318 (Shape command allows creating submodel without a parent model) closed by
- fixed: Fixed in ChimeraX 1.1 Rewrote Models.add() and added extensive error …
- 10:46 PM Ticket #3324 (Wrong parent model assigned when shape command modelId given) closed by
- fixed: Fixed in ChimeraX 1.1 Rewrote Models.add() and added extensive error …
- 5:16 PM Ticket #3329 (Changing 2D label model id can cause problems) created by
- […]
- 4:32 PM Ticket #3328 (Make Surface model show clip caps by default) created by
- I think it would be good to have models that are instances of the …
- 3:35 PM Ticket #3279 (Prevent bad model hierarchies from being formed) closed by
- duplicate
- 2:45 PM Ticket #2876 (core import hook makes non-equivalent classes) closed by
- fixed
- 2:14 PM Ticket #3160 (Install updated bundle into 1.0) closed by
- fixed: Verified that an updated standard bundle will install into the …
- 11:28 AM Ticket #3322 (Blast Protein has trouble with sequences that include UNK) closed by
- fixed: Fixed in 2ddcddb1e. Use 'X' instead of '?' for unknown …
- 10:40 AM Ticket #3326 ('rename' command: maximum recursion depth exceeded) closed by
- fixed: Fixed. The rename command didn't handle the case where a model id …
- 9:46 AM Ticket #3315 (Lighting dark in stereo mode) closed by
- duplicate: This is very likely the same problem as #3226 that everything inside …
- 9:16 AM Ticket #3320 (No bug reported) closed by
- not a bug
- 5:01 AM Ticket #3327 (mmCIF output problem for inserted residues) created by
- […] building_bug.cxs
- 3:00 AM Ticket #3326 ('rename' command: maximum recursion depth exceeded) created by
- […]
May 26, 2020:
- 8:40 PM Ticket #3325 (Crash when clicking on logged "silhouette false" command) created by
- […]
- 6:28 PM Ticket #3324 (Wrong parent model assigned when shape command modelId given) created by
- […]
- 6:20 PM Ticket #3323 (Side View should log a clipping command) created by
- Side View should log a clip command when the user moves a clip plane. …
- 6:17 PM Ticket #3292 (Circular dependency saving surface ("shape icosahedron"?)) closed by
- fixed: Fixed. Session save of surface geometry was incorrectly trying to …
- 6:14 PM Ticket #3200 (configfile/configparser not handling encoding) closed by
- fixed: No response. Assume it's been fixed.
- 5:37 PM Ticket #3309 (some color commands should only target atomic models) closed by
- wontfix: MarkerSet is a Structure. There is another class called …
- 4:59 PM Ticket #3302 ("tool show" expanding to "toolshed show") closed by
- fixed: Done. Also suppressed "tool" is a prefix of existing command …
- 4:25 PM Ticket #3296 (volume "subregion" keyword inconsistent with documentation) closed by
- wontfix: Named volume regions are a Chimera feature not currently supported in …
- 4:19 PM Ticket #3290 (selected_residues(session) very slow for large models) closed by
- fixed: After looking at the code, I'm not looping in Python. The lesson is …
- 4:03 PM Ticket #3298 (Crash getting global interpreter lock) reopened by
- 3:50 PM Ticket #3294 (Deleted color-blob check box still being used) closed by
- fixed: Fixed. Pick blobs mouse mode used after pick blobs gui panel was …
- 3:34 PM Ticket #3322 (Blast Protein has trouble with sequences that include UNK) created by
- […]
- 2:54 PM Ticket #3321 (remotecontrol subcommands on/off keywords inconsistent) created by
- Currently the REST subcommand takes start/stop and the XMLRPC one …
- 12:58 PM Ticket #3320 (No bug reported) created by
- […]
- 11:34 AM Ticket #3319 (cartoon style modeHelix wrap: 'NoneType' object does not support item ...) created by
- […]
- 11:12 AM Ticket #3318 (Shape command allows creating submodel without a parent model) created by
- […]
- 11:06 AM Ticket #3317 (CCD fetch failures need to be cached) created by
- […] big_membrane_lipids_only.cif
- 11:04 AM Ticket #3314 (Non-functional selectors) closed by
- not a bug: Hi Phil, The basic "name" command takes literally what you typed as …
- 10:29 AM Ticket #3310 (Session restore failure: ValueError: int is not allowed for map key) closed by
- duplicate: Hi Doreen, This bug was fixed the day after the version you are …
- 10:23 AM Ticket #3316 (Test if bug report log contains all commands) closed by
- not a bug: All commands in this test seemed to make it into the bug report log.
- 10:18 AM Ticket #3308 (User-supplied template does not match the residue) closed by
- duplicate
- 10:17 AM Ticket #3316 (Test if bug report log contains all commands) created by
- […]
- 10:13 AM Ticket #3307 (Model panel, list index out of range, restoring session) closed by
- duplicate: Similar to #3279 -- same user, related session.
- 10:10 AM Ticket #3305 (Save dialog failure) closed by
- duplicate: Hi Raoul, This problem was fixed in the build immediately after the …
- 9:54 AM Ticket #3304 (safeguard chain IDs) closed by
- wontfix: Hi Tristan, I do not envision "setattr" as being the command for …
- 9:40 AM Ticket #3315 (Lighting dark in stereo mode) created by
- Begin forwarded message: From: Kenneth Satyshur Subject: …
- 9:39 AM Ticket #3280 (Error saving session in Clipper symmetry, CORE_STATE_VERSION gone) closed by
- fixed: All sorted. Saving and restoring happily again.
- 9:06 AM Ticket #3311 (Installing ISOLDE in old ChimeraX version) closed by
- fixed
- 6:36 AM Ticket #3314 (Non-functional selectors) created by
- […] InducedFit_model1_rec.mae
- 6:09 AM Ticket #3313 ("Vestigial" ViewDockX can interfere with session restore) created by
- […] ViewDocX_bug.cxs
- 5:35 AM Ticket #3312 (Help Viewer crash) created by
- […]
- 3:08 AM Ticket #3311 (Installing ISOLDE in old ChimeraX version) created by
- […]
- 2:38 AM Ticket #3310 (Session restore failure: ValueError: int is not allowed for map key) created by
- […] chimera bug opening csx file.PNG
- 2:06 AM Ticket #3309 (some color commands should only target atomic models) created by
- […]
May 25, 2020:
- 6:13 PM Ticket #3308 (User-supplied template does not match the residue) created by
- […]
- 5:51 PM Ticket #3307 (Model panel, list index out of range, restoring session) created by
- […]
- 5:30 PM Ticket #3306 (ChimeraX startup: unsupported locale setting) created by
- […]
- 4:28 PM Ticket #3305 (Save dialog failure) created by
- […]
- 3:55 PM Ticket #3284 (Unknown command: linux xdg-install system true) closed by
- fixed: Sorry about that. The fixed will be in the next release candidate, …
- 2:49 PM Ticket #3304 (safeguard chain IDs) created by
- […]
- 12:49 PM Ticket #3303 (Weird copy/paste behavior) created by
- […]
- 12:46 PM Ticket #3302 ("tool show" expanding to "toolshed show") created by
- […]
- 9:43 AM Ticket #3299 (unexpected unindent running Volume Viewer) closed by
- duplicate: Was fixed a week ago. Get current ChimeraX.
- 9:43 AM Ticket #3293 (unexpected unindent running Volume Viewer) closed by
- duplicate: Was fixed a week ago. Get current ChimeraX build.
- 9:38 AM Ticket #3301 (Model panel, list index out of range, restoring session) closed by
- duplicate: Similar to #3279 -- same user, related session. Would be nice if …
- 9:30 AM Ticket #3298 (Crash getting global interpreter lock) closed by
- can't reproduce
- 9:12 AM Ticket #3286 (ISOLDE: KeyError in find_glycan_template_name_and_link) closed by
- fixed: Arg! Didn't notice that this was an anonymous report. Sigh. Closing as …
- 9:06 AM Ticket #3291 (Model panel, list index out of range, restoring session) closed by
- duplicate: Exact duplicate of #3279 (same user/session)
- 9:02 AM Ticket #3289 (Model panel, list index out of range, restoring session) closed by
- duplicate: Exact duplicate of #3279 (same user/session)
- 9:00 AM Ticket #3288 (Model panel, list index out of range, restoring session) closed by
- duplicate: Exact duplicate of #3279 (same user/session)
- 8:59 AM Ticket #3287 (Model panel, list index out of range, restoring session) closed by
- duplicate: Exact duplicate of #3279 (same user/session)
- 8:57 AM Ticket #3300 (ISOLDE and reporting error) closed by
- fixed: The new ISOLDE builds (once released) will give more helpful error …
- 8:41 AM Ticket #3301 (Model panel, list index out of range, restoring session) created by
- […]
- 4:47 AM Ticket #3300 (ISOLDE and reporting error) created by
- […]
- 2:04 AM Ticket #3299 (unexpected unindent running Volume Viewer) created by
- […] emd_9333_msk_1.map
May 24, 2020:
- 7:21 PM Ticket #3298 (Crash getting global interpreter lock) created by
- […]
- 4:35 PM Ticket #3297 (Error opening grayscale + alpha 2D image) created by
- […] gray_alpha.tif
- 1:37 AM Ticket #3296 (volume "subregion" keyword inconsistent with documentation) created by
- […]
- 1:27 AM Ticket #3295 (Help Viewer back-button bug) created by
- […]
- 12:51 AM Ticket #3294 (Deleted color-blob check box still being used) created by
- […]
May 23, 2020:
- 11:46 AM Ticket #3293 (unexpected unindent running Volume Viewer) created by
- […]
- 9:38 AM Ticket #3292 (Circular dependency saving surface ("shape icosahedron"?)) created by
- […]
- 5:52 AM Ticket #3291 (Model panel, list index out of range, restoring session) created by
- […]
- 4:14 AM Ticket #3290 (selected_residues(session) very slow for large models) created by
- From #3285. For 3j3y, with all atoms selected: […] The actual …
May 22, 2020:
- 8:48 PM Ticket #3289 (Model panel, list index out of range, restoring session) created by
- […]
- 6:25 PM Ticket #3288 (Model panel, list index out of range, restoring session) created by
- […]
- 6:16 PM Ticket #3275 (Registration server unavailable) closed by
- fixed: The registration script should be able to handle UTF-8 characters now. …
- 6:12 PM Ticket #3287 (Model panel, list index out of range, restoring session) created by
- […]
- 5:00 PM Ticket #1885 (error using BLOSUM100 in blast) closed by
- fixed: Fixed in 7510c8922. The list of supported similarity …
- 3:01 PM Ticket #3286 (ISOLDE: KeyError in find_glycan_template_name_and_link) created by
- […]
- 2:59 PM Ticket #3285 (Slow graphics updates) created by
- […]
- 2:21 PM Ticket #3234 (ISOLDE Tool Shed install button not appearing) closed by
- fixed: Heard from Tristan that this was fixed. If not, please let us know.
- 1:57 PM Ticket #3232 (Tool Shed download problem) closed by
- fixed: The production toolshed has been updated with the new code.
- 1:47 PM Ticket #3281 (Garbled PostiveIntArg error message) closed by
- fixed: Fixed the error message.
- 11:59 AM Ticket #3284 (Unknown command: linux xdg-install system true) created by
- […] 20200522_Chimerax_ubuntu_20_04_install_fail_log
- 11:23 AM Ticket #3283 (Truncated fetched file produces error when fetched again) created by
- […]
- 11:18 AM Ticket #1311 (Windows 10 display scaling gives wrong GUI text sizes) closed by
- fixed: Font sizes currently look reasonable at 100%, 125% and 175% scaling on …
- 11:13 AM Ticket #1134 (VR gui panel does not work hidden on desktop) closed by
- fixed: VR now shows each ChimeraX tool and a separate pane and those panels …
- 10:55 AM Ticket #3251 (Another clEnqueueReadBuffer problem) closed by
- fixed: Great! I'll go ahead and close this then.
- 10:30 AM Ticket #151 (Rendering ribbon with stick is slow) closed by
- can't reproduce: Retried this test on a newer Mac laptop with larger system 4v88, …
- 10:24 AM Ticket #61 (Rendering takes minutes, Mac Nvidia Geforce GT 330M graphics) closed by
- nonchimerax: The computers that have these extremely limited graphics seem rare …
- 10:20 AM Ticket #947 (Image save only includes lower left quadrant, Mac retina display) closed by
- can't reproduce: This was a macOS graphics driver issue. I have not seen it reported …
- 10:18 AM Ticket #1041 (Surprising slowdown when drawing multiple drawings) closed by
- fixed: Seems performance was made adequate with some bounding box optimization.
- 10:12 AM Ticket #2408 (Cannot use Lenobo explorer for VR) closed by
- can't reproduce: No response from user debugging VR setup.
- 10:09 AM Ticket #2536 (Tug mouse mode bad allocation error) closed by
- fixed: ChimeraX now uses the updated OpenMM 7.4.1
- 10:08 AM Ticket #2566 (Can't start ChimeraX) closed by
- can't reproduce: Some kind of OpenGL / graphics driver problem on reporter's computer. …
- 10:06 AM Ticket #2565 (Problems using previously fetched files) closed by
- can't reproduce: Haven't seen this reported again. So I suspect improvements to macOS …
- 9:52 AM Ticket #2961 (Tips for remote use) closed by
- wontfix: In general my recommendation for running ChimeraX remotely is "Don't …
- 9:43 AM Ticket #3037 (Selection problems) closed by
- can't reproduce: Could be that the default framebuffer depth was not 24 as assumed by …
- 9:39 AM Ticket #3222 (During ChimeraX quit: Could not make graphics context current) closed by
- can't reproduce: I added code so that if an OpenGL error occurs when deleting a Drawing …
- 9:36 AM Ticket #3239 (Graphics window banks to gray) closed by
- can't reproduce
- 9:21 AM Ticket #3282 (Add mcopy command) created by
- The mcopy command is useful for replacing a model in a figure and …
- 7:38 AM Ticket #3281 (Garbled PostiveIntArg error message) created by
- […]
- 6:21 AM Ticket #3280 (Error saving session in Clipper symmetry, CORE_STATE_VERSION gone) created by
- […]
May 21, 2020:
- 7:00 PM Ticket #3278 (Bogus capitalization of SimpleXMLRPCServer.__Init__) closed by
- fixed: Fixed. Jeez, I guess I managed to upcase the word with an errant key …
- 6:49 PM Ticket #3279 (Prevent bad model hierarchies from being formed) created by
- […]
- 5:52 PM Ticket #2080 (Awkward text copy from Help Viewer (HTML widgets?)) closed by
- fixed: Was able to move the log window's workaround into the base class, but …
- 5:39 PM Ticket #3278 (Bogus capitalization of SimpleXMLRPCServer.__Init__) created by
- […]
- 4:03 PM Ticket #3277 (Import error running Linux installer) closed by
- fixed: Hi John, Thanks for reporting this problem. It is fixed now and the …
- 3:52 PM Ticket #3274 (Re: [chimerax-users] Recreating views) closed by
- invalid: intended for chimerax-users
- 3:36 PM Ticket #3277 (Import error running Linux installer) created by
- […] 20200521_Chimerax_ubuntu_20_04_install_log
- 2:46 PM Ticket #3270 (Bfactor sharpening on resampled map) closed by
- not a bug: This is not a bug. I attached an image showing that the resampling …
- 2:21 PM Ticket #3257 (unable to reopen data from file history) closed by
- fixed: I wound up change FileHistory as per Tom's suggestion to map the old …
- 12:50 PM Ticket #3276 (nucleotide sugar-tubes disconnected from ribbon in restored session) created by
- open 2bna save nuctest.cxs close open nuctext.cxs .... now …
- 12:28 PM Ticket #3275 (Registration server unavailable) created by
- […]
- 11:24 AM Ticket #3272 (MAV: region name is None) closed by
- fixed: If the setting for showing the selection region was off, then fetching …
- 10:35 AM Ticket #2712 (A lot of array size mismatches after deletions) closed by
- can't reproduce: This does not look like a ribbon error. It was caused by deleting …
- 10:26 AM Ticket #3213 (REST: broken pipe) closed by
- fixed: The fix worked!
- 10:05 AM Ticket #3273 (Missed a "toolshed show" conversion) closed by
- fixed: That was fixed shortly after you downloaded the candidate release. …
- 9:47 AM Ticket #3274 (Re: [chimerax-users] Recreating views) created by
- […]
- 2:30 AM Ticket #3273 (Missed a "toolshed show" conversion) created by
- […]
May 20, 2020:
- 9:38 PM Ticket #3272 (MAV: region name is None) created by
- […]
- 6:27 PM Ticket #3271 (Line-ending issues for resaved PDB files) created by
- […] pdb-export-eol-test-case.zip
- 6:00 PM Ticket #3270 (Bfactor sharpening on resampled map) created by
- […] Screenshot 2020-05-20 20.56.53.png
- 5:04 PM Ticket #3064 (Adding images and descriptions to RBVI bundles) closed by
- fixed: "maestro" is already on the toolshed. "speech" should not see the …
- 4:59 PM Ticket #2917 (BlaST web service: No alias or index file found for protein database) closed by
- fixed: Fixed in b62257089. Instead of catching one specific …
- 4:52 PM Ticket #3014 (Blast Protein tool: threading) reopened by
- This is an RFE not a bug report. Request is to allow entering …
- 4:43 PM Ticket #3014 (Blast Protein tool: threading) closed by
- not a bug: Currently, the Blast Protein tool can only use the sequence from a …
- 4:32 PM Ticket #2373 (Registration failure) closed by
- can't reproduce: Not sure where a self-signed cert would be used when connecting to …
- 4:30 PM Ticket #2993 (KeyError picking ribbon) closed by
- wontfix: Ribbon code has been completely revamped.
- 4:21 PM Ticket #3079 (Registration failure (while plato was down)) closed by
- fixed: Fixed in d60748b6c. Looks like a "Connection refused" …
- 4:03 PM Ticket #3256 (ViewDockX save broken) closed by
- fixed: Fixed in 1baab4c05. Some code got indented too far and …
- 3:29 PM Ticket #3267 (REST https responses garbled) closed by
- not a bug: The server got gobbledygook on input and logged it as such. Not sure …
- 3:25 PM Ticket #3268 (ssl.SSLError starting REST server with 'ssl true') closed by
- fixed: Fixed in 82e20c048. The code works, but uses a …
- 2:54 PM Ticket #2818 (Improve sample bundle code) closed by
- fixed: Hi Tristan, Thanks for this -- it's really excellent and it must have …
- 12:57 PM Ticket #3191 (remove dead I/O code) closed by
- fixed
- 9:50 AM Ticket #3269 (Custom multitouch trackpad bindings) created by
- This has been on the to-do list for a while, and I was recently …
- 9:36 AM Ticket #3268 (ssl.SSLError starting REST server with 'ssl true') created by
- […]
- 9:27 AM Ticket #3267 (REST https responses garbled) created by
- […]
- 8:38 AM Ticket #3262 (Problems both saving and restoring nucleotides) closed by
- duplicate: duplicate of #3263
- 8:03 AM Ticket #3266 (RFE: have matchmaker maintain original SS assignments) created by
- […]
- 7:55 AM Ticket #3264 (glTF save error) closed by
- fixed: Hi Jonathan Thanks for reporting this problem. I have just fixed it …
- 7:53 AM Ticket #3265 (glTF save error) closed by
- fixed: Hi Thibault, Thanks for reporting this problem. I have just fixed it …
- 1:05 AM Ticket #3265 (glTF save error) created by
- […] error_chimeraX.txt
- 12:44 AM Ticket #3264 (glTF save error) created by
- […] adenine.mol
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