id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17132 Crash on Mac waking from sleep halle.andrews-clark@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.0.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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: { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/haandrew/Downloads/fold_2025_03_11_10_31/fold_2025_03_11_10_31_model_0.cif Chain information for fold_2025_03_11_10_31_model_0.cif #1 --- Chain | Description A | . > open /Users/haandrew/Downloads/fold_25s_snd/fold_25s_snd_model_0.cif Chain information for fold_25s_snd_model_0.cif #2 --- Chain | Description A | . B | . > hide #1 models > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > ~hide Unknown command: ~hide > hide ~select Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~sel > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 79532 atoms, 88302 bonds, 4274 residues, 2 models selected > hide (#2 & sel) target a > cartoon hide (#2 & sel) > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /PDB 8BQX.cif"" PDB 8BQX.cif title: Yeast 80S ribosome in complex with Map1 (conformation 2) [more info...] Chain information for PDB 8BQX.cif #3 --- Chain | Description | UniProt 2 | 18S rRNA | A | 40S ribosomal protein S3 | RS3_YEAST 4-225 AA | 60S ribosomal protein L8-A | RL8A_YEAST 24-256 AB | 60S ribosomal protein L23-A | RL23A_YEAST 2-137 AC | 60S ribosomal protein L36-A | RL36A_YEAST 2-100 AD | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 AE | 60S ribosomal protein L24-A | RL24A_YEAST 1-126 AF | 60S ribosomal protein L37-A | RL37A_YEAST 2-82 AG | RPL11B isoform 1 | A0A6A5PYM2_YEASX 6-174 AH | 60S ribosomal protein L25 | RL25_YEAST 22-142 AI | RPL38 isoform 1 | A0A6A5PUL8_YEASX 2-78 AJ | 60S ribosomal protein L13-A | RL13A_YEAST 2-194 AK | 60S ribosomal protein L26-A | RL26A_YEAST 2-126 AL | 60S ribosomal protein L39 | RL39_YEAST 2-51 AM | 60S ribosomal protein L14-A | RL14A_YEAST 3-138 AN | 60S ribosomal protein L27-A | RL27A_YEAST 2-136 AO | 60S ribosomal protein L40-A | RL40A_YEAST 77-128 AP | 60S ribosomal protein L42-A | RL44A_YEAST 2-104 AQ | 60S ribosomal protein L15-A | RL15A_YEAST 2-204 AR | 60S ribosomal protein L28 | RL28_YEAST 2-149 AS | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 AT | 60S ribosomal protein L43-A | RL43A_YEAST 2-92 AU | 60S ribosomal protein L16-A | RL16A_YEAST 3-199 AV | 60S ribosomal protein L29 | A0A6A5PWR1_YEASX 2-59 AW | 60S ribosomal protein L2-A | RL2A_YEAST 2-252 AX | 60S ribosomal protein L17-A | RL17A_YEAST 2-184 AY | 60S ribosomal protein L30 | RL30_YEAST 9-104 B | 40S ribosomal protein S5 | RS5_YEAST 20-225 BA | 60S ribosomal protein L3 | RL3_YEAST 2-387 BB | 60S ribosomal protein L18-A | RL18A_YEAST 2-186 BC | 60S ribosomal protein L31-A | RL31A_YEAST 4-112 BD | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 2-219 BE | 60S ribosomal protein L4-A | RL4A_YEAST 2-362 BF | 60S ribosomal protein L19-A | RL19A_YEAST 2-189 BG | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 2-128 BH | 60S ribosomal protein L20-A | RL20A_YEAST 2-172 BI | 60S ribosomal protein L5 | RL5_YEAST 4-297 BJ | 60S ribosomal protein L21-A | RL21A_YEAST 2-160 BK | 60S ribosomal protein L33-A | RL33A_YEAST 2-107 BL | 60S ribosomal protein L22-A | RL22A_YEAST 9-108 BM | 60S ribosomal protein L6-B | RL6B_YEAST 2-176 BN | 60S ribosomal protein L34-A | RL34A_YEAST 2-113 BO | 60S ribosomal protein L7-A | RL7A_YEAST 23-244 BP | 60S ribosomal protein L35-A | RL35A_YEAST 2-120 BQ | 25S rRNA | BR | 5S rRNA | BS | 5.8S rRNA | BT | 60S ribosomal protein L1-A | RL1A_YEAST 1-217 C | 40S ribosomal protein S10-A | RS10A_YEAST 1-92 D | 40S ribosomal protein S12 | RS12_YEAST 23-143 E | 40S ribosomal protein S15 | RS15_YEAST 1-142 F | 40S ribosomal protein S16-A | RS16A_YEAST 3-143 G | 40S ribosomal protein S17-A | RS17A_YEAST 2-126 H | 40S ribosomal protein S18-A | RS18A_YEAST 2-146 I | 40S ribosomal protein S19-A | RS19A_YEAST 2-144 J | 40S ribosomal protein S20 | RS20_YEAST 20-119 K | 40S ribosomal protein S25-A | RS25A_YEAST 24-105 L | 40S ribosomal protein S28-A | RS28A_YEAST 5-67 M | 40S ribosomal protein S29-A | RS29A_YEAST 4-56 N | 40S ribosomal protein S31 | RS31_YEAST 80-152 O | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 5-316 P | 40S ribosomal protein S0-A | RSSA1_YEAS1 2-207 Q | 40S ribosomal protein S1-A | RS3A1_YEAS1 2-233 R | 40S ribosomal protein S2 | RS2_YEAST 34-249 S | 40S ribosomal protein S4-A | RS4A_YEAST 2-259 T | 40S ribosomal protein S6-A | RS6A_YEAST 1-228 U | 40S ribosomal protein S7-A | RS7A_YEAST 4-187 V | 40S ribosomal protein S8-A | RS8A_YEAST 2-199 W | 40S ribosomal protein S9-A | RS9A_YEAST 2-185 X | 40S ribosomal protein S11-A | RS11A_YEAST 4-145 Y | 40S ribosomal protein S13 | RS13_YEAST 2-151 Z | 40S ribosomal protein S14-B | RS14B_YEAST 11-137 a | 40S ribosomal protein S21-A | RS21A_YEAST 1-87 b | 40S ribosomal protein S22-A | RS22A_YEAST 2-130 c | 40S ribosomal protein S23-A | RS23A_YEAST 2-145 d | 40S ribosomal protein S24-A | RS24A_YEAST 2-135 e | 40S ribosomal protein S26-B | RS26B_YEAST 2-98 f | 40S ribosomal protein S27-A | RS27A_YEAST 2-82 g | 40S ribosomal protein S30-A | RS30A_YEAST 2-61 x | Methionine aminopeptidase 1 | MAP1_YEAST 1-387 Non-standard residues in PDB 8BQX.cif #3 --- ZN — zinc ion 1555 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!3 models > show #!3 models > select add #3 285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models selected > select subtract #3 79532 atoms, 88302 bonds, 4274 residues, 2 models selected > sequence chain #3/BQ Alignment identifier is 3/BQ > select add #3 285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models selected > cartoon (#2#!3 & sel) > hide (#2#!3 & sel) target a > select add #2 292254 atoms, 316312 bonds, 5155 pseudobonds, 22220 residues, 6 models selected > select subtract #2 212723 atoms, 228010 bonds, 5155 pseudobonds, 17947 residues, 5 models selected > select subtract #3 6915 atoms, 7029 bonds, 878 residues, 1 model selected > select subtract #1 Nothing selected > sequence chain #3/BQ Destroying pre-existing alignment with identifier 3/BQ Alignment identifier is 3/BQ > select #3/BQ:3-3396 70586 atoms, 79003 bonds, 3108 pseudobonds, 3301 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_0.cif, chain B (#2), sequence alignment score = 19589.3 RMSD between 2666 pruned atom pairs is 0.915 angstroms; (across all 3301 pairs: 5.800) > ~struts sel > select clear > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select clear > log metadata #3 Metadata for PDB 8BQX.cif #3 --- Title | Yeast 80S ribosome in complex with Map1 (conformation 2) Citation | Knorr, A.G., Mackens-Kiani, T., Musial, J., Berninghausen, O., Becker, T., Beatrix, B., Beckmann, R. (2023). The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains. Plos Biol., 21, e3001995-e3001995. PMID: 37079644. DOI: 10.1371/journal.pbio.3001995 Non-standard residue | ZN — zinc ion Sources (natural) | Saccharomyces cerevisiae Saccharomyces cerevisiae (baker's yeast) CryoEM Map | EMDB 16191 — open map Experimental method | Electron microscopy Resolution | 3.8Å > select add #3 205808 atoms, 220981 bonds, 5155 pseudobonds, 17069 residues, 4 models selected > color (#!3 & sel) gray > select subtract #3 Nothing selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models selected > hide (#2#!3 & sel) target a > cartoon hide (#2#!3 & sel) > cartoon (#2#!3 & sel) > ~struts sel > select clear > hide #!3 models > select #2/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #2/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 285340 atoms, 309283 bonds, 5155 pseudobonds, 21343 residues, 6 models selected > cartoon hide (#2 & sel) > show #!3 models > select ~ sel 6914 atoms, 7029 bonds, 877 residues, 1 model selected > ~struts sel > select clear > save /Users/haandrew/Desktop/image24.png supersample 3 > movie record > turn y 2 180 > wait 180 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/movie.py"", line 176, in capture_image i.save(save_path, self.img_fmt) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/PIL/Image.py"", line 2459, in save save_handler(self, fp, filename) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/PIL/PpmImagePlugin.py"", line 356, in _save ImageFile._save(im, fp, [(""raw"", (0, 0) + im.size, 0, (rawmode, 0, row_order))]) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/PIL/ImageFile.py"", line 538, in _save _encode_tile(im, fp, tile, bufsize, fh) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/PIL/ImageFile.py"", line 565, in _encode_tile errcode = encoder.encode_to_file(fh, bufsize) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ OSError: [Errno 28] No space left on device Out of disk space > movie encode /Users/haandrew/Desktop/movie2.mp4 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 351, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 456, in add self._history.enqueue((item, typed)) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/history.py"", line 182, in enqueue self.save() File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/history.py"", line 212, in save