id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9596 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 minhducdkh@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff850901700 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-08-17 00:01:36.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.5 (22G74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""FF85DC01-52F8-43EE-8584-419CD39FCC33""} { ""uptime"" : 650000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 29557, ""osVersion"" : { ""train"" : ""macOS 13.5"", ""build"" : ""22G74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-08-17 00:01:29.0035 +0200"", ""incident"" : ""FF85DC01-52F8-43EE-8584-419CD39FCC33"", ""pid"" : 83438, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-08-16 16:45:52.5821 +0200"", ""procStartAbsTime"" : 635216170973013, ""procExitAbsTime"" : 656436675524308, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""1B621CC7-A08E-58E5-A30C-B64306F232D4"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""5A8EFE95-C9B8-50CB-3111-3AE68D059CBA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 2, ""bridgeVersion"" : {""build"":""20P6072"",""train"":""7.6""}, ""sleepWakeUUID"" : ""7E43A03C-6243-4EE3-95FF-CDC43B020D9D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Processing_1-202208/Refinement- > March/Anas refinement/monosome_P-site_no-H_RS-R_50.pdb"" format pdb Summary of feedback from opening /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- KarolinskaInstitutet/KI/Jurkat_monosome_project/Processing_1-202208/Refinement- March/Anas refinement/monosome_P-site_no-H_RS-R_50.pdb --- warnings | Ignored bad PDB record found on line 12 SSBOND 1 CYS A2 45 CYS A2 76 Cannot find LINK/SSBOND residue FES (7099121) Cannot find LINK/SSBOND residue FES (7099121) Cannot find LINK/SSBOND residue FES (8965361) Cannot find LINK/SSBOND residue FES (8965361) Cannot find LINK/SSBOND residue FES (7099121) 4 messages similar to the above omitted Chain information for monosome_P-site_no-H_RS-R_50.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available A0 | No description available A1 | No description available A2 | No description available A3 | No description available A4 | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AM | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Ax | No description available Ay | No description available Az | No description available B | No description available D | No description available E | No description available F | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available z | No description available > open 6spf format mmcif fromDatabase pdb 6spf title: Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate [more info...] Chain information for 6spf #2 --- Chain | Description | UniProt 1 | 50S ribosomal protein L31 | A0A072ZJG4_PSEAI 2-32 2 | 50S ribosomal protein L32 | A0A069QB25_PSEAI 2-54 3 | 50S ribosomal protein L33 | A0A140SG33_PSEAI 2-51 4 | 50S ribosomal protein L34 | A0A087L9L7_PSEAI 1-44 5 | 50S ribosomal protein L35 | A0A069QC44_PSEAI 2-64 6 | 50S ribosomal protein L36 | E2RXU2_PSEAI 1-38 A | Pseudomonas aeruginosa strain PAO1 23S ribosomal RNA | B | 5S rRNA | C | 50S ribosomal protein L2 | A0A241XHA2_PSEAI 3-273 D | 50S ribosomal protein L3 | A0A072ZBZ2_PSEAI 3-209 E | 50S ribosomal protein L4 | A0A241XH26_PSEAI 2-200 F | 50S ribosomal protein L5 | A0A072ZMU2_PSEAI 3-176 G | 50S ribosomal protein L6 | A0A2V3F3S9_PSEAI 2-170 H | 50S ribosomal protein L9 | A0A072ZKF0_PSEAI 2-79 I | 50S ribosomal protein L11 | A0A2V3GYK0_PSEAI 3-142 J | 50S ribosomal protein L13 | A0A071L356_PSEAI 2-142 K | 50S ribosomal protein L14 | E2RXT6_PSEAI 1-120 L | 50S ribosomal protein L15 | A0A2V3D5Z8_PSEAI 1-144 M | 50S ribosomal protein L16 | A0A069QEB6_PSEAI 1-136 N | 50S ribosomal protein L17 | A0A072ZCA1_PSEAI 1-120 O | 50S ribosomal protein L18 | E2RXU0_PSEAI 2-116 P | 50S ribosomal protein L19 | A0A263PZC6_PSEAI 2-115 Q | 50S ribosomal protein L20 | A0A069QEE3_PSEAI 2-118 R | 50S ribosomal protein L21 | A0A072ZDZ0_PSEAI 1-102 S | 50S ribosomal protein L22 | A0A1C7BCP0_PSEAI 1-110 T | 50S ribosomal protein L23 | E2RXT1_PSEAI 1-94 U | 50S ribosomal protein L24 | E2RXT7_PSEAI 1-103 V | 50S ribosomal protein L25 | A0A072ZBM5_PSEAI 4-191 W | 50S ribosomal protein L27 | A0A071LFT4_PSEAI 10-85 X | 50S ribosomal protein L28 | A0A072ZIQ9_PSEAI 2-78 Y | Ribosomal protein uL29 | Z | 50S ribosomal protein L30 | E2RXU1_PSEAI 2-58 a | 16S rRNA | b | 30S ribosomal protein S2 | A0A072ZPV8_PSEAI 3-228 c | 30S ribosomal protein S3 | A0A140S919_PSEAI 5-207 d | 30S ribosomal protein S4 | A0A072ZDF7_PSEAI 3-206 e | 30S ribosomal protein S5 | A0A241XG65_PSEAI 11-159 f | 30S ribosomal protein S6 | A0A069Q263_PSEAI 2-101 g | 30S ribosomal protein S7 | A0A2V3F2U6_PSEAI 3-156 h | 30S ribosomal protein S8 | E2RXT9_PSEAI 2-130 i | 30S ribosomal protein S9 | A0A069PXX1_PSEAI 3-128 j | 30S ribosomal protein S10 | E2RXT0_PSEAI 8-103 k | 30S ribosomal protein S11 | E2RXU4_PSEAI 14-128 l | 30S ribosomal protein S12 | A0A071L394_PSEAI 2-121 m | 30S ribosomal protein S13 | E2RXU3_PSEAI 3-112 n | 30S ribosomal protein S14 | E2RXT8_PSEAI 3-100 o | 30S ribosomal protein S15 | A0A071L3R7_PSEAI 2-88 p | 30S ribosomal protein S16 | A0A2V4FRZ2_PSEAI 1-78 q | 30S ribosomal protein S17 | E2RXT5_PSEAI 9-84 r | 30S ribosomal protein S18 | A0A2V3DLV3_PSEAI 19-74 s | 30S ribosomal protein S19 | E2RXT2_PSEAI 2-81 t | 30S ribosomal protein S20 | A0A072ZDZ9_PSEAI 2-87 u | 30S ribosomal protein S21 | A0A069QC99_PSEAI 34-67 > open 7m4v format mmcif fromDatabase pdb 7m4v title: A. baumannii Ribosome-Eravacycline complex: 50S [more info...] Chain information for 7m4v #3 --- Chain | Description | UniProt 0 | 50S ribosomal protein L33 | A0A062FI44_ACIBA 1-51 1 | 50S ribosomal protein L34 | A0A1J6Y3G0_9GAMM 1-44 2 | 50S ribosomal protein L35 | RL35_ACIB5 1-64 3 | 50S ribosomal protein L36 | A0A372FJT1_9GAMM 1-38 A | 23s ribosomal RNA | B | 5s ribosomal RNA | C | 50S ribosomal protein L2 | RL2_ACIB5 1-274 D | 50S ribosomal protein L3 | RL3_ACIB5 1-212 E | 50S ribosomal protein L4 | RL4_ACIB5 1-200 F | 50S ribosomal protein L5 | RL5_ACIB5 1-178 G | 50S ribosomal protein L6 | RL6_ACIB5 1-177 H | 50S ribosomal protein L9 | RL9_ACIB5 1-148 I | 50S ribosomal protein L13 | RL13_ACIB5 1-142 J | 50S ribosomal protein L14 | N8SHC6_9GAMM 1-122 K | 50S ribosomal protein L15 | RL15_ACIB5 1-146 L | 50S ribosomal protein L16 | RL16_ACIB5 1-137 M | 50S ribosomal protein L17 | RL17_ACIB5 1-125 N | 50S ribosomal protein L18 | RL18_ACIB5 1-116 O | 50S ribosomal protein L19 | RL19_ACIB5 1-122 P | 50S ribosomal protein L20 | V5VGC9_ACIBA 1-119 Q | 50S ribosomal protein L21 | RL21_ACIB5 1-103 R | 50S ribosomal protein L22 | A0A009I821_ACIB9 1-109 S | 50S ribosomal protein L23 | RL23_ACIB5 1-106 T | 50S ribosomal protein L24 | RL24_ACIB5 1-105 U | 50S ribosomal protein L25 | RL25_ACIB5 1-98 V | 50S ribosomal protein L27 | RL27_ACIB5 1-85 W | 50S ribosomal protein L28 | N9N7A0_9GAMM 1-78 X | 50S ribosomal protein L29 | RL29_ACIB5 1-65 Y | 50S ribosomal protein L30 | A0A062FG91_ACIBA 1-58 Z | 50S ribosomal protein L32 | RL32_ACIB5 1-61 Non-standard residues in 7m4v #3 --- MG — magnesium ion YQM — Eravacycline ZN — zinc ion > open 7qi4 format mmcif fromDatabase pdb Summary of feedback from opening 7qi4 fetched from pdb --- warnings | Atom H is not in the residue template for PRO /s:135 Atom HN10 is not in the residue template for SPM /AA:1702 Atom H103 is not in the residue template for SPD /AA:1703 Atom H103 is not in the residue template for SPD /A:3301 Atom H103 is not in the residue template for SPD /A:3302 Atom H103 is not in the residue template for SPD /A:3303 Atom HN13 is not in the residue template for PUT /A:3304 Atom H1 is not in the residue template for VAL /B:101 7qi4 title: Human mitochondrial ribosome at 2.2 A resolution [more info...] Chain information for 7qi4 #4 --- Chain | Description | UniProt 0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188 1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65 2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92 3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188 4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103 5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423 6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380 7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338 8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206 9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137 A | 16S mitochondrial rRNA | A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 2-218 A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323 A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118 A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199 A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689 AA | 12S mitochondrial rRNA | AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296 AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167 AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430 AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125 AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242 AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396 AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201 AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194 AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138 AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128 AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257 AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137 AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130 AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258 AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142 AQ | MRPS21 isoform 1 | A0A2J8VEN6_PONAB 1-87 AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360 AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190 AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173 AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205 AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414 AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187 AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398 AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395 AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106 Aw | A/A-tRNA | Ax | P/P-tRNA | Ay | E/E-tRNA | Az | mRNA | B | mitochondrial tRNAVal | D | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305 E | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348 F | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311 H | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267 I | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261 J | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192 K | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178 L | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145 M | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296 N | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251 O | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175 P | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 1-180 Q | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292 R | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149 S | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205 T | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 1-206 U | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153 V | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216 W | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148 X | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256 Y | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250 Z | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161 a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142 b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215 c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332 d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306 e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279 f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212 g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166 h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158 i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128 j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123 k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112 l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138 m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128 o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102 p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206 q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222 r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196 s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439 t u v w x y | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN 1-198 z | 39S ribosomal protein L1, mitochondrial | RM01_HUMAN 1-325 Non-standard residues in 7qi4 #4 --- 5F0 — (3~{S})-3-azanyl-4-methoxy-4-oxidanylidene-butanoic acid ATP — adenosine-5'-triphosphate FES — FE2/S2 (inorganic) cluster GDP — guanosine-5'-diphosphate K — potassium ion MG — magnesium ion NAD — nicotinamide-adenine-dinucleotide PUT — 1,4-diaminobutane (putrescine) SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) SPM — spermine VAL — valine ZN — zinc ion > open 8crx format mmcif fromDatabase pdb Summary of feedback from opening 8crx fetched from pdb --- warning | Atom O3' has no neighbors to form bonds with according to residue template for U /a:1730 8crx title: Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound [more info...] Chain information for 8crx #5 --- Chain | Description | UniProt 0 | 50S ribosomal protein L33 | A0A2C6LJM0_CUTAC 1-56 1 | 50S ribosomal protein L34 | A0A2B7IDI8_CUTAC 1-44 2 | 50S ribosomal protein L35 | A0A371N4N9_CUTAC 1-68 3 | 50S ribosomal protein L36 | A0A2B7JN22_CUTAC 1-37 4 | 50S ribosomal protein L31 | A0A2B7JUW7_CUTAC 1-69 A | RNA (1537-MER) | B | 30S ribosomal protein S2 | A0A2B7I756_CUTAC 1-283 C | P-site initiator tRNA | D | 30S ribosomal protein S4 | A0A2B7JMY9_CUTAC 1-201 E | 30S ribosomal protein S5 | A0A2B7I5L8_CUTAC 1-215 F | 30S ribosomal protein S6 | A0A2C6L3A1_CUTAC 1-96 G | 30S ribosomal protein S3 | A0A2B7I5Y3_CUTAC 1-269 H | 30S ribosomal protein S8 | A0A2B7ITQ7_CUTAC 1-135 I | 30S ribosomal protein S7 | A0A2B7ITZ4_CUTAC 1-156 J | 30S ribosomal protein S9 | A0A2B7JN42_CUTAC 1-173 K | 30S ribosomal protein S11 | A0A2B7I645_CUTAC 1-135 L | 30S ribosomal protein S12 | A0A2C6LJN0_CUTAC 1-123 M | 30S ribosomal protein S10 | A0A085B5E4_CUTAC 1-103 N | 30S ribosomal protein S13 | A0A2C6LKT6_CUTAC 1-123 O | 30S ribosomal protein S15 | A0A2B7I743_CUTAC 1-87 P | 30S ribosomal protein S16 | A0A2B7IXM7_CUTAC 1-147 Q | 30S ribosomal protein S17 | A0A2B7JMS7_CUTAC 1-90 R | 30S ribosomal protein S18 | A0A2C6LI71_CUTAC -3-75 S | 30S ribosomal protein S14 type Z | A0A2B7JMX1_CUTAC 1-61 T | 30S ribosomal protein S20 | A0A2B7I592_CUTAC 1-88 U | 30S ribosomal protein S19 | A0A2B7ITR7_CUTAC 1-93 V | 50S ribosomal protein bL37 | X | 30S ribosomal protein bS22 | A0A533INE0_CUTAC 1-33 Y | 32MF mRNA | a | 23S ribosomal RNA | b | 5S ribosomal RNA | c | 50S ribosomal protein L2 | A0A2B7JMV5_CUTAC 1-278 d | 50S ribosomal protein L3 | A0A1G9KW65_CUTAC 1-223 e | 50S ribosomal protein L4 | A0A2B7I5M5_CUTAC 1-301 f | 50S ribosomal protein L5 | A0A3E2DDM1_CUTAC 1-210 g | 50S ribosomal protein L6 | A0A2B7I5S3_CUTAC 1-180 i | 50S ribosomal protein L13 | A0A2B7I6I7_CUTAC 1-147 j | 50S ribosomal protein L14 | A0A2B7JMZ8_CUTAC 1-122 k | 50S ribosomal protein L15 | A0A2B7IUA0_CUTAC 1-146 l | 50S ribosomal protein L16 | A0A2B7I5M8_CUTAC 1-139 m | 50S ribosomal protein L17 | A0A085AZY3_CUTAC 1-187 n | 50S ribosomal protein L18 | A0A2B7JN02_CUTAC 1-127 o | 50S ribosomal protein L19 | A0A2C6LKT3_CUTAC 1-117 p | 50S ribosomal protein L20 | A0A2B7I6V3_CUTAC 1-123 q | 50S ribosomal protein L21 | A0A085B4N9_CUTAC 1-102 r | 50S ribosomal protein L22 | A0A2B7ITY5_CUTAC 1-153 s | 50S ribosomal protein L23 | A0A2C6LEQ5_CUTAC 1-102 t | 50S ribosomal protein L24 | A0A085B5D2_CUTAC 1-122 u | 50S ribosomal protein L25 | A0A2B7IYF8_CUTAC 1-205 v | 50S ribosomal protein L27 | A0A2B7IGT1_CUTAC 1-89 w | 50S ribosomal protein L28 | A0A2B7I7B7_CUTAC 1-61 x | 50S ribosomal protein L29 | A0A2B7JB12_CUTAC 1-77 y | 50S ribosomal protein L30 | A0A2B7I5Y4_CUTAC 2-61 z | 50S ribosomal protein L32 | A0A2B7I771_CUTAC 1-63 Non-standard residues in 8crx #5 --- MG — magnesium ion V7A — Sarecycline ZN — zinc ion > hide atoms > show cartoons > lighting soft > ui tool show Matchmaker > matchmaker #!2-5 to #1 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 monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 6spf, chain A (#2), sequence alignment score = 5975.7 RMSD between 382 pruned atom pairs is 0.903 angstroms; (across all 1547 pairs: 67.816) Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 7m4v, chain A (#3), sequence alignment score = 5875.2 RMSD between 450 pruned atom pairs is 1.236 angstroms; (across all 1538 pairs: 49.351) Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 7qi4, chain A (#4), sequence alignment score = 9157.7 RMSD between 1467 pruned atom pairs is 0.481 angstroms; (across all 1556 pairs: 0.995) Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 8crx, chain a (#5), sequence alignment score = 5770.9 RMSD between 361 pruned atom pairs is 0.913 angstroms; (across all 1492 pairs: 70.485) > hide #!2 models > hide #!3 models > hide #!5 models > hide #!1 models > open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tige-LSU-1.pdb Summary of feedback from opening /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tige-LSU-1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184 ALA D 186 1 3 Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254 1 3 Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262 1 3 Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265 1 3 Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1 17 996 messages similar to the above omitted Cannot find LINK/SSBOND residue FES (201 ) Cannot find LINK/SSBOND residue FES (201 ) > select #4/A:3078 31 atoms, 32 bonds, 1 residue, 1 model selected > select up 49872 atoms, 53804 bonds, 1558 residues, 1 model selected > cartoon style width 1.5 thickness 1 > lighting flat > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > lighting soft > set bgColor white > ui tool show ""Side View"" > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 872908 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 10 days, 18 hours, 55 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal B277U: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 70.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: TDBEE003853B Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX