![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Nov 21, 2022:
- 6:59 PM Ticket #6774 (Unknown crash) closed by
- can't reproduce: This looks like a crash in the Qt window toolkit, but there is not …
- 6:57 PM Ticket #6924 (QXcbConnection: XCB error:) closed by
- nonchimerax: No reply from reporter.
- 6:57 PM Ticket #6961 (AlphaFold prediction: A UTF-8 locale is required. Got ANSI_X3.4-1968) closed by
- can't reproduce: I have not seen this error in 6 months. Maybe our switch to using …
- 6:55 PM Ticket #7209 (Mac notarization fails about 1/4 of the time: "A timestamp was ...) closed by
- fixed: I increased the number of notarization retries from 1 to 4 and …
- 6:51 PM Ticket #7417 ("cofr" info misleading) closed by
- limitation
- 6:50 PM Ticket #7428 (Inconsistent stack trace information) closed by
- limitation: I may improve the log handling in the future to allow for multiple …
- 6:46 PM Ticket #7524 (Save image to desktop: permission denied) closed by
- duplicate: ChimeraX was changed more than a year ago so it will not set the …
- 6:42 PM Ticket #7678 (Crashes creating QWebEngineProfile on Windows) closed by
- nonchimerax
- 6:41 PM Ticket #7739 (QPainter::begin: Paint device returned engine == 0, type: 2) closed by
- can't reproduce
- 6:40 PM Ticket #7878 ('show' unexpectedly showing whole chains) closed by
- can't reproduce: No reply from reporter.
- 6:38 PM Ticket #8010 (Image stack:tuple index out of range) closed by
- can't reproduce: Probably requires an incomplete set of files to reproduce this.
- 5:18 PM Ticket #8064 (clicking Model Panel Info to show DICOM Browser either gives traceback ...) closed by
- fixed: This should be fixed tomorrow. The DICOM browser was rewritten to make …
- 4:58 PM Ticket #8065 (Log chain table with RMSD for AlphaFold multimer predictions) created by
- […]
- 4:44 PM Ticket #8015 ('DICOMBrowserTool' object has no attribute '_see_what_happened') closed by
- fixed: Should be fixed in tomorrow's daily build and release candidate.
- 2:42 PM Ticket #8019 (Bad alternate locations) closed by
- limitation: Okay, I submitted a pull request that will skip a preset when these …
- 1:26 PM Ticket #8055 (AlphaFold: I/O operation on closed file) closed by
- fixed
- 1:25 PM Ticket #8055 (AlphaFold: I/O operation on closed file) reopened by
- Fixed. The release of jax 0.3.25 broke ColabFold. Unfortunately …
- 11:58 AM Ticket #8064 (clicking Model Panel Info to show DICOM Browser either gives traceback ...) created by
- […]
- 10:30 AM Ticket #8063 (Crash running AlphaFold prediction) closed by
- can't reproduce
- 10:29 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) closed by
- duplicate: This bug was fixed about a year ago. It happens when running ChimeraX …
- 10:23 AM Ticket #8055 (AlphaFold: I/O operation on closed file) closed by
- nonchimerax: That is an error in AlphaFold code, not in ChimeraX. It says it is …
- 10:21 AM Ticket #8061 (MD viewer: No self.atomLocations) closed by
- not a bug: Not a trajectory (self.atomLocations only set on ENDMDL record).
- 10:19 AM Ticket #8063 (Crash running AlphaFold prediction) created by
- […]
- 9:29 AM Ticket #8060 (crash running modal dialog) closed by
- can't reproduce
- 9:26 AM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Uzay, Thanks for reporting this problem. We believe it is fixed …
- 9:21 AM Ticket #8057 (Save session: Basic Actions: 'QEventLoop' object has no attribute 'exec_') closed by
- duplicate
- 9:14 AM Ticket #8054 (Crash processing geometry change) closed by
- can't reproduce
- 9:12 AM Ticket #8053 (Crash creating QTimer) closed by
- can't reproduce
- 8:58 AM Ticket #8050 (Crash in event loop) closed by
- can't reproduce
- 6:10 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) created by
- […]
- 5:43 AM Ticket #8061 (MD viewer: No self.atomLocations) created by
- […]
- 3:03 AM Ticket #8060 (crash running modal dialog) created by
- […]
- 2:51 AM Ticket #8059 (chimeraX freezing) created by
- […]
Nov 20, 2022:
- 5:47 PM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 10:58 AM Ticket #8057 (Save session: Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by
- […]
Nov 19, 2022:
- 9:05 PM Ticket #8056 (Problem opening Gaussian output: Unknown element detected: Variables) created by
- […] gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log
- 10:04 AM Ticket #8055 (AlphaFold: I/O operation on closed file) created by
- […] Screen Shot 2022-11-19 at 11.00.32 AM.png
- 7:17 AM Ticket #8054 (Crash processing geometry change) created by
- […]
- 6:45 AM Ticket #8053 (Crash creating QTimer) created by
- […]
Nov 18, 2022:
- 5:04 PM Ticket #7997 (Add Charges: Nonstandard name for heavy atom) closed by
- fixed: Tomorrow's daily build will handle phosphorylated 5' termini.
- 3:13 PM Ticket #8052 (limit formats in Save dialog to ones appropriate for current models) created by
- It would be nice if the list of output formats in the Save dialog …
- 1:14 PM Ticket #8051 (ISOLDE: matplotlib: 'box_aspect' and 'fig_aspect' must be positive + ...) created by
- […]
- 10:41 AM Ticket #8049 (MemoryError saving large image) closed by
- nonchimerax: Ran out of memory trying to save an 6000 x 4000 image. PIL tried to …
- 10:01 AM Ticket #8050 (Crash in event loop) created by
- […]
Nov 17, 2022:
- 11:23 PM Ticket #8049 (MemoryError saving large image) created by
- […]
- 3:40 PM 2022-11-17 edited by
- (diff)
- 3:40 PM 2022-11-17 edited by
- (diff)
- 3:02 PM Dev2022-11-17 created by
- 2:54 PM DeveloperMeetings edited by
- (diff)
- 1:25 PM Ticket #7992 (Modeller target is None) closed by
- fixed: Fix: …
- 1:23 PM Ticket #8048 (Crash in timer callback) created by
- […]
- 10:36 AM ChangeLog edited by
- (diff)
- 10:22 AM 2022-11-17 edited by
- (diff)
- 9:53 AM Ticket #8047 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 9:51 AM Ticket #8046 (Crash in garbage collection after showing 30000+ pseudobonds) closed by
- can't reproduce
- 4:39 AM Ticket #8047 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
Nov 16, 2022:
- 4:18 PM Ticket #7769 (Crash reading mmCIF) closed by
- can't reproduce: Learned on 11 October 2022 that the .cif file had been deleted.
- 4:02 PM Ticket #3534 (Parsing complaint about Ligand Expo cif files) closed by
- nonchimerax: Yes, that is illegal according to the CIF standard, …
- 3:45 PM Ticket #7925 (DICOM Browser: bundle forgot to override start_tool method) closed by
- fixed
- 2:54 PM Ticket #8045 (Bad symmetry table entries) closed by
- fixed
- 2:42 PM Ticket #8034 ("make clean" compiles bundle) closed by
- fixed: Should be fixed by …
- 1:35 PM Ticket #8022 (Bad residue names from Mol2 file) closed by
- fixed: The Mol2 reader wasn't adding missing-structure pseudobonds when …
- 1:23 PM Ticket #8046 (Crash in garbage collection after showing 30000+ pseudobonds) created by
- […]
- 1:02 PM Ticket #8045 (Bad symmetry table entries) created by
- Click on entry 1 of the symmetry table for the attached file works …
- 12:06 PM 2022-11-17 edited by
- (diff)
- 10:32 AM Ticket #8043 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by
- limitation: ChimeraX requires Windows 10 or 11. Maybe it will run on Windows 7 …
- 9:26 AM Ticket #8037 (Charge-determination failure for CAS in 1fyw) closed by
- limitation: Neither charge-determination method can handle the arsenic in the CAS …
- 8:56 AM Ticket #8044 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by
- duplicate
- 8:53 AM Ticket #8042 (Unknown crash) closed by
- can't reproduce
- 8:51 AM Ticket #8039 (Charge-determination convergence failure for 4pk2) closed by
- limitation: The charge determination works with the Gasteiger method, and …
- 7:49 AM Ticket #8044 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by
- […]
- 6:52 AM Ticket #8043 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by
- […]
Nov 15, 2022:
- 11:10 PM Ticket #7993 (Mesa-Utils package required) closed by
- can't reproduce: I don't know where those errors are coming from. But if you uninstall …
- 6:24 PM Ticket #8040 (alphafold pae command with no structure gives AttributeError) closed by
- fixed: Fixed in ChimeraX 1.5 and daily build. The chain divider lines on the …
- 6:20 PM Ticket #8042 (Unknown crash) created by
- […]
- 6:11 PM Ticket #8041 (Add ESMFold database to BlastProtein) created by
- The ESMFold metagenomic atlas is very similar to the AlphaFold …
- 5:49 PM Ticket #7945 (Read PAE matrix: No module named 'jax') closed by
- fixed: Duplicate of #8032. Fixed.
- 5:36 PM Ticket #8023 (All white coulombic) closed by
- not a bug: The PDB has a spurious TER card in the middle of chain A, between …
- 5:28 PM Ticket #8032 (Read PAE matrix: No module named 'jax') closed by
- fixed: Fixed in ChimeraX 1.5 release candidate and daily build. I put in a …
- 5:16 PM Ticket #8024 (PubChem: #charges != #atoms) closed by
- fixed: Now in addition to a missing charges section of the SDF file meaning …
- 5:04 PM Ticket #7967 (Ubuntu 22 ChimeraX installer is replacing symlinks by copies of libraries) closed by
- fixed: Needed syslinks=True argument to shutil.copytree()
- 4:57 PM Ticket #8036 (Not able to sign in to Google Colab for AlphaFold prediction) closed by
- worksforme
- 4:40 PM Ticket #8026 (sqm failure on all-nonstandard nucleic acid) closed by
- fixed: Switched the coulombic preset to use Gasteiger charge-determination …
- 4:40 PM Ticket #8040 (alphafold pae command with no structure gives AttributeError) created by
- […]
- 4:03 PM Ticket #8028 (microheterogeneity) closed by
- limitation: ChimeraX simply does not handle microheterogeneity (e.g residue 782 in …
- 2:38 PM Ticket #8029 (non-standard C-terminal oxygen name) closed by
- fixed: Add Charge will allow 1OCT and 2OCT as C-terminal oxygen names …
- 2:05 PM ChangeLog edited by
- (diff)
- 2:04 PM ChangeLog edited by
- (diff)
- 1:54 PM Ticket #8039 (Charge-determination convergence failure for 4pk2) created by
- […] 4pk2.pdb
- 1:53 PM ChangeLog edited by
- (diff)
- 1:22 PM Ticket #8038 (Compressed .cif without .gz suffix) created by
- […] 2fae-assembly-1.cif
- 1:16 PM Ticket #8037 (Charge-determination failure for CAS in 1fyw) created by
- […]
- 12:01 PM Ticket #8031 (Incorrect element column in PDB file) closed by
- not a bug: The input PDB file is just bad. The "element' column is *mostly* the …
- 11:35 AM Ticket #8035 (Bad formal charge estimate) closed by
- limitation: The ChargeError does get caught by the command processing code, but …
- 10:14 AM Ticket #8036 (Not able to sign in to Google Colab for AlphaFold prediction) created by
- […]
- 10:02 AM 2022-11-17 created by
- 10:01 AM DeveloperMeetings edited by
- (diff)
- 9:56 AM Ticket #8035 (Bad formal charge estimate) created by
- […] 1av7.pdb
Nov 14, 2022:
- 6:09 PM Ticket #8034 ("make clean" compiles bundle) created by
- When doing "make clean" in the mmcif bundle with an error in …[…]
- 5:26 PM Ticket #8033 (SEQCROW: memory reporting: unsupported operand type(s) for *: ...) created by
- […]
- 3:07 PM Ticket #8030 (PDB file reader accepts "nan" coordinates without warning) closed by
- fixed: Use numpy.isnan() to check the coordinates coming from the PDB reader. …
- 2:17 PM Ticket #8032 (Read PAE matrix: No module named 'jax') created by
- […]
- 2:01 PM Ticket #8025 (Small molecule CIF) closed by
- duplicate: Duplicate of #4479 -- will add Kristen to recipient list for that ticket
- 1:14 PM Ticket #8031 (Incorrect element column in PDB file) created by
- […] 2.5F phyre prediction.pdb
- 11:31 AM Ticket #8020 (Encode movie: Output directory does not exist) closed by
- duplicate: You probably are using Microsoft OneDrive which relocates your Desktop …
- 11:16 AM Ticket #8014 (Surface computation: cannot convert float NaN to integer) closed by
- nonchimerax: Probable bad PDB file with NaN atom coordinates. User opened a file …
- 11:14 AM Ticket #8030 (PDB file reader accepts "nan" coordinates without warning) created by
- A few times we have seen users open PDB files which have coordinates …
- 10:58 AM Ticket #8011 (Movie encoding: No space left on device) closed by
- nonchimerax: Making a spin movie of 180 frames, temp directory had no disk space. …
- 10:52 AM Ticket #8029 (non-standard C-terminal oxygen name) created by
- […] 3ZG6-SIRT6.pdb
- 10:48 AM Ticket #8007 (Picking: Singular matrix) closed by
- nonchimerax: Opened 7ud4.pdb then "sym #1 biomt" then mouse over causes an error …
- 10:33 AM Ticket #8028 (microheterogeneity) created by
- […] 4gfh.pdb
- 10:29 AM Ticket #8027 (Add "save image" context menu entry for AlphaFold PAE plots) closed by
- fixed: Added to daily build, not in 1.5.
- 10:27 AM Ticket #8027 (Add "save image" context menu entry for AlphaFold PAE plots) created by
- […]
- 10:19 AM Ticket #8018 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 10:09 AM Ticket #8026 (sqm failure on all-nonstandard nucleic acid) created by
- […]
- 9:44 AM Ticket #8008 (ISOLDE: dead Structure model) closed by
- fixed: ... what. Why on earth would a user be installing ISOLDE into ChimeraX …
- 9:42 AM Ticket #8012 (Crash using File→Save on Windows and/or in return statement) closed by
- can't reproduce: Hi Andrew, We believe this problem is fixed in the latest release of …
- 9:35 AM Ticket #8009 (ISOLDE: dead Structure model) closed by
- duplicate: Same as #8008, except additional follow-on errors.
- 9:26 AM Ticket #8025 (Small molecule CIF) created by
- […] 168875.cif
- 9:22 AM Ticket #8003 (Crash adjusting window sizes) closed by
- can't reproduce: Hi Chai, Thanks for reporting this problem. From the code traceback, …
- 9:21 AM Ticket #8024 (PubChem: #charges != #atoms) created by
- […]
- 9:11 AM Ticket #8023 (All white coulombic) created by
- […] NTD_CCD_CTD_pymol_1-coot-0_modified.pdb
- 9:06 AM Ticket #8022 (Bad residue names from Mol2 file) created by
- […] CCR5.mol2
- 9:01 AM Ticket #8021 (Coulombic all white) created by
- […] dyn1_dimer.pdb
- 8:46 AM Ticket #8020 (Encode movie: Output directory does not exist) created by
- […]
- 7:15 AM Ticket #8019 (Bad alternate locations) created by
- […] out_15898.pdb
- 4:46 AM Ticket #8018 (Crash showing Rapid Access at startup) created by
- […]
- 4:12 AM Ticket #8017 (Clipper: Spgr_descr: No such HM symbol) created by
- […]
- 4:12 AM Ticket #8016 (Clipper: Unrecognised space group string (empty string)) created by
- […]
Nov 13, 2022:
- 2:58 PM Ticket #8015 ('DICOMBrowserTool' object has no attribute '_see_what_happened') created by
- […]
- 10:22 AM Ticket #8014 (Surface computation: cannot convert float NaN to integer) created by
- […]
Nov 12, 2022:
- 2:59 PM Ticket #8013 (Compare alphafold database structure conformations for all sequences ...) created by
- It might be informative to see the different conformations AlphaFold …
- 1:25 PM Ticket #8012 (Crash using File→Save on Windows and/or in return statement) created by
- […]
- 11:46 AM Ticket #8011 (Movie encoding: No space left on device) created by
- […]
- 8:23 AM Ticket #8010 (Image stack:tuple index out of range) created by
- […]
- 1:07 AM Ticket #8009 (ISOLDE: dead Structure model) created by
- […]
- 1:06 AM Ticket #8008 (ISOLDE: dead Structure model) created by
- […]
Nov 11, 2022:
- 5:47 PM Ticket #7725 (Update to AlphaFold database version 4) closed by
- fixed: Fixed in 1.5 and daily build. I've updated the alphafold and …
- 5:28 PM ChangeLog edited by
- (diff)
- 5:27 PM ChangeLog edited by
- (diff)
- 5:19 PM ChangeLog edited by
- (diff)
- 2:36 PM Ticket #8007 (Picking: Singular matrix) created by
- […]
- 1:51 PM Ticket #8006 (Improve granularity of webservice poll timing) created by
- We use client-side polling to determine when webservice jobs are …
- 12:58 PM Ticket #7984 (Segger: Color array dimension 3 must be one more than index array ...) closed by
- fixed
- 12:50 AM Ticket #7976 (Toolshed upload internal server error) closed by
- fixed: I put a fix in, please try uploading again and confirm that it works. …
Nov 10, 2022:
- 6:29 PM 2022-11-10 edited by
- (diff)
- 6:25 PM Ticket #8005 (Make a mouse mode to extract non-axis aligned volume subregions) created by
- For extracting features from electron tomograms it is useful to drag a …
- 6:16 PM NIAID2022 edited by
- (diff)
- 6:15 PM NIAID2022 edited by
- (diff)
- 6:07 PM Ticket #7989 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 5:43 PM Ticket #8004 (ChimeraX sometimes very slow to start) created by
- ChimeraX sometimes takes 30 seconds to a minute to startup. We should …
- 5:38 PM Ticket #8003 (Crash adjusting window sizes) created by
- […]
- 5:30 PM Ticket #7801 (Out of memory opening 7f1q) closed by
- can't reproduce
- 5:08 PM Ticket #8002 (Blast error searching Alphafold database version 4) closed by
- duplicate
- 5:07 PM Ticket #8002 (Blast error searching Alphafold database version 4) reopened by
- 5:05 PM Ticket #8002 (Blast error searching Alphafold database version 4) closed by
- duplicate: Testing alphafold database version 4 blast search for ticket #7725. …
- 4:45 PM Ticket #8002 (Blast error searching Alphafold database version 4) created by
- […]
- 3:22 PM Ticket #7988 (chimerax.add_charge.settings missing) closed by
- fixed: Yay!
- 3:19 PM Ticket #8001 (H-bonds: More than 2 coplanar positions specified) closed by
- not a bug: Hi Phil, It looks like several residues are missing alternate …
- 3:05 PM Ticket #8000 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 3:03 PM Ticket #7998 (Crash in event loop after "select") closed by
- can't reproduce
- 2:31 PM Ticket #7991 (Crash in event loop) closed by
- can't reproduce
- 2:22 PM Ticket #8001 (H-bonds: More than 2 coplanar positions specified) created by
- […] out_15898.pdb
- 1:55 PM NIAID2022 edited by
- (diff)
- 1:44 PM NIAID2022 edited by
- (diff)
- 12:59 PM Ticket #7990 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 12:47 PM 2022-11-10 edited by
- (diff)
- 11:23 AM Ticket #8000 (Crash showing Rapid Access at startup) created by
- […]
- 10:56 AM Ticket #7999 (Marker operations don't work through transparent surfaces) created by
- […]
- 10:39 AM Ticket #7998 (Crash in event loop after "select") created by
- […]
- 9:02 AM Ticket #7997 (Add Charges: Nonstandard name for heavy atom) created by
- […]
- 8:36 AM Ticket #7987 (Crash in event loop) closed by
- can't reproduce
- 7:48 AM Ticket #7996 (Rebuild residue to template: template problem) created by
- […]
- 7:15 AM Ticket #7995 (Crash in color chooser) created by
- […]
- 7:10 AM Ticket #7994 (Crash in color chooser) created by
- […]
- 4:42 AM Ticket #7993 (Mesa-Utils package required) created by
- […]
- 4:36 AM Ticket #7992 (Modeller target is None) created by
- […]
- 4:01 AM Ticket #7991 (Crash in event loop) created by
- […]
Nov 9, 2022:
- 6:51 PM Ticket #7990 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 3:55 PM ChangeLog edited by
- (diff)
- 2:01 PM Ticket #7989 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) created by
- […]
- 1:08 PM Ticket #7982 (Cannot upload bundle) closed by
- fixed: New apache configuration had limit of default limit of 12.5Mbytes. …
- 12:55 PM Ticket #7988 (chimerax.add_charge.settings missing) created by
- […]
- 11:35 AM Ticket #6593 (CentOS 7 daily build still Qt5) closed by
- fixed: No longer building for CentOS 7.
- 11:12 AM Ticket #7981 (devel install failure) closed by
- fixed: Fixed. The current Mac universal build release candidate on the …
- 11:09 AM Ticket #7987 (Crash in event loop) created by
- […]
- 10:42 AM Ticket #7985 (Graphics crash, macOS 13.0, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:19 AM Ticket #7986 (Make side view clip plane lines thicker) created by
- […] […] […]
- 10:03 AM Ticket #7979 (Graphics crash, macOS 11.6, Intel Iris Plus Graphics 655) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:00 AM Ticket #7983 (open PDB file: 'utf-8' codec can't decode byte) closed by
- can't reproduce: Would need the PDB file to assess whether this has already been fixed …
- 8:44 AM Ticket #7985 (Graphics crash, macOS 13.0, Intel Iris Plus Graphics 645) created by
- […]
- 8:39 AM Ticket #7984 (Segger: Color array dimension 3 must be one more than index array ...) created by
- […]
- 7:29 AM Ticket #7983 (open PDB file: 'utf-8' codec can't decode byte) created by
- […]
- 1:59 AM Ticket #7982 (Cannot upload bundle) created by
- […]
- 1:21 AM Ticket #7981 (devel install failure) created by
- […]
Nov 8, 2022:
- 11:52 PM Ticket #7959 (WSL2: Attempt to retrieve context when no valid context) closed by
- nonchimerax: Glad to hear it was an OpenGL bug and it was fixed by updating mesa. …
- 1:53 PM Ticket #7980 (Unknown crash) created by
- […]
- 1:28 PM Ticket #7979 (Graphics crash, macOS 11.6, Intel Iris Plus Graphics 655) created by
- […]
- 11:39 AM Ticket #7978 (ISOLDE monkey patch for alphafold sequence search gives obsolete warning) closed by
- fixed: Fixed in next ISOLDE release.
- 11:20 AM Ticket #7978 (ISOLDE monkey patch for alphafold sequence search gives obsolete warning) created by
- […]
- 10:51 AM Ticket #7977 (DICOM: SEG models not aligned with CT 4) created by
- In the RIDER lung example for one patient (data …
- 10:44 AM Ticket #7222 (Make universal Intel/ARM Mac distribution) closed by
- fixed: Done. Mac universal builds have been on the download page about a month.
- 10:10 AM 2022-11-10 created by
- 10:07 AM 2022-11-3 edited by
- (diff)
- 10:06 AM DeveloperMeetings edited by
- (diff)
- 9:04 AM Ticket #7975 (Restore new session in old ChimeraX) closed by
- limitation: Hi Anja, ChimeraX sessions are guaranteed to restore in the same …
- 9:00 AM Ticket #7974 (Non alphanumeric atom names) closed by
- limitation: Hi Yunhao, Since the atom-specifier syntax uses a lot of …
- 8:43 AM Ticket #7972 (Crash in QDockWidget::event) closed by
- can't reproduce: No Python traceback
- 8:41 AM Ticket #7976 (Toolshed upload internal server error) created by
- […] upload2.jpg upload1.jpg
- 2:09 AM Ticket #7975 (Restore new session in old ChimeraX) created by
- […]
- 12:09 AM Ticket #7896 (DICOM: volume models not assigned unique colors) closed by
- fixed: Fixed on develop and in the 1.5 release candidate …
- 12:07 AM Ticket #7965 (Usage: arg_type is str) closed by
- limitation: It is the "measure composite"'s palette argument on line 267 of …
Nov 7, 2022:
- 8:39 PM Ticket #7974 (Non alphanumeric atom names) created by
- […]
- 5:28 PM Ticket #7966 (Update EMDB fetch to not use deprecated ftp protocol.) closed by
- fixed: Fixed in 1.5 and daily build. Made wwpdb fetches use https by default …
- 4:12 PM Ticket #7973 (Update Blast tool to use version 3 of AlphaFold database) closed by
- fixed: Fixed in 1.5 and daily build. Updated blast gui to use alphafold …
- 3:44 PM Ticket #7973 (Update Blast tool to use version 3 of AlphaFold database) created by
- […]
- 3:19 PM Ticket #7972 (Crash in QDockWidget::event) created by
- […]
- 3:14 PM Ticket #7962 (split submodels not hiding) closed by
- fixed: I couldn't think of a case where overlapping atom specifications seems …
- 3:06 PM Ticket #7574 (Choose next tool for Phenix ChimeraX user interface) closed by
- fixed: Chose Randy's new EMPlacement method
- 2:53 PM Ticket #7971 (sym command with t,z3 symmetry gives an error) closed by
- fixed: Fixed in 1.5 and daily build. Tetrahedral symmetry with z3 …
- 2:45 PM Ticket #7971 (sym command with t,z3 symmetry gives an error) created by
- […]
- 1:35 PM Ticket #7960 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by
- nonchimerax: ChimeraX is not able to show graphics because you have a bad graphics …
- 1:20 PM Ticket #7970 (Allow running ESMFold structure prediction and kmer and blast search ...) created by
- Twitter comment …
- 1:17 PM Ticket #7969 (Crash in QDockWidget::event) closed by
- can't reproduce: No Python stack trace
- 1:08 PM Ticket #7964 (Crash in event loop after ISOLDE sim start) closed by
- can't reproduce
- 12:36 PM Ticket #7946 (partially initialized module 'jax._src.device_array' has no attribute ...) closed by
- nonchimerax: This looks like an attempt to fix #7945 where an AlphaFold .pkl file …
- 12:30 PM Ticket #7969 (Crash in QDockWidget::event) created by
- […]
- 12:23 PM Ticket #7857 (OpenMM binary compatibility) closed by
- fixed: Tristan confirms that the new OpenMM is working with ISOLDE (comment …
- 12:22 PM Ticket #7968 (Try OpenMM 8.0 in daily builds) created by
- Tristan provided an OpenMM 8.0 beta builds we could try in the daily …
- 12:18 PM Ticket #7967 (Ubuntu 22 ChimeraX installer is replacing symlinks by copies of libraries) created by
- Tristan notes that the ChimeraX Ubuntu 22 installer is copying …
- 12:11 PM Ticket #7966 (Update EMDB fetch to not use deprecated ftp protocol.) created by
- ChimeraX EMDB fetch is using these URLs which will be deprecated in …
- 11:47 AM Ticket #7965 (Usage: arg_type is str) created by
- […]
- 11:38 AM Ticket #7964 (Crash in event loop after ISOLDE sim start) created by
- […]
- 11:17 AM Ticket #7963 (toolshed install with no arguments gives traceback) created by
- […]
- 11:14 AM Ticket #7962 (split submodels not hiding) created by
- I am mystified as to why after using this splitting example open …
- 10:37 AM Ticket #7935 (Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash. I have reproduced these Mac Intel …
- 9:00 AM Ticket #7958 (Crash using color chooser) closed by
- can't reproduce
- 8:58 AM Ticket #7956 (Session save: function 'set_pbgroup_py_instance' not found) closed by
- duplicate
- 8:54 AM Ticket #7957 (Crash using the color chooser: illegal backingScaleFactor) closed by
- can't reproduce
- 8:51 AM Ticket #7955 (Crash in QMainWindow::removeDockWidget) closed by
- can't reproduce: No Python stack trace
- 8:49 AM Ticket #7954 (Crash using the color chooser) closed by
- can't reproduce
- 8:47 AM Ticket #7953 (Restore new session in old ChimeraX) closed by
- not a bug
- 8:44 AM Ticket #7951 (Crash in QFileDialog.getOpenFileNames()) closed by
- can't reproduce
- 8:41 AM Ticket #7950 (Crash in event loop at startup) closed by
- can't reproduce
- 8:38 AM Ticket #7949 (Restore new session in old ChimeraX) closed by
- not a bug: Hi Karolin, Whereas sessions saved in old versions of ChimeraX are …
- 8:24 AM Ticket #7961 (Clipper fails to build in Windows - Nov 3 release candidate) created by
- Installed the Nov 3 release candidate and attempted to rebuild …
- 8:16 AM Ticket #7960 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by
- […]
- 3:42 AM Ticket #7959 (WSL2: Attempt to retrieve context when no valid context) created by
- […]
Nov 6, 2022:
- 7:50 PM Ticket #7958 (Crash using color chooser) created by
- […]
- 1:55 PM Ticket #7957 (Crash using the color chooser: illegal backingScaleFactor) created by
- […]
- 4:35 AM Ticket #7956 (Session save: function 'set_pbgroup_py_instance' not found) created by
- […]
- 2:52 AM Ticket #7955 (Crash in QMainWindow::removeDockWidget) created by
- […]
Nov 5, 2022:
- 3:50 PM Ticket #7954 (Crash using the color chooser) created by
- […]
- 12:33 PM Ticket #7953 (Restore new session in old ChimeraX) created by
- […]
- 2:53 AM Ticket #7952 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Nov 4, 2022:
- 4:38 PM Ticket #7951 (Crash in QFileDialog.getOpenFileNames()) created by
- […]
- 3:58 PM Ticket #7948 (Restore session: LZ4F_decompress failed with code: ERROR_frameType_unknown) closed by
- limitation: Where was that error reported? I searched for "but it was too large" …
- 2:34 PM Ticket #7950 (Crash in event loop at startup) created by
- […]
- 12:36 PM Ticket #7949 (Restore new session in old ChimeraX) created by
- […]
- 11:52 AM Ticket #7947 (Restore session: LZ4F_decompress failed with code: ERROR_frameType_unknown) closed by
- can't reproduce: Would need the session file to investigate this.
- 7:46 AM Ticket #7944 (CUDA_ERROR_UNSUPPORTED_PTX_VERSION) closed by
- duplicate: Ugh... only just noticed it was an anonymous report.
- 4:12 AM Ticket #7948 (Restore session: LZ4F_decompress failed with code: ERROR_frameType_unknown) created by
- […] 西æ¹å€§åŠ-æœäžå ¬å¢é-å±åæš¡å.cxs
- 3:33 AM Ticket #7947 (Restore session: LZ4F_decompress failed with code: ERROR_frameType_unknown) created by
- […]
- 2:12 AM Ticket #7946 (partially initialized module 'jax._src.device_array' has no attribute ...) created by
- […]
- 1:41 AM Ticket #7945 (Read PAE matrix: No module named 'jax') created by
- […]
- 12:53 AM Ticket #7944 (CUDA_ERROR_UNSUPPORTED_PTX_VERSION) created by
- […]
Nov 3, 2022:
- 5:14 PM Ticket #7943 (Document how user puts ChimeraX icon on desktop) created by
- How to install the ChimeraX icon on the desktop is poorly documented. …
- 4:34 PM Ticket #7824 (Toolshed install of wiggle wheel file error installing dependencies) closed by
- fixed: It turns out that a recursive call to sys.executable by pip sometimes …
- 3:53 PM Ticket #7940 (MemoryError saving session) closed by
- limitation: Probably a huge volume. Try a newer ChimeraX.
- 3:28 PM Ticket #7942 (MemoryError saving session) closed by
- duplicate
- 3:28 PM Ticket #7941 (MemoryError saving session) closed by
- duplicate
- 3:25 PM Ticket #7939 (Modeller: Invalid license key) closed by
- not a bug: Dear Dr. Tang, In order to use the Model Loops tool, you need to …
- 3:19 PM Ticket #7938 (Restore new session in old ChimeraX) closed by
- not a bug: Hi Nitesh, Sessions saved in old versions of ChimeraX are guaranteed …
- 3:15 PM Ticket #7937 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 10:58 AM phenix-11-3-22 edited by
- (diff)
- 10:58 AM phenix-11-3-22 created by
- 10:46 AM Features edited by
- (diff)
- 7:38 AM Ticket #7942 (MemoryError saving session) created by
- […]
- 7:36 AM Ticket #7941 (MemoryError saving session) created by
- […]
- 7:36 AM Ticket #7940 (MemoryError saving session) created by
- […]
- 4:47 AM Ticket #7939 (Modeller: Invalid license key) created by
- […]
Nov 2, 2022:
- 6:35 PM Ticket #7938 (Restore new session in old ChimeraX) created by
- […]
- 5:52 PM Ticket #7674 (Report sqm.out; try to make quotes "reusable") closed by
- fixed: The contents of sqm.out are now also dumped on an antechamber failure …
- 5:25 PM Ticket #7937 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 2:10 PM Ticket #7936 (ResidueStepper refers to dead Structure) created by
- […]
- 1:26 PM Ticket #7934 (Crash after opening session) closed by
- can't reproduce
- 1:25 PM Ticket #7933 (Crash using the color chooser) closed by
- nonchimerax
- 1:20 PM Ticket #7932 (Crash in QDockWidget::event) closed by
- can't reproduce: Hi James, Thanks for reporting this problem. The information in the …
- 11:45 AM Ticket #7935 (Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645) created by
- […]
- 5:23 AM Ticket #7934 (Crash after opening session) created by
- […]
Nov 1, 2022:
- 2:05 PM Ticket #7933 (Crash using the color chooser) created by
- […]
- 1:35 PM Ticket #7897 (Hanging 6B1T) closed by
- fixed: Fixes for other similar structures has cut down the execution time …
- 11:58 AM Ticket #7898 (FW: Hanging QS PDB 6CGV) closed by
- fixed: Put "enclose #1" into the blob presets' surface command. Will send …
- 11:19 AM Ticket #7918 (MemoryError saving session) closed by
- worksforme: Try a newer version of ChimeraX.
- 10:58 AM Ticket #7932 (Crash in QDockWidget::event) created by
- […]
- 9:34 AM Ticket #7929 (Crash coloring volume, Intel Mac, no C++ stack trace) closed by
- can't reproduce: Possible Intel graphics driver crash. No stack symbols, so nothing to …
- 9:28 AM 2022-11-3 created by
- 9:25 AM DeveloperMeetings edited by
- (diff)
- 8:47 AM Ticket #7930 (Crash in event loop) closed by
- can't reproduce
Oct 31, 2022:
- 11:12 PM Ticket #7931 (Port topography command from Chimera to ChimeraX) closed by
- fixed: Done. The topography command is mostly the same as in Chimera with …
- 11:05 PM Ticket #7931 (Port topography command from Chimera to ChimeraX) created by
- The topography command might be useful for visualization atomic force …
- 10:40 PM Ticket #7930 (Crash in event loop) created by
- […]
- 4:53 PM Ticket #7929 (Crash coloring volume, Intel Mac, no C++ stack trace) created by
- […]
- 4:14 PM Ticket #7170 (Session restore: decompression failure) closed by
- fixed: The fix is finally in.
- 4:09 PM Ticket #7900 (4v4u.cif hangs then fails) closed by
- fixed: Due to the changes in #7901, operations on this structure now finish …
- 3:17 PM Ticket #5866 (Registration time-format error) closed by
- fixed: Fixed on 22 July 2022.
- 3:17 PM Ticket #7595 (Registration code: ValueError: tuple.index(x): x not in tuple) closed by
- duplicate: #5866
- 3:16 PM Ticket #6580 (Registration time-format error) closed by
- duplicate: #5866
- 1:47 PM Ticket #7917 (Cannot access Downloads folder) closed by
- fixed: daily build only
- 1:15 PM Ticket #7901 (PDB QS 2CSE) closed by
- fixed: In addition to using the faster "surface" command for large …
- 11:22 AM Ticket #7926 (glClear: invalid framebuffer operation) closed by
- nonchimerax: ChimeraX does not start because the Qt window toolkit fails to create …
- 11:08 AM Ticket #7911 (Crash saving image) closed by
- duplicate: Duplicate of #7910. Same reporter, same crash.
- 11:06 AM Ticket #7910 (Crash saving large image) closed by
- duplicate: This crash has been reported about 7 times in the past 2 months, …
- 10:08 AM Ticket #7928 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 10:08 AM ChangeLog edited by
- (diff)
- 10:04 AM Ticket #7927 (Unknown crash) closed by
- can't reproduce
- 9:56 AM Ticket #7924 (Crash in QMainWindow::removeDockWidget) closed by
- can't reproduce
- 9:50 AM Ticket #7928 (Crash showing Rapid Access at startup) created by
- […]
- 9:47 AM Ticket #7922 (Read PDB file: 'utf-8' codec can't decode byte) closed by
- can't reproduce
- 9:45 AM Ticket #7921 (Read PDB file: 'utf-8' codec can't decode byte) closed by
- can't reproduce
- 9:43 AM Ticket #7920 (MemoryError saving session) closed by
- duplicate: duplicate of #7918
- 9:41 AM Ticket #7919 (MemoryError saving session) closed by
- duplicate: duplicate of #7918
- 9:20 AM Ticket #7913 (Crash in event loop) closed by
- can't reproduce
- 9:19 AM Ticket #7912 (Get version info: lookup failure) closed by
- nonchimerax
- 9:10 AM Ticket #7909 (Crash in event loop) closed by
- can't reproduce
- 9:09 AM Ticket #7908 (Crash in event loop) closed by
- can't reproduce
- 9:06 AM Ticket #7902 (Crash destroying tool during garbage collection) closed by
- can't reproduce
- 8:53 AM Ticket #7927 (Unknown crash) created by
- […]
- 5:14 AM Ticket #7926 (glClear: invalid framebuffer operation) created by
- […]
Oct 30, 2022:
- 7:58 AM Ticket #7925 (DICOM Browser: bundle forgot to override start_tool method) created by
- […]
- 12:08 AM Ticket #7924 (Crash in QMainWindow::removeDockWidget) created by
- […]
Oct 29, 2022:
- 12:36 PM Ticket #7923 (Read PDB file: 'utf-8' codec can't decode byte) created by
- […]
- 12:31 PM Ticket #7922 (Read PDB file: 'utf-8' codec can't decode byte) created by
- […]
- 12:30 PM Ticket #7921 (Read PDB file: 'utf-8' codec can't decode byte) created by
- […]
- 5:30 AM Ticket #7920 (MemoryError saving session) created by
- […]
- 5:27 AM Ticket #7919 (MemoryError saving session) created by
- […]
- 5:27 AM Ticket #7918 (MemoryError saving session) created by
- […]
- 2:27 AM Ticket #7917 (Cannot access Downloads folder) created by
- […]
Oct 28, 2022:
- 4:43 PM Ticket #7916 (openmm.OpenMMException: There is no registered Platform called "CPU") closed by
- not a bug: False alarm. I got this error after I did a test import of openmm …
- 4:15 PM Ticket #7915 (New OpenMM 7.7 on Linux import error) closed by
- fixed: Ok, so this problem importing OpenMM is solved with chrpath. But then …
- 4:08 PM Ticket #7916 (openmm.OpenMMException: There is no registered Platform called "CPU") created by
- The new OpenMM 7.7.0 for Linux provided by Tristan in #7857 apparently …
- 2:39 PM Ticket #7915 (New OpenMM 7.7 on Linux import error) created by
- […]
- 2:21 PM Ticket #7914 (Document Linux compilation system prerequisites such as sqlite to get ...) created by
- […]
- 10:49 AM Ticket #7903 (Info from sym command) closed by
- fixed: Done. Examples of messages logged: […]
- 9:46 AM Ticket #7913 (Crash in event loop) created by
- […]
- 6:59 AM Ticket #7912 (Get version info: lookup failure) created by
- […]
- 6:49 AM Ticket #7911 (Crash saving image) created by
- […]
- 6:48 AM Ticket #7910 (Crash saving large image) created by
- […]
- 3:46 AM Ticket #7909 (Crash in event loop) created by
- […]
- 3:17 AM Ticket #7908 (Crash in event loop) created by
- […]
Oct 27, 2022:
- 8:20 PM Ticket #7907 (Allow Collada scene export) created by
- Kristen said at today's NIAID / ChimeraX meeting that in addition to …
- 8:15 PM NIAID2022 edited by
- (diff)
- 7:45 PM 2022-10-27 edited by
- (diff)
- 7:34 PM Ticket #7905 (Bus Error computing surface of 2cse biological assembly) closed by
- limitation: I duplicated this crash and reported in #7906. It is using 69 Gbytes …
- 7:20 PM Ticket #7906 (Crash making SES surface for 1 million atom 2cse virus) closed by
- duplicate
- 7:14 PM Ticket #7906 (Crash making SES surface for 1 million atom 2cse virus) created by
- […] ChimeraX-2022-10-27-190959.ips
- 6:49 PM Ticket #7895 (Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 6:25 PM Ticket #7905 (Bus Error computing surface of 2cse biological assembly) created by
- […]
- 5:57 PM Ticket #7882 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by
- fixed: Fix will be in tomorrow's release candidate and daily build. Fix: …
- 4:16 PM Ticket #7748 (Cloud documentation) closed by
- fixed: https://chimerax.readthedocs.io/en/latest/
- 4:11 PM Ticket #7858 (pip command puts packages in ~/Library/Python and not ...) closed by
- fixed: Fixed in …
- 3:55 PM Ticket #7904 (RCSB biological unit: PDBx/mmCIF styling lost) created by
- Opening the attached biological unit downloaded from the RCSB results …
- 3:15 PM Ticket #7903 (Info from sym command) created by
- It would be useful if the sym command reported how many copies it …
- 3:09 PM Ticket #7381 (ISOLDE GUI startup: __init__() got an unexpected keyword argument ...) closed by
- fixed: See https://peps.python.org/pep-0440/#compatible-release. …
- 3:00 PM Ticket #7830 (Can't install ChimeraX 1.5 on Ubuntu 22) closed by
- fixed: This is fixed. And is in the daily builds since October 21st.
- 2:37 PM Ticket #7902 (Crash destroying tool during garbage collection) created by
- […]
- 2:20 PM Ticket #7810 (UNK residues that should not be UNK) closed by
- nonchimerax: The RCSB will be releasing a corrected version of 3j5q next week..
- 2:19 PM Ticket #7888 (Grouping model hidden) closed by
- fixed: The fixed bundle is on the Toolshed now. Will mail the wheel separately.
- 2:10 PM NIAID2022 edited by
- (diff)
- 2:06 PM Ticket #7901 (PDB QS 2CSE) created by
- […] logs (10).txt
- 2:05 PM Ticket #7900 (4v4u.cif hangs then fails) created by
- […] logs (9).txt 4v4u.cif
- 2:02 PM Ticket #7899 (FW: Hanging on PDB file) created by
- […] 1fvm-monomer-blue.pdb logs (8).txt
- 2:02 PM Ticket #7898 (FW: Hanging QS PDB 6CGV) created by
- […] logs (7).txt
- 1:33 PM Ticket #7897 (Hanging 6B1T) created by
- […] logs (6).txt
- 1:32 PM NIAID2022 edited by
- (diff)
- 1:30 PM NIAID2022 edited by
- (diff)
- 12:54 PM Ticket #7896 (DICOM: volume models not assigned unique colors) created by
- If you open a DICOM folder with more than one series, they are all …
- 12:10 PM Dev2022-10-27 edited by
- (diff)
- 11:24 AM Dev2022-10-27 edited by
- (diff)
- 11:22 AM Ticket #7895 (Graphics crash, macOS 12.6, Intel Iris Plus Graphics 645) created by
- […]
- 11:07 AM Dev2022-10-27 created by
- 11:05 AM DeveloperMeetings edited by
- (diff)
- 11:02 AM Ticket #7889 (Error for render involving missing attrs) closed by
- fixed: Wasn't handling structures where the attribute was missing correctly.
- 10:23 AM Ticket #7894 (Probable hang on Linux) closed by
- can't reproduce
- 10:21 AM Ticket #7893 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 10:20 AM Ticket #7892 (Negative decimal places for distance format) closed by
- duplicate: Duplicate #7881
- 6:57 AM Ticket #7894 (Probable hang on Linux) created by
- […]
- 4:26 AM Ticket #7893 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
Oct 26, 2022:
- 6:54 PM Ticket #7884 (CIF file: atom_site category: Missing column 'label_asym_id) closed by
- limitation: This is a limitation. Added a warning saying small-molecule CIF files …
- 5:17 PM Ticket #7892 (Negative decimal places for distance format) created by
- […]
- 5:09 PM Ticket #7891 (hide/show slow with many structures) created by
- Using the 14,000 structure Mol2 file attached to ticket #7890 and with …
- 5:06 PM Ticket #7890 (Slow Mol2 reading) created by
- Reading the attached 14,000 structure Mol2 file takes >6 minutes on my …
- 4:45 PM Ticket #7889 (Error for render involving missing attrs) created by
- […] 3models.cxs
- 2:14 PM Ticket #7888 (Grouping model hidden) created by
- […]
- 1:25 PM Ticket #7887 (ViewDockX error reading mol2 file: KeyError: None) closed by
- fixed: Fixed in next daily build and 1.5 release candidate: …
- 12:09 PM Ticket #7887 (ViewDockX error reading mol2 file: KeyError: None) created by
- […] AcCAA.mol2
- 11:48 AM Ticket #7886 (Optional PDB fields) created by
- Have optional/variant PDB fields like segment ID, formal charge, etc. …
- 11:42 AM Ticket #7885 (unwanted whole-chain selection) created by
- […]
- 11:17 AM Ticket #7884 (CIF file: atom_site category: Missing column 'label_asym_id) created by
- […] 9253.cif
- 10:56 AM Ticket #7877 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:52 AM Ticket #7871 (Graphics crash, macOS 11.4, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:03 AM Ticket #7883 (Saving various files: No space left on device) closed by
- nonchimerax: In current versions of ChimeraX, this will be a UserError
- 9:23 AM Ticket #7881 (Negative decimal places for distance format) closed by
- can't reproduce: If negative decimal places was indeed the problem, I don't know how …
- 9:09 AM Ticket #7880 (No error reported) closed by
- invalid
- 9:08 AM Ticket #7879 (Permission Denied saving MRC file) closed by
- fixed: In current versions, this is a UserError.
- 9:01 AM Ticket #7876 (Crash destroying Qt widget during garbage collection) closed by
- can't reproduce: Seems to be correlated with using XMAS
- 5:08 AM Ticket #7883 (Saving various files: No space left on device) created by
- […]
- 2:43 AM Ticket #7882 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
- 2:25 AM Ticket #7881 (Negative decimal places for distance format) created by
- […]
- 12:24 AM Ticket #7880 (No error reported) created by
- […]
Oct 25, 2022:
- 8:32 PM Ticket #7879 (Permission Denied saving MRC file) created by
- […]
- 6:11 PM Ticket #5366 (Volume contour level for NIH 3D printable surface) closed by
- fixed
- 6:11 PM Ticket #5366 (Volume contour level for NIH 3D printable surface) reopened by
- 5:59 PM Ticket #5366 (Volume contour level for NIH 3D printable surface) closed by
- fixed: The current code detects if the threshold level hides two much of the …
- 5:34 PM Ticket #7863 (Histogram: super(type, obj): obj must be an instance or subtype of type) closed by
- fixed
- 4:46 PM Ticket #7878 ('show' unexpectedly showing whole chains) created by
- […]
- 4:28 PM Ticket #7877 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) created by
- […]
- 4:24 PM ChangeLog edited by
- (diff)
- 4:23 PM ChangeLog edited by
- (diff)
- 4:22 PM ChangeLog edited by
- (diff)
- 2:56 PM Ticket #7876 (Crash destroying Qt widget during garbage collection) created by
- […]
- 2:31 PM Ticket #7875 (XMAS: AttributeError: 'Tabular' object has no attribute 'peptide_pairs') created by
- […]
- 2:26 PM Ticket #7715 (DICOM: TypeError: %d format: a number is required, not NoneType) closed by
- fixed: Left out the modality but did reword it to be more concise as in the …
- 2:23 PM Ticket #7860 (Add other bundles' lib dirs to rpaths) closed by
- fixed: I was able to build that bundle after adding the import to pdb_lib. So …
- 2:21 PM Ticket #7874 (Improve ambient shadows with transparent surface) created by
- […] 7rpi_surf.png
- 12:26 PM Ticket #7873 (ISOLDE: wrapped C/C++ object of type WinAutoResizeQComboBox has been ...) created by
- […]
- 11:57 AM Ticket #7872 (Add surface smooth command) closed by
- fixed: Done in ChimeraX daily builds, not in 1.5. Syntax is […] with …
- 11:53 AM Ticket #7872 (Add surface smooth command) created by
- Add the equivalent of the Chimera "sop smooth" command to smooth any …
- 11:27 AM Ticket #7871 (Graphics crash, macOS 11.4, Intel Iris Plus Graphics) created by
- […]
- 11:14 AM Ticket #7870 (Add segmentation surfaces smoothing) closed by
- fixed: Done. Added to ChimeraX 1.5 and daily builds. I added an option …
- 11:06 AM Ticket #7870 (Add segmentation surfaces smoothing) created by
- […]
- 10:10 AM 2022-10-27 created by
- 10:09 AM 2022-10-20 edited by
- (diff)
- 10:08 AM DeveloperMeetings edited by
- (diff)
- 9:12 AM Ticket #7869 (Problem fetching mmCIF template: URL can't contain control characters) closed by
- duplicate: duplicate of #6508
- 9:09 AM Ticket #7868 (Crash in modal dialog exec()) closed by
- can't reproduce
- 9:07 AM Ticket #7867 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Seems to be Linux a lot
- 9:05 AM Ticket #7866 (Crash in event loop after MatchMaker) closed by
- can't reproduce
- 8:55 AM Ticket #7865 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:52 AM Ticket #7864 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 8:49 AM Ticket #7861 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:48 AM Ticket #7859 (Crash in event loop) closed by
- can't reproduce
- 7:15 AM Ticket #7869 (Problem fetching mmCIF template: URL can't contain control characters) created by
- […]
- 3:48 AM Ticket #7868 (Crash in modal dialog exec()) created by
- […]
- 2:49 AM Ticket #7867 (Crash showing Rapid Access at startup) created by
- […]
- 2:11 AM Ticket #7866 (Crash in event loop after MatchMaker) created by
- […]
- 1:48 AM Ticket #7865 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Oct 24, 2022:
- 6:29 PM Ticket #7864 (Crash showing Rapid Access at startup) created by
- […]
- 6:14 PM Ticket #7863 (Histogram: super(type, obj): obj must be an instance or subtype of type) created by
- […]
- 5:14 PM Ticket #7862 (No way to set segmentation colors when coloring image style volume) created by
- […]
- 4:57 PM Ticket #7861 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:51 PM Ticket #7860 (Add other bundles' lib dirs to rpaths) created by
- Trying to install mmcif into a virtual environment for readthedocs, I …
- 4:24 PM Dev2022-10-24 edited by
- (diff)
- 3:23 PM Ticket #7826 (Charge addition problem for FRD) closed by
- fixed: Due to an overzealous optimization, the backbone C of the FRD residue …
- 2:20 PM Ticket #7859 (Crash in event loop) created by
- […]
- 2:10 PM Ticket #7715 (DICOM: TypeError: %d format: a number is required, not NoneType) reopened by
- Mostly fixed but changing warning text as in comments 6 and 7 still to …
- 12:42 PM Ticket #7854 (Error opening ORCA file: KeyError: 'multiplicity') closed by
- fixed
- 12:01 PM Ticket #7728 (chimerax daily logs many errors in nogui mode) closed by
- fixed: I personally don't like imports in functions because in long (>500 …
- 11:47 AM Ticket #7856 (Crash saving PNG) closed by
- can't reproduce: I am not sure why ChimeraX crashed when saving an image. I don't …
- 11:37 AM Ticket #7849 (MPEG conversion failed) closed by
- not a bug: ffmpeg failed due to no disk space av_interleaved_write_frame(): No …
- 11:35 AM Ticket #7858 (pip command puts packages in ~/Library/Python and not ...) created by
- 11:08 AM Ticket #7827 (Hydrogen added to C terminus) closed by
- fixed: Was expecting the OXT to be missing, not the O. Now the code handles …
- 9:39 AM Ticket #7855 (Version conflict opening MTZ file in 1.5) closed by
- duplicate: Sorry about this - due to my misunderstanding of the Python dependency …
- 9:38 AM Ticket #7853 (transparency not working) closed by
- not a bug: Hello Guipeun Kang, Your transparency command is wrong ... should be …
- 9:28 AM Ticket #7852 ('Sequence' object has no attribute 'structure') closed by
- duplicate: Essentially a duplicate of #7851
- 8:59 AM Ticket #7850 (MPEG conversion failed) closed by
- duplicate
- 8:00 AM Ticket #7857 (OpenMM binary compatibility) created by
- […]
- 3:43 AM Ticket #7856 (Crash saving PNG) created by
- […]
- 2:46 AM Ticket #7855 (Version conflict opening MTZ file in 1.5) created by
- […]
Oct 23, 2022:
- 11:36 AM Ticket #7854 (Error opening ORCA file: KeyError: 'multiplicity') created by
- […] test.out
- 11:30 AM Ticket #7853 (transparency not working) created by
- […] [[Image(...)]]
- 7:08 AM Ticket #7852 ('Sequence' object has no attribute 'structure') created by
- […]
- 7:07 AM Ticket #7851 ('Sequence' object has no attribute 'structure') created by
- […]
- 1:52 AM Ticket #7850 (MPEG conversion failed) created by
- […]
- 1:52 AM Ticket #7849 (MPEG conversion failed) created by
- […]
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