self._history.save(self._queue) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/history.py"", line 120, in save json.dump(obj, f, ensure_ascii=False) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py"", line 180, in dump fp.write(chunk) OSError: [Errno 28] No space left on device Out of disk space An error occurred during encoding. See Reply Log for details. > save /Users/haandrew/Desktop/image25.png supersample 3 > save /Users/haandrew/Desktop/image26.png supersample 3 > ui tool show ""Side View"" > save /Users/haandrew/Desktop/image27.png supersample 3 > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /fold_25s_snd/fold_25s_snd_model_1.cif"" Chain information for fold_25s_snd_model_1.cif #4 --- Chain | Description A | . B | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /fold_25s_snd/fold_25s_snd_model_2.cif"" Chain information for fold_25s_snd_model_2.cif #5 --- Chain | Description A | . B | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /fold_25s_snd/fold_25s_snd_model_3.cif"" Chain information for fold_25s_snd_model_3.cif #6 --- Chain | Description A | . B | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /fold_25s_snd/fold_25s_snd_model_4.cif"" Chain information for fold_25s_snd_model_4.cif #7 --- Chain | Description A | . B | . > hide #4 models > hide #5 models > hide #6 models > hide #7 models > show #4 models > select #4/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #4/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > hide #!3 models > hide #2 models > select #4/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models selected > select clear > select #4/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #4/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select clear > ui tool show Matchmaker > matchmaker #4-7 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_1.cif, chain B (#4), sequence alignment score = 19589.3 RMSD between 2667 pruned atom pairs is 0.941 angstroms; (across all 3301 pairs: 6.096) Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_2.cif, chain B (#5), sequence alignment score = 19589.3 RMSD between 2688 pruned atom pairs is 0.943 angstroms; (across all 3301 pairs: 10.416) Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_3.cif, chain B (#6), sequence alignment score = 19589.3 RMSD between 2726 pruned atom pairs is 0.987 angstroms; (across all 3301 pairs: 7.361) Matchmaker PDB 8BQX.cif, chain BQ (#3) with fold_25s_snd_model_4.cif, chain B (#7), sequence alignment score = 19589.3 RMSD between 2634 pruned atom pairs is 0.964 angstroms; (across all 3301 pairs: 7.614) > select #4/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #4/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > cartoon hide sel > hide sel target a > hide #4 models > show #5 models > select #5/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #5/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models selected > cartoon hide (#5 & sel) > hide (#5 & sel) target a > hide #5 models > show #6 models > select #6/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #6/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models selected > hide (#6 & sel) target a > cartoon hide (#6 & sel) > hide #6 models > show #7 models > select #7/B:1-3396 72617 atoms, 81273 bonds, 3396 residues, 1 model selected > select #7/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~ sel 603464 atoms, 662491 bonds, 5155 pseudobonds, 38435 residues, 10 models selected > hide (#7 & sel) target a > cartoon hide (#7 & sel) > show #6 models > show #5 models > show #4 models > show #!3 models > show #2 models > select clear > ui tool show Matchmaker > matchmaker #!3 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_25s_snd_model_1.cif, chain B (#4) with PDB 8BQX.cif, chain BQ (#3), sequence alignment score = 19589.3 RMSD between 2667 pruned atom pairs is 0.941 angstroms; (across all 3301 pairs: 6.096) > sequence chain #3/BQ Alignment identifier is 3/BQ > select #3/BQ:3-3396 70586 atoms, 79003 bonds, 3108 pseudobonds, 3301 residues, 2 models selected > color (#!3 & sel) cyan > select clear > save ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /80s ribosome + 25S SND1 model ALL.jpg"" width 706 height 608 > supersample 3 > select #3/x:21-387 2899 atoms, 2970 bonds, 367 residues, 1 model selected > hide sel target a > cartoon hide sel > select clear ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11D000L9D/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 4 days, 2 hours, 39 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2722H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX