id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15104 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4-arm64-arm-64bit ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 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 0x00000001efee5e00 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.25.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-rc2023.04.25.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-rc2023.04.25.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-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6-rc2023.04.25.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"":""2024-04-29 16:37:10.00 -0400"",""app_version"":""1.6.0"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.4 (22F66)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""513D6C63-B7A5-4337-A4A8-52D9A3DAF0EC""} { ""uptime"" : 390000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 23847, ""osVersion"" : { ""train"" : ""macOS 13.4"", ""build"" : ""22F66"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-04-29 16:33:46.7545 -0400"", ""incident"" : ""513D6C63-B7A5-4337-A4A8-52D9A3DAF0EC"", ""pid"" : 46087, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-04-25 16:04:55.2687 -0400"", ""procStartAbsTime"" : 8117922785634, ""procExitAbsTime"" : 9393364879568, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6-rc2023.04.25.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C3C49ABA-19BA-5F65-922B-BF1C622C9267"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""4C23F015-FEA2-97D2-0E0F-B6A4AD618697"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 3002, ""sleepWakeUUID"" : ""D5200120-4CAE-4793-9442-57E28F154E88"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 105557813886952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600118000000-600120000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""vmregioninfo"" : ""0x18 is not in any region. 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294912, ""uuid"" : ""c2fd3094-b465-39a4-b774-16583ff53c4b"", ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"", ""name"" : ""libdispatch.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6790094848, ""size"" : 582996, ""uuid"" : ""bd993f39-c902-37d6-8bd8-6d827c7f121e"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6949109760, ""CFBundleShortVersionString"" : ""306.7.4"", ""CFBundleIdentifier"" : ""com.apple.Metal"", ""size"" : 2002944, ""uuid"" : ""2bab169c-42da-36e3-955a-f30b709ec2ad"", ""path"" : ""\/System\/Library\/Frameworks\/Metal.framework\/Versions\/A\/Metal"", ""name"" : ""Metal"", ""CFBundleVersion"" : ""306.7.4"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 6789431296, ""size"" : 3551805440, ""uuid"" : ""7d9faa84-5c6b-3ef4-9379-faba64346673"" }, ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""ef45c3c799d687e7c3aadbc0025924581155042f"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62fe74515312cd4599bd3c80"", ""factorPackIds"" : { ""MYRIAD_BOOSTS"" : ""62fe74805312cd4599bd3c81"" }, ""deploymentId"" : 240000006 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ { ""treatmentId"" : ""5d51a80d-93ec-47e1-9027-675002e78e4a"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000023 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Feb 23 15:56:32 2024UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Tue Jan 30 16:17:55 2024UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Nov 3 09:32:22 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:54:08 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:24:47 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:08:11 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 14:52:35 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/stefhed/Library/Mobile > Documents/com~apple~CloudDocs/Downloads/6elz 2.cif"" 6elz 2.cif title: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes [more info...] Chain information for 6elz 2.cif #1 --- Chain | Description | UniProt 1 | 25S ribosomal RNA | 2 | 5.8S ribosomal RNA | 6 | Internal transcribed spacer 2 | A | Ribosome biogenesis protein BRX1 | BRX1_YEAST 1-291 B | 60S ribosomal protein L3 | RL3_YEAST 1-387 C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362 D | ATP-dependent RNA helicase HAS1 | HAS1_YEAST 1-505 E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 I | Nucleolar complex-associated protein 3 | NOC3_YEAST 1-663 J | rRNA-processing protein EBP2 | EBP2_YEAST 1-427 K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376 L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236 X | 60S ribosomal protein L25 | RL25_YEAST 1-142 Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 a | 60S ribosomal protein L28 | RL28_YEAST 1-149 b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647 c | 60S ribosomal protein L30 | RL30_YEAST 1-105 d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 e | 60S ribosomal protein L32 | RL32_YEAST 1-130 f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 k | 60S ribosomal protein L38 | RL38_YEAST 1-78 l | 60S ribosome subunit biogenesis protein NIP7 | NIP7_YEAST 1-181 m | Ribosome biogenesis protein ERB1 | ERB1_YEAST 1-807 n | Pescadillo homolog | PESC_YEAS7 1-605 o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220 p | Ribosome biogenesis protein YTM1 | YTM1_YEAS7 1-460 q | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | NOP2_YEAST 1-618 r | Ribosome biogenesis protein NSA2 | NSA2_YEAS7 1-261 s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520 t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322 u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199 v | Nucleolar protein 16 | NOP16_YEAST 1-231 w | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | SPB1_YEAST 1-841 y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245 z | UPF0642 protein YBL028C | YBC8_YEAST 1-106 Non-standard residues in 6elz 2.cif #1 --- ZN — zinc ion > select all 134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models selected > hide sel > show nucleic > hide sel surfaces > show sel cartoons > hide sel surfaces > hide surfaces > select all 134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models selected > hide all > select clear > select #1:I, y, s, K, W, A, r, u, t, p, z 29269 atoms, 32087 bonds, 715 pseudobonds, 1392 residues, 3 models selected > hide sel > hide sel cartoons > hide sel surfaces > select #1:K Nothing selected > select #1/K 2073 atoms, 2107 bonds, 1 pseudobond, 257 residues, 2 models selected > hide sel > hide sel cartoons > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > hide sel cartoons > select #1/y, s, K, W, A, r, u, t, p, z 15075 atoms, 15315 bonds, 10 pseudobonds, 1883 residues, 2 models selected > hide sel cartoons > select nucleic 57318 atoms, 64137 bonds, 2412 pseudobonds, 2680 residues, 3 models selected > show sel cartoons > ladder nucleotides Unknown command: ladder nucleotides > show nucleotides ladder Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > nucleotides sel ladder [Repeated 2 time(s)] > select #1/A-Z 38689 atoms, 39375 bonds, 15 pseudobonds, 4848 residues, 2 models selected > hide sel > hide sel cartoons > select #1/a, c-k 7802 atoms, 7921 bonds, 4 pseudobonds, 981 residues, 2 models selected > hide sel cartoons > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > show sel surfaces > hide sel cartoons > color sel yellow > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel red > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > hide sel cartoons > show sel surfaces > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > hide sel cartoons > show sel surfaces > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected > hide sel cartoons > show sel surfaces > color sel blue > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > hide sel surfaces > hide sel cartoons > show sel surfaces > color sel light green > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel orange > select clear > select #1/b 3410 atoms, 3474 bonds, 3 pseudobonds, 421 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel light blue > select clear > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > hide sel cartoons > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > hide sel cartoons > show sel surfaces > select clear > select #1/:42-635 Expected an objects specifier or a keyword > select #1/1:42-635 11543 atoms, 12934 bonds, 447 pseudobonds, 537 residues, 3 models selected > color sel lightblue red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel red > color sel lightred Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lightblue red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #1/1:662-1435 14182 atoms, 15879 bonds, 569 pseudobonds, 661 residues, 3 models selected > color sel orange > select #1/1:1452-1878 8891 atoms, 9946 bonds, 390 pseudobonds, 416 residues, 3 models selected > color sel yellow > select up 52595 atoms, 58864 bonds, 390 pseudobonds, 2457 residues, 3 models selected > select up 134887 atoms, 143091 bonds, 2448 pseudobonds, 12372 residues, 3 models selected > select #1/1:1911-2332 902 atoms, 1007 bonds, 48 pseudobonds, 42 residues, 3 models selected > color sel light green > color sel forest green > select #1/1:2400-2980 4471 atoms, 4995 bonds, 172 pseudobonds, 210 residues, 3 models selected > color sel medium blue > select #1/1:2995-3396 8560 atoms, 9569 bonds, 344 pseudobonds, 402 residues, 2 models selected > color sel lightblue purple Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel purple > color medium purple > color sel medium purple > select #1/2 3353 atoms, 3746 bonds, 83 pseudobonds, 158 residues, 2 models selected > color sel pink > color sel hot pink > select clear > sequence chain #1/D Alignment identifier is 1/D > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select /I:132-601 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select /I:132-601 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > sequence chain #1/I Alignment identifier is 1/I > select /I:132-133 18 atoms, 17 bonds, 2 residues, 1 model selected > select /I:132-133 18 atoms, 17 bonds, 2 residues, 1 model selected > color sel white > select clear Alignment identifier is 1/1 Alignment identifier is 1/2 Alignment identifier is 1/6 Alignment identifier is 1/L Alignment identifier is 1/N Alignment identifier is 1/Q Alignment identifier is 1/R Alignment identifier is 1/S Alignment identifier is 1/T Alignment identifier is 1/U Alignment identifier is 1/Z Alignment identifier is 1/c Alignment identifier is 1/d Alignment identifier is 1/e Alignment identifier is 1/f Alignment identifier is 1/g Alignment identifier is 1/i Alignment identifier is 1/j Alignment identifier is 1/k Alignment identifier is 1/O Alignment identifier is 1/V Alignment identifier is 1/a Alignment identifier is 1/P Alignment identifier is 1/X Alignment identifier is 1/Y Alignment identifier is 1/h Alignment identifier is 1/F Alignment identifier is 1/B Alignment identifier is 1/C Alignment identifier is 1/H Alignment identifier is 1/A Alignment identifier is 1/K Alignment identifier is 1/m Alignment identifier is 1/D Alignment identifier is 1/W Alignment identifier is 1/l Alignment identifier is 1/b Alignment identifier is 1/o Alignment identifier is 1/n Alignment identifier is 1/r Alignment identifier is 1/s Alignment identifier is 1/t Alignment identifier is 1/y Alignment identifier is 1/z Alignment identifier is 1/p Alignment identifier is 1/q Alignment identifier is 1/u Alignment identifier is 1/v Alignment identifier is 1/w Destroying pre-existing alignment with identifier 1/I Alignment identifier is 1/I Alignment identifier is 1/J Alignment identifier is 1/E Alignment identifier is 1/G Alignment identifier is 1/M Window position QRect(2176,1854 100x30) outside any known screen, using primary screen > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected Alignment identifier is 1/J > select /J:196 8 atoms, 7 bonds, 1 residue, 1 model selected > select /J:196-197 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select /J:339 6 atoms, 5 bonds, 1 residue, 1 model selected > select /J:339-340 14 atoms, 13 bonds, 2 residues, 1 model selected > color sel white > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected Alignment identifier is 1/m > select /m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select /m:125-126 18 atoms, 18 bonds, 2 residues, 1 model selected > color sel white > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected Alignment identifier is 1/o > select /o:88-89 21 atoms, 21 bonds, 2 residues, 1 model selected > select /o:88-89 21 atoms, 21 bonds, 2 residues, 1 model selected > color sel white > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected Alignment identifier is 1/q > select /q:227 12 atoms, 12 bonds, 1 residue, 1 model selected > select /q:227-229 27 atoms, 27 bonds, 3 residues, 1 model selected > color sel white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select /q:549 8 atoms, 7 bonds, 1 residue, 1 model selected > select /q:549-550 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected Alignment identifier is 1/v > select /v:65 4 atoms, 3 bonds, 1 residue, 1 model selected > select /v:65-66 13 atoms, 12 bonds, 2 residues, 1 model selected > color sel white > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > select /v:155 9 atoms, 8 bonds, 1 residue, 1 model selected > select /v:155-156 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected Alignment identifier is 1/w > select /w:328 8 atoms, 7 bonds, 1 residue, 1 model selected > select /w:328-329 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected > select /w:639-640 15 atoms, 14 bonds, 2 residues, 1 model selected > select /w:639-640 15 atoms, 14 bonds, 2 residues, 1 model selected > color sel white > select clear > ui mousemode right ""move markers"" [Repeated 1 time(s)] > lighting soft > lighting simple [Repeated 1 time(s)] > lighting soft > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set bgColor gray > set bgColor black > set bgColor white > set bgColor black > select clear > ui tool show ""Side View"" > view orient > ui mousemode right ""mark maximum"" > ui mousemode right ""mark plane"" > ui mousemode right ""mark surface"" > ui mousemode right ""mark center"" > ui mousemode right ""mark point"" > ui mousemode right ""link markers"" > ui mousemode right ""move markers"" > ui mousemode right ""resize markers"" > select /D:267-481 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected Alignment identifier is 1/D > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting soft > select clear > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected Alignment identifier is 1/I > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected Alignment identifier is 1/v > select /v:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select /v:3-45 352 atoms, 355 bonds, 43 residues, 1 model selected > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 14:52:35 2023 ——— opened ChimeraX session > lighting simple > lighting soft > lighting full > lighting soft > select /L 998 atoms, 1017 bonds, 122 residues, 1 model selected > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/3jct-nog2state1.cif"" 3jct-nog2state1.cif title: Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...] Chain information for 3jct-nog2state1.cif #2 --- Chain | Description | UniProt 1 | RDN25-1 rRNA | 2 | RDN58-1 rRNA | 3 | RDN5-2 rRNA | 4 | Probable metalloprotease ARX1 | Q03862 1-593 5 | rRNA-processing protein CGR1 | P53188 1-120 6 | ITS2-1 miscRNA | A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254 B | 60S ribosomal protein L3 | RL3_YEAST 1-387 C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362 D | 60S ribosomal protein L5 | RL5_YEAST 1-297 E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 I | Bud site selection protein 20 | BUD20_YEAST 1-166 J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174 K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376 L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236 X | 60S ribosomal protein L25 | RL25_YEAST 1-142 Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 a | 60S ribosomal protein L28 | RL28_YEAST 1-149 b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647 c | 60S ribosomal protein L30 | RL30_YEAST 1-105 d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 e | 60S ribosomal protein L32 | RL32_YEAST 1-130 f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 k | 60S ribosomal protein L38 | RL38_YEAST 1-78 l | 60S ribosomal protein L39 | RL39_YEAST 1-51 m | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486 n | Pescadillo homolog | PESC_YEAST 1-605 o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220 p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92 q | Ribosome biogenesis protein NOP53 | NOP53_YEAST 1-455 r | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261 s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520 t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322 u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199 v | Ribosome biogenesis protein RPF2 | RPF2_YEAST 1-344 w | Regulator of ribosome biosynthesis | RRS1_YEAST 1-203 x | Ribosome assembly protein 4 | NLE1_YEAST 1-515 y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245 z | UPF0642 protein YBL028C | YBC8_YEAST 1-106 Non-standard residues in 3jct-nog2state1.cif #2 --- GTP — guanosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide all > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:08:11 2023 ——— opened ChimeraX session > select #1/A 1623 atoms, 1663 bonds, 2 pseudobonds, 198 residues, 2 models selected > show sel surfaces > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected Alignment identifier is 1/m > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:24:47 2023 ——— opened ChimeraX session > select #1/m:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/m:156-169 105 atoms, 107 bonds, 14 residues, 1 model selected > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-155 246 atoms, 250 bonds, 31 residues, 1 model selected > color sel lightblue orange Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color (#!1 & sel) #fff125ff [Repeated 1 time(s)] > color (#!1 & sel) #ffd00bff [Repeated 1 time(s)] > color (#!1 & sel) #ffb80cff [Repeated 1 time(s)] > color (#!1 & sel) #ffdc10ff [Repeated 1 time(s)] > color (#!1 & sel) #fff612ff > color (#!1 & sel) #fff613ff > color (#!1 & sel) #ffdd16ff [Repeated 1 time(s)] > color (#!1 & sel) #ffd617ff [Repeated 1 time(s)] > color (#!1 & sel) #ffcf13ff [Repeated 1 time(s)] > color (#!1 & sel) #ffbc13ff [Repeated 1 time(s)] > color (#!1 & sel) #ffa50aff > select clear > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-155 246 atoms, 250 bonds, 31 residues, 1 model selected > color (#!1 & sel) #ffb51dff > color (#!1 & sel) #ffbf40ff > color (#!1 & sel) #ffd8aeff > color (#!1 & sel) #ffdbb2ff > color (#!1 & sel) #ffe0b5ff > color (#!1 & sel) #ffe5bbff > color (#!1 & sel) #fff2c7ff > color (#!1 & sel) #ffe2b1ff > select clear > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-126 18 atoms, 18 bonds, 2 residues, 1 model selected > color sel white > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:54:08 2023 ——— opened ChimeraX session > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > show sel surfaces Alignment identifier is 1/n > select clear > color sel red [Repeated 1 time(s)] > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > select #1/n:594 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/n:591-594 31 atoms, 30 bonds, 4 residues, 1 model selected > color sel red > select clear > select #1/u 976 atoms, 996 bonds, 116 residues, 1 model selected > show sel surfaces > hide sel surfaces > select #1/l 1377 atoms, 1408 bonds, 174 residues, 1 model selected > hide sel > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected Alignment identifier is 1/I > select clear > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Nov 3 09:32:22 2023 ——— opened ChimeraX session > hide #!2 models > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected Alignment identifier is 1/q > color (#!1 & sel) red > undo > color (#!1 & sel) red > undo > select #1/I:562,564,599,605 27 atoms, 25 bonds, 3 residues, 1 model selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/w:562,564,599,605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q:562,564,599,605 Nothing selected > color #1 red > undo > select clear > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q:562,564,599,605 Nothing selected > select #1/q :562,564,599,605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q: 562, 564, 599, 605 Nothing selected > select #1/ q:562, 564, 599, 605 Nothing selected > select #1/ q: 562, 564, 599, 605 Nothing selected > select #1/q: 562, 564, 599, 605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > color #1 red > undo > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q: 388, 392, 449, 482, 510 39 atoms, 35 bonds, 5 residues, 1 model selected > color (#!1 & sel) red > select clear > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Tue Jan 30 16:17:55 2024 ——— opened ChimeraX session > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select #1/l 1377 atoms, 1408 bonds, 174 residues, 1 model selected Alignment identifier is 1/l > select #1/G 1438 atoms, 1463 bonds, 1 pseudobond, 184 residues, 2 models selected > show sel cartoons > select #1/P 1442 atoms, 1465 bonds, 183 residues, 1 model selected > show sel cartoons > select clear > select #1/s 301 atoms, 301 bonds, 36 residues, 1 model selected > show sel cartoons > select #1/W 1870 atoms, 1902 bonds, 232 residues, 1 model selected > show sel cartoons > select clear > select #1/z 444 atoms, 445 bonds, 55 residues, 1 model selected > show sel cartoons > select #1/r 1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected > show sel cartoons > select #1/u 976 atoms, 996 bonds, 116 residues, 1 model selected > show sel cartoons > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Feb 23 15:56:32 2024 ——— opened ChimeraX session > select #1/1 52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected > select 1:970-1110 Expected an objects specifier or a keyword > select 1/1:970-1110 Expected an objects specifier or a keyword > select 2/1:970-1110 Expected an objects specifier or a keyword > select 1/1:970-1110 Expected an objects specifier or a keyword > select 1/1: 970-1110 Expected an objects specifier or a keyword > select clear > select 1/1:970-1110 Expected an objects specifier or a keyword > select #1/1 52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected Alignment identifier is 1/1 > select #1/1:990 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/1:977-990 292 atoms, 324 bonds, 14 residues, 1 model selected > select clear > select #1/1 52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected > select #1/1:2826 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/1:2826 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/1:2823-2824 46 atoms, 51 bonds, 2 residues, 1 model selected > select #1/1:2824-2880 850 atoms, 947 bonds, 19 pseudobonds, 40 residues, 3 models selected > select #1/1:2611 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/1:2611-2925 2295 atoms, 2562 bonds, 43 pseudobonds, 108 residues, 3 models selected > select clear > select #1/1:2820 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel red > select #1/1:2922 23 atoms, 25 bonds, 1 residue, 1 model selected > select #1/1:2922 23 atoms, 25 bonds, 1 residue, 1 model selected > color sel red > select #1/q:510 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/q:510-511 18 atoms, 17 bonds, 2 residues, 1 model selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > color (#!1 & sel) #b5ffcdff > color (#!1 & sel) #a7ffe4ff > color (#!1 & sel) #76ffb2ff > color (#!1 & sel) #56ff7dff > color (#!1 & sel) #6dffa9ff > color (#!1 & sel) #4dccffff > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > color (#!1 & sel) #6fffb0ff > color (#!1 & sel) #3aff92ff > select clear > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > color (#!1 & sel) white > undo > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > color (#!1 & sel) white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q:227-228 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/q:227 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!1 & sel) white > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected Alignment identifier is 1/J > select #1/J:196-197 16 atoms, 15 bonds, 2 residues, 1 model selected > color (#!1 & sel) white > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select #1/J:340 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:340 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!1 & sel) white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/q:550 4 atoms, 3 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > select clear > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q:227 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/q:227 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select #1/J:196 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:196 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select #1/J:340 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:340 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > color (#!1 & sel) #62ffb0ff > color (#!1 & sel) #acff7eff > color (#!1 & sel) #c3ffadff > select clear > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > color (#!1 & sel) dark gray > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > color (#!1 & sel) dark gray > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > color (#!1 & sel) dark gray > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected > color (#!1 & sel) dim gray > color (#!1 & sel) gray > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected > color (#!1 & sel) dark gray > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > color (#!1 & sel) gray > select #1/W 1870 atoms, 1902 bonds, 232 residues, 1 model selected > show sel surfaces > color sel gray > select #1/l 1377 atoms, 1408 bonds, 174 residues, 1 model selected > show sel surfaces > select clear > select #1/r 1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected > select #1/t 2328 atoms, 2355 bonds, 1 pseudobond, 290 residues, 2 models selected > select #1/u 976 atoms, 996 bonds, 116 residues, 1 model selected > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select #1/J:196 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/J:196-197 16 atoms, 15 bonds, 2 residues, 1 model selected > color (#!1 & sel) red > select #1/1:2858 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/1:2855-2858 83 atoms, 91 bonds, 4 residues, 1 model selected > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs-grey.cxs"" > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > set bgColor gray > set bgColor white > set bgColor black 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: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Feb 23 15:56:32 2024UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Tue Jan 30 16:17:55 2024UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Nov 3 09:32:22 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:54:08 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:24:47 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 15:08:11 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/state E IDRs.cxs"" Log from Fri Oct 20 14:52:35 2023UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/stefhed/Library/Mobile > Documents/com~apple~CloudDocs/Downloads/6elz 2.cif"" 6elz 2.cif title: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes [more info...] Chain information for 6elz 2.cif #1 --- Chain | Description | UniProt 1 | 25S ribosomal RNA | 2 | 5.8S ribosomal RNA | 6 | Internal transcribed spacer 2 | A | Ribosome biogenesis protein BRX1 | BRX1_YEAST 1-291 B | 60S ribosomal protein L3 | RL3_YEAST 1-387 C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362 D | ATP-dependent RNA helicase HAS1 | HAS1_YEAST 1-505 E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 I | Nucleolar complex-associated protein 3 | NOC3_YEAST 1-663 J | rRNA-processing protein EBP2 | EBP2_YEAST 1-427 K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376 L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236 X | 60S ribosomal protein L25 | RL25_YEAST 1-142 Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 a | 60S ribosomal protein L28 | RL28_YEAST 1-149 b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647 c | 60S ribosomal protein L30 | RL30_YEAST 1-105 d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 e | 60S ribosomal protein L32 | RL32_YEAST 1-130 f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 k | 60S ribosomal protein L38 | RL38_YEAST 1-78 l | 60S ribosome subunit biogenesis protein NIP7 | NIP7_YEAST 1-181 m | Ribosome biogenesis protein ERB1 | ERB1_YEAST 1-807 n | Pescadillo homolog | PESC_YEAS7 1-605 o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220 p | Ribosome biogenesis protein YTM1 | YTM1_YEAS7 1-460 q | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | NOP2_YEAST 1-618 r | Ribosome biogenesis protein NSA2 | NSA2_YEAS7 1-261 s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520 t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322 u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199 v | Nucleolar protein 16 | NOP16_YEAST 1-231 w | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | SPB1_YEAST 1-841 y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245 z | UPF0642 protein YBL028C | YBC8_YEAST 1-106 Non-standard residues in 6elz 2.cif #1 --- ZN — zinc ion > select all 134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models selected > hide sel > show nucleic > hide sel surfaces > show sel cartoons > hide sel surfaces > hide surfaces > select all 134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models selected > hide all > select clear > select #1:I, y, s, K, W, A, r, u, t, p, z 29269 atoms, 32087 bonds, 715 pseudobonds, 1392 residues, 3 models selected > hide sel > hide sel cartoons > hide sel surfaces > select #1:K Nothing selected > select #1/K 2073 atoms, 2107 bonds, 1 pseudobond, 257 residues, 2 models selected > hide sel > hide sel cartoons > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > hide sel cartoons > select #1/y, s, K, W, A, r, u, t, p, z 15075 atoms, 15315 bonds, 10 pseudobonds, 1883 residues, 2 models selected > hide sel cartoons > select nucleic 57318 atoms, 64137 bonds, 2412 pseudobonds, 2680 residues, 3 models selected > show sel cartoons > ladder nucleotides Unknown command: ladder nucleotides > show nucleotides ladder Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > nucleotides sel ladder [Repeated 2 time(s)] > select #1/A-Z 38689 atoms, 39375 bonds, 15 pseudobonds, 4848 residues, 2 models selected > hide sel > hide sel cartoons > select #1/a, c-k 7802 atoms, 7921 bonds, 4 pseudobonds, 981 residues, 2 models selected > hide sel cartoons > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > show sel surfaces > hide sel cartoons > color sel yellow > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel red > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > hide sel cartoons > show sel surfaces > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > hide sel cartoons > show sel surfaces > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected > hide sel cartoons > show sel surfaces > color sel blue > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > hide sel surfaces > hide sel cartoons > show sel surfaces > color sel light green > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel orange > select clear > select #1/b 3410 atoms, 3474 bonds, 3 pseudobonds, 421 residues, 2 models selected > hide sel cartoons > show sel surfaces > color sel light blue > select clear > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > hide sel cartoons > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > hide sel cartoons > show sel surfaces > select clear > select #1/:42-635 Expected an objects specifier or a keyword > select #1/1:42-635 11543 atoms, 12934 bonds, 447 pseudobonds, 537 residues, 3 models selected > color sel lightblue red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel red > color sel lightred Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lightblue red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #1/1:662-1435 14182 atoms, 15879 bonds, 569 pseudobonds, 661 residues, 3 models selected > color sel orange > select #1/1:1452-1878 8891 atoms, 9946 bonds, 390 pseudobonds, 416 residues, 3 models selected > color sel yellow > select up 52595 atoms, 58864 bonds, 390 pseudobonds, 2457 residues, 3 models selected > select up 134887 atoms, 143091 bonds, 2448 pseudobonds, 12372 residues, 3 models selected > select #1/1:1911-2332 902 atoms, 1007 bonds, 48 pseudobonds, 42 residues, 3 models selected > color sel light green > color sel forest green > select #1/1:2400-2980 4471 atoms, 4995 bonds, 172 pseudobonds, 210 residues, 3 models selected > color sel medium blue > select #1/1:2995-3396 8560 atoms, 9569 bonds, 344 pseudobonds, 402 residues, 2 models selected > color sel lightblue purple Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel purple > color medium purple > color sel medium purple > select #1/2 3353 atoms, 3746 bonds, 83 pseudobonds, 158 residues, 2 models selected > color sel pink > color sel hot pink > select clear > sequence chain #1/D Alignment identifier is 1/D > select #1/D 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select /I:132-601 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select /I:132-601 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > sequence chain #1/I Alignment identifier is 1/I > select /I:132-133 18 atoms, 17 bonds, 2 residues, 1 model selected > select /I:132-133 18 atoms, 17 bonds, 2 residues, 1 model selected > color sel white > select clear Alignment identifier is 1/1 Alignment identifier is 1/2 Alignment identifier is 1/6 Alignment identifier is 1/L Alignment identifier is 1/N Alignment identifier is 1/Q Alignment identifier is 1/R Alignment identifier is 1/S Alignment identifier is 1/T Alignment identifier is 1/U Alignment identifier is 1/Z Alignment identifier is 1/c Alignment identifier is 1/d Alignment identifier is 1/e Alignment identifier is 1/f Alignment identifier is 1/g Alignment identifier is 1/i Alignment identifier is 1/j Alignment identifier is 1/k Alignment identifier is 1/O Alignment identifier is 1/V Alignment identifier is 1/a Alignment identifier is 1/P Alignment identifier is 1/X Alignment identifier is 1/Y Alignment identifier is 1/h Alignment identifier is 1/F Alignment identifier is 1/B Alignment identifier is 1/C Alignment identifier is 1/H Alignment identifier is 1/A Alignment identifier is 1/K Alignment identifier is 1/m Alignment identifier is 1/D Alignment identifier is 1/W Alignment identifier is 1/l Alignment identifier is 1/b Alignment identifier is 1/o Alignment identifier is 1/n Alignment identifier is 1/r Alignment identifier is 1/s Alignment identifier is 1/t Alignment identifier is 1/y Alignment identifier is 1/z Alignment identifier is 1/p Alignment identifier is 1/q Alignment identifier is 1/u Alignment identifier is 1/v Alignment identifier is 1/w Destroying pre-existing alignment with identifier 1/I Alignment identifier is 1/I Alignment identifier is 1/J Alignment identifier is 1/E Alignment identifier is 1/G Alignment identifier is 1/M Window position QRect(2176,1854 100x30) outside any known screen, using primary screen > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected Alignment identifier is 1/J > select /J:196 8 atoms, 7 bonds, 1 residue, 1 model selected > select /J:196-197 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/J 1215 atoms, 1232 bonds, 145 residues, 1 model selected > select /J:339 6 atoms, 5 bonds, 1 residue, 1 model selected > select /J:339-340 14 atoms, 13 bonds, 2 residues, 1 model selected > color sel white > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected Alignment identifier is 1/m > select /m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select /m:125-126 18 atoms, 18 bonds, 2 residues, 1 model selected > color sel white > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected Alignment identifier is 1/o > select /o:88-89 21 atoms, 21 bonds, 2 residues, 1 model selected > select /o:88-89 21 atoms, 21 bonds, 2 residues, 1 model selected > color sel white > select #1/o 1107 atoms, 1129 bonds, 133 residues, 1 model selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected Alignment identifier is 1/q > select /q:227 12 atoms, 12 bonds, 1 residue, 1 model selected > select /q:227-229 27 atoms, 27 bonds, 3 residues, 1 model selected > color sel white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select /q:549 8 atoms, 7 bonds, 1 residue, 1 model selected > select /q:549-550 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel white > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected Alignment identifier is 1/v > select /v:65 4 atoms, 3 bonds, 1 residue, 1 model selected > select /v:65-66 13 atoms, 12 bonds, 2 residues, 1 model selected > color sel white > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > select /v:155 9 atoms, 8 bonds, 1 residue, 1 model selected > select /v:155-156 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected Alignment identifier is 1/w > select /w:328 8 atoms, 7 bonds, 1 residue, 1 model selected > select /w:328-329 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel white > select #1/w 3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected > select /w:639-640 15 atoms, 14 bonds, 2 residues, 1 model selected > select /w:639-640 15 atoms, 14 bonds, 2 residues, 1 model selected > color sel white > select clear > ui mousemode right ""move markers"" [Repeated 1 time(s)] > lighting soft > lighting simple [Repeated 1 time(s)] > lighting soft > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set bgColor gray > set bgColor black > set bgColor white > set bgColor black > select clear > ui tool show ""Side View"" > view orient > ui mousemode right ""mark maximum"" > ui mousemode right ""mark plane"" > ui mousemode right ""mark surface"" > ui mousemode right ""mark center"" > ui mousemode right ""mark point"" > ui mousemode right ""link markers"" > ui mousemode right ""move markers"" > ui mousemode right ""resize markers"" > select /D:267-481 1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected Alignment identifier is 1/D > lighting simple > lighting soft > lighting full > lighting flat > lighting full > lighting soft > select clear > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected Alignment identifier is 1/I > select #1/v 1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected Alignment identifier is 1/v > select /v:3 6 atoms, 5 bonds, 1 residue, 1 model selected > select /v:3-45 352 atoms, 355 bonds, 43 residues, 1 model selected > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 14:52:35 2023 ——— opened ChimeraX session > lighting simple > lighting soft > lighting full > lighting soft > select /L 998 atoms, 1017 bonds, 122 residues, 1 model selected > open ""/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford > Lab/Structures-chimera stuff/3jct-nog2state1.cif"" 3jct-nog2state1.cif title: Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...] Chain information for 3jct-nog2state1.cif #2 --- Chain | Description | UniProt 1 | RDN25-1 rRNA | 2 | RDN58-1 rRNA | 3 | RDN5-2 rRNA | 4 | Probable metalloprotease ARX1 | Q03862 1-593 5 | rRNA-processing protein CGR1 | P53188 1-120 6 | ITS2-1 miscRNA | A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254 B | 60S ribosomal protein L3 | RL3_YEAST 1-387 C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362 D | 60S ribosomal protein L5 | RL5_YEAST 1-297 E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 I | Bud site selection protein 20 | BUD20_YEAST 1-166 J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174 K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376 L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236 X | 60S ribosomal protein L25 | RL25_YEAST 1-142 Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 a | 60S ribosomal protein L28 | RL28_YEAST 1-149 b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647 c | 60S ribosomal protein L30 | RL30_YEAST 1-105 d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 e | 60S ribosomal protein L32 | RL32_YEAST 1-130 f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 k | 60S ribosomal protein L38 | RL38_YEAST 1-78 l | 60S ribosomal protein L39 | RL39_YEAST 1-51 m | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486 n | Pescadillo homolog | PESC_YEAST 1-605 o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220 p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92 q | Ribosome biogenesis protein NOP53 | NOP53_YEAST 1-455 r | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261 s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520 t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322 u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199 v | Ribosome biogenesis protein RPF2 | RPF2_YEAST 1-344 w | Regulator of ribosome biosynthesis | RRS1_YEAST 1-203 x | Ribosome assembly protein 4 | NLE1_YEAST 1-515 y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245 z | UPF0642 protein YBL028C | YBC8_YEAST 1-106 Non-standard residues in 3jct-nog2state1.cif #2 --- GTP — guanosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide all > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:08:11 2023 ——— opened ChimeraX session > select #1/A 1623 atoms, 1663 bonds, 2 pseudobonds, 198 residues, 2 models selected > show sel surfaces > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected Alignment identifier is 1/m > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:24:47 2023 ——— opened ChimeraX session > select #1/m:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/m:156-169 105 atoms, 107 bonds, 14 residues, 1 model selected > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-155 246 atoms, 250 bonds, 31 residues, 1 model selected > color sel lightblue orange Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color (#!1 & sel) #fff125ff [Repeated 1 time(s)] > color (#!1 & sel) #ffd00bff [Repeated 1 time(s)] > color (#!1 & sel) #ffb80cff [Repeated 1 time(s)] > color (#!1 & sel) #ffdc10ff [Repeated 1 time(s)] > color (#!1 & sel) #fff612ff > color (#!1 & sel) #fff613ff > color (#!1 & sel) #ffdd16ff [Repeated 1 time(s)] > color (#!1 & sel) #ffd617ff [Repeated 1 time(s)] > color (#!1 & sel) #ffcf13ff [Repeated 1 time(s)] > color (#!1 & sel) #ffbc13ff [Repeated 1 time(s)] > color (#!1 & sel) #ffa50aff > select clear > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-155 246 atoms, 250 bonds, 31 residues, 1 model selected > color (#!1 & sel) #ffb51dff > color (#!1 & sel) #ffbf40ff > color (#!1 & sel) #ffd8aeff > color (#!1 & sel) #ffdbb2ff > color (#!1 & sel) #ffe0b5ff > color (#!1 & sel) #ffe5bbff > color (#!1 & sel) #fff2c7ff > color (#!1 & sel) #ffe2b1ff > select clear > select #1/m 5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected > select #1/m:125 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/m:125-126 18 atoms, 18 bonds, 2 residues, 1 model selected > color sel white > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Oct 20 15:54:08 2023 ——— opened ChimeraX session > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > show sel surfaces Alignment identifier is 1/n > select clear > color sel red [Repeated 1 time(s)] > select #1/n 3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected > select #1/n:594 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/n:591-594 31 atoms, 30 bonds, 4 residues, 1 model selected > color sel red > select clear > select #1/u 976 atoms, 996 bonds, 116 residues, 1 model selected > show sel surfaces > hide sel surfaces > select #1/l 1377 atoms, 1408 bonds, 174 residues, 1 model selected > hide sel > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected Alignment identifier is 1/I > select clear > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Nov 3 09:32:22 2023 ——— opened ChimeraX session > hide #!2 models > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected Alignment identifier is 1/q > color (#!1 & sel) red > undo > color (#!1 & sel) red > undo > select #1/I:562,564,599,605 27 atoms, 25 bonds, 3 residues, 1 model selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/w:562,564,599,605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q:562,564,599,605 Nothing selected > color #1 red > undo > select clear > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q:562,564,599,605 Nothing selected > select #1/q :562,564,599,605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > select #1/q: 562, 564, 599, 605 Nothing selected > select #1/ q:562, 564, 599, 605 Nothing selected > select #1/ q: 562, 564, 599, 605 Nothing selected > select #1/q: 562, 564, 599, 605 Nothing selected > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select clear > color #1 red > undo > select #1/q 2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected > select #1/q: 388, 392, 449, 482, 510 39 atoms, 35 bonds, 5 residues, 1 model selected > color (#!1 & sel) red > select clear > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Tue Jan 30 16:17:55 2024 ——— opened ChimeraX session > select #1/I 3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected > select #1/l 1377 atoms, 1408 bonds, 174 residues, 1 model selected Alignment identifier is 1/l > select #1/G 1438 atoms, 1463 bonds, 1 pseudobond, 184 residues, 2 models selected > show sel cartoons > select #1/P 1442 atoms, 1465 bonds, 183 residues, 1 model selected > show sel cartoons > select clear > select #1/s 301 atoms, 301 bonds, 36 residues, 1 model selected > show sel cartoons > select #1/W 1870 atoms, 1902 bonds, 232 residues, 1 model selected > show sel cartoons > select clear > select #1/z 444 atoms, 445 bonds, 55 residues, 1 model selected > show sel cartoons > select #1/r 1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected > show sel cartoons > select #1/u 976 atoms, 996 bonds, 116 residues, 1 model selected > show sel cartoons > save ""/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E > IDRs.cxs"" ——— End of log from Fri Feb 23 15:56:32 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple 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 Air Model Identifier: Mac14,2 Model Number: FLY33LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 28 days, 15 hours, 25 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL SE2422HX: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz 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: 2.2.4 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-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: 1.6rc202304252053 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-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: 3.3.0 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