id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17199 Crash in graphics driver during Qt drawing chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.7-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00000001e9284f40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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All rights reserved. > open ""/Users/phonghoa/Desktop/L24 human vs yeast.cxs"" Log from Wed Mar 26 17:09:16 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4ug0 fromDatabase pdb format mmcif Summary of feedback from opening 4ug0 fetched from pdb --- note | Fetching compressed mmCIF 4ug0 from http://files.rcsb.org/download/4ug0.cif 4ug0 title: Structure of the human 80S ribosome [more info...] Chain information for 4ug0 #1 --- Chain | Description | UniProt L5 | 28S ribosomal RNA | L7 | 5S ribosomal RNA | L8 | 5.8S ribosomal RNA | LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN 1-257 LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN 1-403 LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN 1-427 LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN 1-297 LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN 1-288 LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN 1-248 LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN 1-266 LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN 1-192 LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN 1-214 LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN 1-178 LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN 1-211 LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN 1-215 LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN 1-204 LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN 1-203 LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN 1-184 LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN 1-188 LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN 1-196 LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN 1-176 LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN 1-160 LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN 1-128 LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN 1-140 LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN 1-157 LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN 1-156 LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN 1-145 LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN 1-136 La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN 1-148 Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN 1-159 Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN 1-115 Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN 1-125 Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN 1-135 Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN 1-110 Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN 1-117 Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN 1-123 Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN 1-105 Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN 1-97 Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN 1-70 Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN 1-51 Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN 1-128 Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN 1-25 Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN 1-106 Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN 1-92 Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN 1-137 Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN 1-217 S2 | 18S ribosomal RNA | S6 | HUMAN INITIATOR MET-TRNA-I | SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN 1-295 SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN 1-264 SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN 1-293 SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN 1-243 SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN 1-263 SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN 1-204 SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN 1-249 SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN 1-194 SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN 1-208 SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN 1-194 SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN 1-165 SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN 1-158 SM | 40S RIBOSOMAL PROTEIN | SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN 1-151 SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN 1-151 SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN 1-145 SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN 1-146 SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN 1-135 SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN 1-152 ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN 1-145 SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN 1-119 SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN 1-83 SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN 1-130 SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN 1-143 SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN 1-133 SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN 1-125 Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN 1-115 Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN 1-84 Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN 1-69 Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN 1-56 Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN 1-59 Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN 1-156 Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN 1-317 Non-standard residues in 4ug0 #1 --- MG — magnesium ion ZN — zinc ion > sequence chain #1/LW Alignment identifier is 1/LW > select /LW:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /LW 1015 atoms, 1030 bonds, 124 residues, 1 model selected > color sel red > sequence chain #1/SG Alignment identifier is 1/SG > select /SG:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /SG 1923 atoms, 1946 bonds, 237 residues, 1 model selected > color sel blue > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > select subtract #1 Nothing selected > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > hide sel atoms > show sel cartoons > select subtract #1 Nothing selected > open 3j77 fromDatabase pdb format mmcif 3j77 title: Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) [more info...] Chain information for 3j77 #2 --- Chain | Description | UniProt 10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105 11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156 12 | 40S ribosomal protein S12 | RS12_YEAST 1-143 13 | 40S ribosomal protein S13 | RS13_YEAST 1-151 14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137 15 | 40S ribosomal protein S15 | RS15_YEAST 1-142 16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143 17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136 18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146 19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144 1S | 18S ribosomal RNA | 20 | 40S ribosomal protein S20 | RS20_YEAST 1-121 21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87 22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130 23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145 24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135 25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108 26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119 27 | 40S ribosomal protein S27 | RS27_YEAST 1-82 28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67 29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56 2S | 25S ribosomal RNA | 30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63 31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152 5S | 5S ribosomal RNA | 60 | 60S ribosomal protein L10 | RL10_YEAST 1-221 61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174 62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165 63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199 64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138 65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204 66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199 67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184 68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186 69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189 70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172 71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160 72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121 73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137 74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155 75 | 60S ribosomal protein L25 | RL25_YEAST 1-142 76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127 77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136 78 | 60S ribosomal protein L28 | RL28_YEAST 1-149 79 | 60S ribosomal protein L29 | RL29_YEAST 1-59 80 | 60S ribosomal protein L30 | RL30_YEAST 1-105 81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113 82 | 60S ribosomal protein L32 | RL32_YEAST 1-130 83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107 84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121 85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120 86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100 87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88 88 | 60S ribosomal protein L38 | RL38_YEAST 1-78 89 | 60S ribosomal protein L39 | RL39_YEAST 1-51 8S | 5.8S ribosomal RNA | 90 | 60S ribosomal protein L40 | RL401_YEAST 1-128 91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25 92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106 93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92 L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217 L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254 L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387 L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362 L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297 L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176 L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244 L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256 L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191 MR | messenger RNA | P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312 PT | P/E-site initiator transfer RNAfMet | RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319 S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252 S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255 S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254 S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240 S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261 S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225 S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236 S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190 S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200 S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197 > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > hide sel atoms > show sel cartoons > select subtract #2 Nothing selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure [Repeated 1 time(s)] 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 4ug0, chain L5 (#1) with 3j77, chain 2S (#2), sequence alignment score = 15359 RMSD between 2164 pruned atom pairs is 1.046 angstroms; (across all 3168 pairs: 14.499) > sequence chain #2/74 Alignment identifier is 2/74 > select clear > select #2/74 1089 atoms, 1103 bonds, 135 residues, 1 model selected > color sel magenta > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > sequence chain #2/S6 Alignment identifier is 2/S6 > select clear > select #2/S6 1820 atoms, 1844 bonds, 226 residues, 1 model selected > color sel cornflower blue > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > save ""/Users/phonghoa/Desktop/human vs yeast 80s )L24=.cxs"" > sequence chain #2/L5 Alignment identifier is 2/L5 > select #2/L5:297 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/L5 2376 atoms, 2426 bonds, 296 residues, 1 model selected > color sel orange > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > sequence chain #1/LD Alignment identifier is 1/LD > select clear > select #1/LD 2382 atoms, 2428 bonds, 293 residues, 1 model selected > color sel orange red > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > select subtract #1 Nothing selected > save ""/Users/phonghoa/Desktop/L24 human vs yeast.cxs"" ——— End of log from Wed Mar 26 17:09:16 2025 ——— opened ChimeraX session > save /Users/phonghoa/Desktop/image1.png supersample 3 > volume appearance airways No volumes specified Alignment identifier is 1/L5 Alignment identifier is 1/L7 Alignment identifier is 1/L8 Alignment identifier is 1/LA Alignment identifier is 1/LB Alignment identifier is 1/LC Alignment identifier is 1/LD Alignment identifier is 1/LE Alignment identifier is 1/LF Alignment identifier is 1/LG Alignment identifier is 1/LH Alignment identifier is 1/LI Alignment identifier is 1/LJ Alignment identifier is 1/LL Alignment identifier is 1/LM Alignment identifier is 1/LN Alignment identifier is 1/LO Alignment identifier is 1/LP Alignment identifier is 1/LQ Alignment identifier is 1/LR Alignment identifier is 1/LS Alignment identifier is 1/LT Alignment identifier is 1/LU Alignment identifier is 1/LV Alignment identifier is 1/LW Alignment identifier is 1/LX Alignment identifier is 1/LY Alignment identifier is 1/LZ Alignment identifier is 1/La Alignment identifier is 1/Lb Alignment identifier is 1/Lc Alignment identifier is 1/Ld Alignment identifier is 1/Le Alignment identifier is 1/Lf Alignment identifier is 1/Lg Alignment identifier is 1/Lh Alignment identifier is 1/Li Alignment identifier is 1/Lj Alignment identifier is 1/Lk Alignment identifier is 1/Ll Alignment identifier is 1/Lm Alignment identifier is 1/Ln Alignment identifier is 1/Lo Alignment identifier is 1/Lp Alignment identifier is 1/Lr Alignment identifier is 1/Lz Alignment identifier is 1/S2 Alignment identifier is 1/S6 Alignment identifier is 1/SA Alignment identifier is 1/SB Alignment identifier is 1/SD Alignment identifier is 1/SE Alignment identifier is 1/SF Alignment identifier is 1/SH Alignment identifier is 1/SI Alignment identifier is 1/SK Alignment identifier is 1/SL Alignment identifier is 1/SP Alignment identifier is 1/SQ Alignment identifier is 1/SR Alignment identifier is 1/SS Alignment identifier is 1/ST Alignment identifier is 1/SU Alignment identifier is 1/SV Alignment identifier is 1/SX Alignment identifier is 1/Sa Alignment identifier is 1/Sc Alignment identifier is 1/Sd Alignment identifier is 1/Sf Alignment identifier is 1/Sg Alignment identifier is 1/SC Alignment identifier is 1/SG Alignment identifier is 1/SJ Alignment identifier is 1/SM Alignment identifier is 1/SN Alignment identifier is 1/SO Alignment identifier is 1/SW Alignment identifier is 1/SY Alignment identifier is 1/SZ Alignment identifier is 1/Sb Alignment identifier is 1/Se Alignment identifier is 2/L1 Alignment identifier is 2/L2 Alignment identifier is 2/L3 Alignment identifier is 2/L4 Alignment identifier is 2/L5 Alignment identifier is 2/L6 Alignment identifier is 2/L7 Alignment identifier is 2/L8 Alignment identifier is 2/L9 Alignment identifier is 2/60 Alignment identifier is 2/61 Alignment identifier is 2/62 Alignment identifier is 2/63 Alignment identifier is 2/64 Alignment identifier is 2/65 Alignment identifier is 2/66 Alignment identifier is 2/67 Alignment identifier is 2/68 Alignment identifier is 2/69 Alignment identifier is 2/70 Alignment identifier is 2/71 Alignment identifier is 2/72 Alignment identifier is 2/73 Alignment identifier is 2/74 Alignment identifier is 2/75 Alignment identifier is 2/76 Alignment identifier is 2/77 Alignment identifier is 2/78 Alignment identifier is 2/79 Alignment identifier is 2/80 Alignment identifier is 2/81 Alignment identifier is 2/82 Alignment identifier is 2/83 Alignment identifier is 2/84 Alignment identifier is 2/85 Alignment identifier is 2/86 Alignment identifier is 2/87 Alignment identifier is 2/88 Alignment identifier is 2/89 Alignment identifier is 2/90 Alignment identifier is 2/91 Alignment identifier is 2/92 Alignment identifier is 2/93 Alignment identifier is 2/P0 Alignment identifier is 2/RC Alignment identifier is 2/S0 Alignment identifier is 2/S1 Alignment identifier is 2/S2 Alignment identifier is 2/S3 Alignment identifier is 2/S4 Alignment identifier is 2/S5 Alignment identifier is 2/S6 Alignment identifier is 2/S7 Alignment identifier is 2/S8 Alignment identifier is 2/S9 Alignment identifier is 2/10 Alignment identifier is 2/11 Alignment identifier is 2/12 Alignment identifier is 2/13 Alignment identifier is 2/14 Alignment identifier is 2/15 Alignment identifier is 2/16 Alignment identifier is 2/17 Alignment identifier is 2/18 Alignment identifier is 2/19 Alignment identifier is 2/20 Alignment identifier is 2/21 Alignment identifier is 2/22 Alignment identifier is 2/23 Alignment identifier is 2/24 Alignment identifier is 2/25 Alignment identifier is 2/26 Alignment identifier is 2/27 Alignment identifier is 2/28 Alignment identifier is 2/29 Alignment identifier is 2/30 Alignment identifier is 2/31 Alignment identifier is 2/1S Alignment identifier is 2/2S Alignment identifier is 2/8S Alignment identifier is 2/5S Alignment identifier is 2/MR Alignment identifier is 2/PT ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/phonghoa/Desktop/L24 human vs yeast.cxs"" Log from Wed Mar 26 17:09:16 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4ug0 fromDatabase pdb format mmcif Summary of feedback from opening 4ug0 fetched from pdb --- note | Fetching compressed mmCIF 4ug0 from http://files.rcsb.org/download/4ug0.cif 4ug0 title: Structure of the human 80S ribosome [more info...] Chain information for 4ug0 #1 --- Chain | Description | UniProt L5 | 28S ribosomal RNA | L7 | 5S ribosomal RNA | L8 | 5.8S ribosomal RNA | LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN 1-257 LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN 1-403 LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN 1-427 LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN 1-297 LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN 1-288 LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN 1-248 LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN 1-266 LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN 1-192 LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN 1-214 LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN 1-178 LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN 1-211 LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN 1-215 LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN 1-204 LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN 1-203 LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN 1-184 LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN 1-188 LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN 1-196 LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN 1-176 LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN 1-160 LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN 1-128 LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN 1-140 LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN 1-157 LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN 1-156 LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN 1-145 LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN 1-136 La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN 1-148 Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN 1-159 Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN 1-115 Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN 1-125 Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN 1-135 Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN 1-110 Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN 1-117 Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN 1-123 Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN 1-105 Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN 1-97 Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN 1-70 Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN 1-51 Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN 1-128 Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN 1-25 Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN 1-106 Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN 1-92 Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN 1-137 Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN 1-217 S2 | 18S ribosomal RNA | S6 | HUMAN INITIATOR MET-TRNA-I | SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN 1-295 SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN 1-264 SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN 1-293 SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN 1-243 SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN 1-263 SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN 1-204 SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN 1-249 SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN 1-194 SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN 1-208 SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN 1-194 SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN 1-165 SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN 1-158 SM | 40S RIBOSOMAL PROTEIN | SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN 1-151 SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN 1-151 SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN 1-145 SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN 1-146 SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN 1-135 SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN 1-152 ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN 1-145 SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN 1-119 SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN 1-83 SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN 1-130 SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN 1-143 SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN 1-133 SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN 1-125 Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN 1-115 Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN 1-84 Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN 1-69 Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN 1-56 Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN 1-59 Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN 1-156 Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN 1-317 Non-standard residues in 4ug0 #1 --- MG — magnesium ion ZN — zinc ion > sequence chain #1/LW Alignment identifier is 1/LW > select /LW:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /LW 1015 atoms, 1030 bonds, 124 residues, 1 model selected > color sel red > sequence chain #1/SG Alignment identifier is 1/SG > select /SG:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /SG 1923 atoms, 1946 bonds, 237 residues, 1 model selected > color sel blue > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > select subtract #1 Nothing selected > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > hide sel atoms > show sel cartoons > select subtract #1 Nothing selected > open 3j77 fromDatabase pdb format mmcif 3j77 title: Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) [more info...] Chain information for 3j77 #2 --- Chain | Description | UniProt 10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105 11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156 12 | 40S ribosomal protein S12 | RS12_YEAST 1-143 13 | 40S ribosomal protein S13 | RS13_YEAST 1-151 14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137 15 | 40S ribosomal protein S15 | RS15_YEAST 1-142 16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143 17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136 18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146 19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144 1S | 18S ribosomal RNA | 20 | 40S ribosomal protein S20 | RS20_YEAST 1-121 21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87 22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130 23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145 24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135 25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108 26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119 27 | 40S ribosomal protein S27 | RS27_YEAST 1-82 28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67 29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56 2S | 25S ribosomal RNA | 30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63 31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152 5S | 5S ribosomal RNA | 60 | 60S ribosomal protein L10 | RL10_YEAST 1-221 61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174 62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165 63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199 64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138 65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204 66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199 67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184 68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186 69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189 70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172 71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160 72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121 73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137 74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155 75 | 60S ribosomal protein L25 | RL25_YEAST 1-142 76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127 77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136 78 | 60S ribosomal protein L28 | RL28_YEAST 1-149 79 | 60S ribosomal protein L29 | RL29_YEAST 1-59 80 | 60S ribosomal protein L30 | RL30_YEAST 1-105 81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113 82 | 60S ribosomal protein L32 | RL32_YEAST 1-130 83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107 84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121 85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120 86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100 87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88 88 | 60S ribosomal protein L38 | RL38_YEAST 1-78 89 | 60S ribosomal protein L39 | RL39_YEAST 1-51 8S | 5.8S ribosomal RNA | 90 | 60S ribosomal protein L40 | RL401_YEAST 1-128 91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25 92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106 93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92 L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217 L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254 L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387 L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362 L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297 L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176 L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244 L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256 L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191 MR | messenger RNA | P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312 PT | P/E-site initiator transfer RNAfMet | RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319 S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252 S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255 S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254 S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240 S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261 S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225 S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236 S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190 S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200 S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197 > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > hide sel atoms > show sel cartoons > select subtract #2 Nothing selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure [Repeated 1 time(s)] 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 4ug0, chain L5 (#1) with 3j77, chain 2S (#2), sequence alignment score = 15359 RMSD between 2164 pruned atom pairs is 1.046 angstroms; (across all 3168 pairs: 14.499) > sequence chain #2/74 Alignment identifier is 2/74 > select clear > select #2/74 1089 atoms, 1103 bonds, 135 residues, 1 model selected > color sel magenta > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > sequence chain #2/S6 Alignment identifier is 2/S6 > select clear > select #2/S6 1820 atoms, 1844 bonds, 226 residues, 1 model selected > color sel cornflower blue > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > save ""/Users/phonghoa/Desktop/human vs yeast 80s )L24=.cxs"" > sequence chain #2/L5 Alignment identifier is 2/L5 > select #2/L5:297 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/L5 2376 atoms, 2426 bonds, 296 residues, 1 model selected > color sel orange > select add #2 207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models selected > select subtract #2 Nothing selected > sequence chain #1/LD Alignment identifier is 1/LD > select clear > select #1/LD 2382 atoms, 2428 bonds, 293 residues, 1 model selected > color sel orange red > select add #1 218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models selected > select subtract #1 Nothing selected > save ""/Users/phonghoa/Desktop/L24 human vs yeast.cxs"" ——— End of log from Wed Mar 26 17:09:16 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: Mac15,4 Model Number: Z1950004VZP/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.1.1 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7 (23H124) Kernel Version: Darwin 23.6.0 Time since boot: 8 days, 6 hours, 35 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 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ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX