id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8903 Crash in ~QGridLayout chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001ebe7000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001dbe4000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File 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""logWritingSignature"" : ""137ac88e6d5f590eee595ac92c2074da44a53d68"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""63f8068a238e7b23a1f30123"" }, ""deploymentId"" : 240000055 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip available: 22.2.2 -> 23.1.2 [notice] To update, run: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/leonpalaoiii/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl Requirement already satisfied: ChimeraX-UI~=1.3 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-XMAS==1.1.2) (1.24.3) Collecting seaborn Downloading seaborn-0.12.2-py3-none-any.whl (293 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 2.9 MB/s eta 0:00:00 Collecting qtrangeslider Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB) Collecting pandas Downloading pandas-2.0.1-cp39-cp39-macosx_10_9_x86_64.whl (11.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.8/11.8 MB 6.8 MB/s eta 0:00:00 Requirement already satisfied: ChimeraX-Core~=1.3 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-XMAS==1.1.2) (1.5) Collecting openpyxl Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 6.4 MB/s eta 0:00:00 Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0) Collecting et-xmlfile Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) Requirement already satisfied: numpy>=1.20.3 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1) Collecting tzdata>=2022.1 Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.8/341.8 kB 4.5 MB/s eta 0:00:00 Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6) Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2) Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.2) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX- XMAS==1.1.2) (1.0.1) Requirement already satisfied: pyparsing>=2.2.1 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9) Requirement already satisfied: fonttools>=4.22.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (4.38.0) Requirement already satisfied: cycler>=0.10 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (0.11.0) Requirement already satisfied: kiwisolver>=1.0.1 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4) Requirement already satisfied: packaging>=20.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3) Requirement already satisfied: pillow>=6.2.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0) Requirement already satisfied: six>=1.5 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from python-dateutil>=2.8.2->pandas->ChimeraX-XMAS==1.1.2) (1.16.0) Installing collected packages: tzdata, qtrangeslider, et-xmlfile, pandas, openpyxl, seaborn, ChimeraX-XMAS Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2 pandas-2.0.1 qtrangeslider-0.1.5 seaborn-0.12.2 tzdata-2023.3 \--- Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2 pandas-2.0.1 qtrangeslider-0.1.5 seaborn-0.12.2 tzdata-2023.3 Installed ChimeraX-XMAS (1.1.2) > toolshed show > ui tool show XMAS > open /Users/leonpalaoiii/Users/leonpalaoiii/Downloads/Chimera/PDB/6T9I.pdb No such file/path: /Users/leonpalaoiii/Users/leonpalaoiii/Downloads/Chimera/PDB/6T9I.pdb > open /Users/leonpalaoiii/Downloads/Chimera/PDB/6T9I.pdb 6T9I.pdb title: Cryo-em structure of transcription coactivator saga [more info...] Chain information for 6T9I.pdb #1 --- Chain | Description | UniProt B | transcription factor SPT20 | SPT20_YEAST C | positive regulator OF TY transcription | SPT3_YEAST D | transcription initiation factor tfiid subunit 5 | TAF5_YEAST E | transcription initiation factor tfiid subunit 6 | TAF6_YEAST F | transcription initiation factor tfiid subunit 9 | TAF9_YEAST G | transcription initiation factor tfiid subunit 10 | TAF10_YEAST H | transcriptional coactivator HFI1/ADA1 | HFI1_YEAST I | transcription initiation factor tfiid subunit 12 | TAF12_YEAST K | transcriptional activator SPT7 | SPT7_YEAST Q | saga-associated factor 73 | SGF73_YEAST T | P400 KDA component OF SAGA | TRA1_YEAST U | unassigned sequence | Peptide pair mapping of Xi evidence file: /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS.csv Unique peptide pairs: 558 out of 1647 Unique peptide pairs with pseudobonds: 93 Pseudobonds are stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1.pb Mapping information is stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS.csv Unique peptide pairs: 558 out of 1647 Unique peptide pairs with pseudobonds: 93 Pseudobonds are stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1.pb Mapping information is stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1.tsv > style stick Changed 48821 atom styles > style ball Changed 48821 atom styles > style ball Changed 48821 atom styles > style sphere Changed 48821 atom styles > hide #2 models > show #2 models > hide #2 models > hide #3 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #3 models > show #2 models > hide #2 models > hide #3 models > open pdb:7UIG Summary of feedback from opening 7UIG fetched from pdb --- note | Fetching compressed mmCIF 7uig from http://files.rcsb.org/download/7uig.cif 7uig title: Mediator-PIC Early (Mediator A) [more info...] Chain information for 7uig #4 --- Chain | Description | UniProt a | Mediator of RNA polymerase II transcription subunit 1 | MED1_YEAST d | Mediator of RNA polymerase II transcription subunit 4 | MED4_YEAST f | Mediator of RNA polymerase II transcription subunit 6 | MED6_YEAST g | Mediator of RNA polymerase II transcription subunit 7 | MED7_YEAST h | Mediator of RNA polymerase II transcription subunit 8 | MED8_YEAST i | Mediator of RNA polymerase II transcription subunit 9 | MED9_YEAST j | Mediator of RNA polymerase II transcription subunit 10 | MED10_YEAST k | Mediator of RNA polymerase II transcription subunit 11 | MED11_YEAST n | Mediator of RNA polymerase II transcription subunit 14 | MED14_YEAST q | Mediator of RNA polymerase II transcription subunit 17 | MED17_YEAST r | Mediator of RNA polymerase II transcription subunit 18 | MED18_YEAST s | Mediator of RNA polymerase II transcription subunit 19 | MED19_YEAST t | Mediator of RNA polymerase II transcription subunit 20 | MED20_YEAST u | Mediator of RNA polymerase II transcription subunit 21 | MED21_YEAST v | Mediator of RNA polymerase II transcription subunit 22 | MED22_YEAST w | Mediator of RNA polymerase II transcription subunit 31 | MED31_YEAST z | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST > select add #4 27580 atoms, 28041 bonds, 29 pseudobonds, 3390 residues, 2 models selected > select subtract #4 Nothing selected > ui mousemode right ""translate selected models"" > ui mousemode right rotate > ui mousemode right translate > hide #!4 models > show #!4 models > show #!4 target m > select add #4 27580 atoms, 28041 bonds, 29 pseudobonds, 3390 residues, 2 models selected > select subtract #4 Nothing selected > ui mousemode right ""translate selected models"" > select add #4 27580 atoms, 28041 bonds, 29 pseudobonds, 3390 residues, 2 models selected > view matrix models #4,1,0,0,20.472,0,1,0,66.652,0,0,1,28.358 > view matrix models #4,1,0,0,24.745,0,1,0,138.12,0,0,1,-22.791 > view matrix models #4,1,0,0,1.583,0,1,0,140.7,0,0,1,-105.09 > view matrix models #4,1,0,0,8.3174,0,1,0,117.1,0,0,1,-28.893 > view matrix models #4,1,0,0,51.498,0,1,0,158.88,0,0,1,17.962 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.059931,0.86063,-0.50569,180.21,0.81252,0.33633,0.47611,42.111,0.57984,-0.38235,-0.71944,355.82 > view matrix models > #4,-0.87749,-0.32018,-0.35707,614.22,-0.27584,0.94598,-0.1704,268.65,0.39234,-0.051033,-0.9184,358.42 > view matrix models > #4,0.19466,-0.8307,0.52159,316.98,-0.97345,-0.22888,-0.0012244,670.74,0.1204,-0.5075,-0.8532,514.95 > view matrix models > #4,0.44435,0.48605,0.75254,-108.71,-0.27664,-0.72452,0.6313,504.36,0.85207,-0.4887,-0.18748,208.14 > close #4 > open pdb:7UI9 Summary of feedback from opening 7UI9 fetched from pdb --- note | Fetching compressed mmCIF 7ui9 from http://files.rcsb.org/download/7ui9.cif 7ui9 title: Core Mediator-PICearly (Copy A) [more info...] Chain information for 7ui9 #4 --- Chain | Description | UniProt A | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST B | DNA-directed RNA polymerase II subunit RPB2 | RPB2_YEAST C | DNA-directed RNA polymerase II subunit RPB3 | RPB3_YEAST D | DNA-directed RNA polymerase II subunit RPB4 | RPB4_YEAST E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_YEAST F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_YEAST G | DNA-directed RNA polymerase II subunit RPB7 | RPB7_YEAST H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_YEAST I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_YEAST J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_YEAST K | DNA-directed RNA polymerase II subunit RPB11 | RPB11_YEAST L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_YEAST M | Transcription initiation factor IIB | TF2B_YEAST P | Transcription initiation factor IIF subunit alpha | T2FA_YEAST Q | Transcription initiation factor IIF subunit beta | T2FB_YEAST S | Transcription elongation factor S-II | TFS2_YEAST a | Mediator of RNA polymerase II transcription subunit 1 | MED1_YEAST d | Mediator of RNA polymerase II transcription subunit 4 | MED4_YEAST f | Mediator of RNA polymerase II transcription subunit 6 | MED6_YEAST g | Mediator of RNA polymerase II transcription subunit 7 | MED7_YEAST h | Mediator of RNA polymerase II transcription subunit 8 | MED8_YEAST i | Mediator of RNA polymerase II transcription subunit 9 | MED9_YEAST j | Mediator of RNA polymerase II transcription subunit 10 | MED10_YEAST k | Mediator of RNA polymerase II transcription subunit 11 | MED11_YEAST n | Mediator of RNA polymerase II transcription subunit 14 | MED14_YEAST q | Mediator of RNA polymerase II transcription subunit 17 | MED17_YEAST r | Mediator of RNA polymerase II transcription subunit 18 | MED18_YEAST s | Mediator of RNA polymerase II transcription subunit 19 | MED19_YEAST t | Mediator of RNA polymerase II transcription subunit 20 | MED20_YEAST u | Mediator of RNA polymerase II transcription subunit 21 | MED21_YEAST v | Mediator of RNA polymerase II transcription subunit 22 | MED22_YEAST w | Mediator of RNA polymerase II transcription subunit 31 | MED31_YEAST z | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST > select add #4 63137 atoms, 64254 bonds, 36 pseudobonds, 7857 residues, 2 models selected > hide #!1 models > select subtract #4 Nothing selected > open pdb:7UIO Summary of feedback from opening 7UIO fetched from pdb --- notes | Fetching compressed mmCIF 7uio from http://files.rcsb.org/download/7uio.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif 7uio title: Mediator-PIC Early (Composite Model) [more info...] Chain information for 7uio #5 --- Chain | Description | UniProt A | DNA (38-MER) | AA BA | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST AB BB | DNA-directed RNA polymerase II subunit RPB2 | RPB2_YEAST AC BC | DNA-directed RNA polymerase II subunit RPB3 | RPB3_YEAST AD BD | DNA-directed RNA polymerase II subunit RPB4 | RPB4_YEAST AE BE | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_YEAST AF BF | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_YEAST AG BG | DNA-directed RNA polymerase II subunit RPB7 | RPB7_YEAST AH BH | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_YEAST AI BI | DNA-directed RNA polymerase II subunit RPB9 | RPB9_YEAST AJ BJ | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_YEAST AK BK | DNA-directed RNA polymerase II subunit RPB11 | RPB11_YEAST AL BL | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_YEAST AM BM | Transcription initiation factor IIB | TF2B_YEAST AP BP | Transcription initiation factor IIF subunit alpha | T2FA_YEAST AQ BQ | Transcription initiation factor IIF subunit beta | T2FB_YEAST AS BS | Transcription elongation factor S-II | TFS2_YEAST Aa Ba | Mediator of RNA polymerase II transcription subunit 1 | MED1_YEAST Ab Bb | Mediator of RNA polymerase II transcription subunit 2 | MED2_YEAST Ac Bc | Mediator of RNA polymerase II transcription subunit 3 | MED3_YEAST Ad Bd | Mediator of RNA polymerase II transcription subunit 4 | MED4_YEAST Ae Be | Mediator of RNA polymerase II transcription subunit 5 | MED5_YEAST Af Bf | Mediator of RNA polymerase II transcription subunit 6 | MED6_YEAST Ag Bg | Mediator of RNA polymerase II transcription subunit 7 | MED7_YEAST Ah Bh | Mediator of RNA polymerase II transcription subunit 8 | MED8_YEAST Ai Bi | Mediator of RNA polymerase II transcription subunit 9 | MED9_YEAST Aj Bj | Mediator of RNA polymerase II transcription subunit 10 | MED10_YEAST Ak Bk | Mediator of RNA polymerase II transcription subunit 11 | MED11_YEAST An Bn | Mediator of RNA polymerase II transcription subunit 14 | MED14_YEAST Ao Bo | Mediator of RNA polymerase II transcription subunit 15 | MED15_YEAST Ap Bp | Mediator of RNA polymerase II transcription subunit 16 | MED16_YEAST Aq Bq | Mediator of RNA polymerase II transcription subunit 17 | MED17_YEAST Ar Br | Mediator of RNA polymerase II transcription subunit 18 | MED18_YEAST As Bs | Mediator of RNA polymerase II transcription subunit 19 | MED19_YEAST At Bt | Mediator of RNA polymerase II transcription subunit 20 | MED20_YEAST Au Bu | Mediator of RNA polymerase II transcription subunit 21 | MED21_YEAST Av Bv | Mediator of RNA polymerase II transcription subunit 22 | MED22_YEAST Aw Bw | Mediator of RNA polymerase II transcription subunit 31 | MED31_YEAST Az Bz | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST B | DNA (37-MER) | GA GB | Regulatory protein GAL4 | GAL4_YEAST Non-standard residues in 7uio #5 --- ALA — alanine ASP — aspartic acid THR — threonine ZN — zinc ion > hide #!4 models > open pdb:7UIG 7uig title: Mediator-PIC Early (Mediator A) [more info...] Chain information for 7uig #6 --- Chain | Description | UniProt a | Mediator of RNA polymerase II transcription subunit 1 | MED1_YEAST d | Mediator of RNA polymerase II transcription subunit 4 | MED4_YEAST f | Mediator of RNA polymerase II transcription subunit 6 | MED6_YEAST g | Mediator of RNA polymerase II transcription subunit 7 | MED7_YEAST h | Mediator of RNA polymerase II transcription subunit 8 | MED8_YEAST i | Mediator of RNA polymerase II transcription subunit 9 | MED9_YEAST j | Mediator of RNA polymerase II transcription subunit 10 | MED10_YEAST k | Mediator of RNA polymerase II transcription subunit 11 | MED11_YEAST n | Mediator of RNA polymerase II transcription subunit 14 | MED14_YEAST q | Mediator of RNA polymerase II transcription subunit 17 | MED17_YEAST r | Mediator of RNA polymerase II transcription subunit 18 | MED18_YEAST s | Mediator of RNA polymerase II transcription subunit 19 | MED19_YEAST t | Mediator of RNA polymerase II transcription subunit 20 | MED20_YEAST u | Mediator of RNA polymerase II transcription subunit 21 | MED21_YEAST v | Mediator of RNA polymerase II transcription subunit 22 | MED22_YEAST w | Mediator of RNA polymerase II transcription subunit 31 | MED31_YEAST z | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > show #3 models > hide #3 models > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!6 models > close #5 > close #6 Peptide pair mapping of Xi evidence file: /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS.csv Unique peptide pairs: 558 out of 1647 Unique peptide pairs with pseudobonds: 202 Pseudobonds are stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,4.pb Mapping information is stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,4.tsv > open 1D66 Summary of feedback from opening 1D66 fetched from pdb --- notes | Fetching compressed mmCIF 1d66 from http://files.rcsb.org/download/1d66.cif Fetching CCD CD from http://ligand-expo.rcsb.org/reports/C/CD/CD.cif 1d66 title: Dna recognition by GAL4: structure of A protein/DNA complex [more info...] Chain information for 1d66 #6 --- Chain | Description | UniProt A B | PROTEIN (GAL4) | GAL4_YEAST D | DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3') | E | DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*TP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3') | Non-standard residues in 1d66 #6 --- CD — cadmium ion Peptide pair mapping of Xi evidence file: /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS.csv Unique peptide pairs: 558 out of 1647 Unique peptide pairs with pseudobonds: 208 Pseudobonds are stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,4,6.pb Mapping information is stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,4,6.tsv > show #3 models > show #2 models > show #!1 models > tile #1,4,6 3 models tiled > set independent Expected a keyword > select subtract #7 Nothing selected > select add #1 48821 atoms, 49821 bonds, 368 pseudobonds, 6047 residues, 6 models selected > view matrix models > #1,0.38337,0.54968,0.74221,-124.87,-0.65141,0.73061,-0.20463,229.89,-0.65475,-0.40503,0.63817,288.21,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,-0.42718,0.44937,-0.78459,344.06,-0.73867,0.32698,0.58945,188.52,0.52143,0.83136,0.19226,-137.19,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,-0.97299,0.15623,0.16995,344.94,0.19548,0.9492,0.24658,-74.875,-0.12279,0.27314,-0.9541,325.02,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.58389,-0.55853,-0.58917,312.97,-0.51486,-0.81587,0.26321,444.93,-0.6277,0.14965,-0.76394,421.22,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.76458,-0.21681,-0.60697,206.05,-0.19703,-0.97527,0.10017,442.75,-0.61368,0.043005,-0.78838,445.47,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.39498,0.90781,-0.14094,-41.826,0.90522,-0.35841,0.22829,59.422,0.15673,-0.21775,-0.96334,373.15,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.92704,-0.28358,-0.2453,120.36,-0.15164,-0.88188,0.44642,350.1,-0.34292,-0.37666,-0.86054,491.79,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.37261,-0.68492,-0.62614,390.45,0.20831,-0.59577,0.77567,154.3,-0.9043,-0.41945,-0.079321,474.37,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.085632,0.73734,-0.67007,155.46,0.72119,-0.5099,-0.46892,257.43,-0.68742,-0.4431,-0.57543,525.21,#2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > select add #6 50583 atoms, 51633 bonds, 443 pseudobonds, 6254 residues, 9 models selected > select subtract #3 50583 atoms, 51633 bonds, 359 pseudobonds, 6254 residues, 8 models selected > select subtract #2 50583 atoms, 51633 bonds, 275 pseudobonds, 6254 residues, 7 models selected > select subtract #1 1762 atoms, 1812 bonds, 75 pseudobonds, 207 residues, 4 models selected > view matrix models > #6,-0.66439,-0.63403,0.39572,176.48,0.21376,-0.66856,-0.71227,306.35,0.71616,-0.38864,0.57972,-87.867,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.66439,-0.63403,0.39572,242.12,0.21376,-0.66856,-0.71227,358.2,0.71616,-0.38864,0.57972,30.036,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.66439,-0.63403,0.39572,247.62,0.21376,-0.66856,-0.71227,361.94,0.71616,-0.38864,0.57972,40.85,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.071266,0.015566,-0.99734,247.59,-0.31681,-0.94846,0.0078344,364.04,-0.94581,0.31652,0.072525,58.372,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,0.6013,-0.7838,0.15525,235.55,-0.56703,-0.55548,-0.60822,369.76,0.56296,0.27769,-0.77844,54.004,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,0.28312,-0.31855,-0.90464,252.1,-0.23084,0.89287,-0.38665,295.25,0.93089,0.31829,0.17926,17.857,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.27052,-0.50574,-0.81917,268.68,-0.63297,0.73456,-0.24447,305.97,0.72537,0.45238,-0.51883,36.001,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.32951,0.011649,-0.94408,251.4,-0.56686,0.79721,0.20768,289.2,0.75505,0.60359,-0.25608,21.554,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.32951,0.011649,-0.94408,246.67,-0.56686,0.79721,0.20768,222.44,0.75505,0.60359,-0.25608,110.21,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.32951,0.011649,-0.94408,245.35,-0.56686,0.79721,0.20768,222.46,0.75505,0.60359,-0.25608,106.22,#7,1,0,0,0,0,1,0,0,0,0,1,0 > select add #1 50583 atoms, 51633 bonds, 443 pseudobonds, 6254 residues, 9 models selected > select subtract #1 1762 atoms, 1812 bonds, 75 pseudobonds, 207 residues, 4 models selected > select subtract #6 Nothing selected > select add #4 63137 atoms, 64254 bonds, 234 pseudobonds, 7857 residues, 4 models selected > view matrix models > #4,1,0,0,47.413,0,1,0,158.13,0,0,1,-26.398,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #4,0.97376,0.20191,0.10503,-4.3999,-0.21217,0.97231,0.097944,223.29,-0.082348,-0.11766,0.98963,30.037,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ~set independent Missing or invalid ""setting"" argument: Should be 'bgColor' > view matrix models > #4,0.96475,0.22187,0.14153,-21.448,-0.23243,0.97058,0.062876,226.29,-0.12342,-0.093557,0.98793,32.34,#7,1,0,0,0,0,1,0,0,0,0,1,0 > select add #6 64899 atoms, 66066 bonds, 210 pseudobonds, 8064 residues, 6 models selected > select subtract #4 1762 atoms, 1812 bonds, 75 pseudobonds, 207 residues, 4 models selected > view matrix models > #6,-0.24627,-0.78861,-0.56342,288.69,-0.96603,0.24672,0.076919,283.26,0.078348,0.56322,-0.82258,163.34,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.24778,-0.43162,-0.86736,272.51,-0.94227,0.31552,0.11217,263.83,0.22525,0.84508,-0.48488,133.02,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.56952,-0.2269,-0.79004,266.13,-0.74219,0.55505,0.37561,237.69,0.35329,0.80027,-0.48451,133.56,#7,1,0,0,0,0,1,0,0,0,0,1,0 > open PDB:5OQM Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 71, in cmd_open provider_args = mgr.fetch_args(fetches[0][1], format_name=fetches[0][2]) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/manager.py"", line 175, in fetch_args args.update(provider_info.bundle_info.run_provider(self.session, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/mmcif/__init__.py"", line 65, in run_provider fetcher = { KeyError: 'PDB' KeyError: 'PDB' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/mmcif/__init__.py"", line 65, in run_provider fetcher = { See log for complete Python traceback. > open 5OQM Summary of feedback from opening 5OQM fetched from pdb --- notes | Fetching compressed mmCIF 5oqm from http://files.rcsb.org/download/5oqm.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif 5oqm title: Structure of yeast transcription pre-initiation complex with tfiih and core mediator [more info...] Chain information for 5oqm #8 --- Chain | Description | UniProt 0 | General transcription and DNA repair factor IIH helicase subunit XPD | RAD3_YEAST 1 | General transcription and DNA repair factor IIH subunit TFB1 | TFB1_YEAST 2 | General transcription and DNA repair factor IIH subunit TFB2 | TFB2_YEAST 3 | RNA polymerase II transcription factor B subunit 3 | TFB3_YEAST 4 | General transcription and DNA repair factor IIH subunit TFB4 | TFB4_YEAST 5 | General transcription and DNA repair factor IIH subunit TFB5 | TFB5_YEAST 6 | General transcription and DNA repair factor IIH subunit SSL1 | SSL1_YEAST 7 | General transcription and DNA repair factor IIH helicase subunit XPB | RAD25_YEAST A | DNA-directed RNA polymerase II subunit RPB1 | RPB1_YEAST B | DNA-directed RNA polymerase II subunit RPB2 | RPB2_YEAST C | DNA-directed RNA polymerase II subunit RPB3 | RPB3_YEAST D | DNA-directed RNA polymerase II subunit RPB4 | RPB4_YEAST E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_YEAST F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_YEAST G | DNA-directed RNA polymerase II subunit RPB7 | RPB7_YEAST H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_YEAST I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_YEAST J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_YEAST K | DNA-directed RNA polymerase II subunit RPB11 | RPB11_YEAST L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_YEAST M | Transcription initiation factor IIB | TF2B_YEAST N | NONTEMPLATE DNA | O | TATA-box-binding protein | TBP_YEAST Q | Transcription initiation factor IIF subunit alpha | A0A250WD40_YEASX R | Transcription initiation factor IIF subunit beta | T2FB_YEAST T | TEMPLATE DNA | U | Transcription initiation factor IIA large subunit | TOA1_YEAST V | Transcription initiation factor IIA subunit 2 | T2AG_YEAST W | Transcription factor TFIIE subunit | T2EA_YEAST X | Transcription initiation factor IIE subunit beta | T2EB_YEAST Z | Unknown protein | a | Mediator of RNA polymerase II transcription subunit 6 | MED6_YEAST b | Mediator of RNA polymerase II transcription subunit 8 | MED8_YEAST c | Mediator of RNA polymerase II transcription subunit 11 | MED11_YEAST d | Mediator of RNA polymerase II transcription subunit 17 | MED17_YEAST e | Mediator of RNA polymerase II transcription subunit 18 | MED18_YEAST f | Mediator of RNA polymerase II transcription subunit 20 | MED20_YEAST g | Mediator of RNA polymerase II transcription subunit 22 | MED22_YEAST h | Mediator of RNA polymerase II transcription subunit 4 | MED4_YEAST i | Mediator of RNA polymerase II transcription subunit 7 | MED7_YEAST j | Mediator of RNA polymerase II transcription subunit 9 | MED9_YEAST k | Mediator of RNA polymerase II transcription subunit 10 | MED10_YEAST l | Mediator of RNA polymerase II transcription subunit 14 | MED14_YEAST m | Mediator of RNA polymerase II transcription subunit 19 | MED19_YEAST n | Mediator of RNA polymerase II transcription subunit 21 | MED21_YEAST o | Mediator of RNA polymerase II transcription subunit 31,Mediator of RNA polymerase II transcription subunit 31 | MED31_YEAST Non-standard residues in 5oqm #8 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > select add #8 81519 atoms, 82910 bonds, 397 pseudobonds, 11198 residues, 8 models selected > select subtract #6 79757 atoms, 81098 bonds, 322 pseudobonds, 10991 residues, 4 models selected > view matrix models > #8,0.98782,0.15416,0.021244,-66.325,-0.15494,0.98704,0.041671,116.99,-0.014545,-0.044455,0.99891,-194.45 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.71099,0.5757,-0.4038,351.76,0.69189,0.67531,-0.25545,65.103,0.12563,-0.46101,-0.87846,359.12 > view matrix models > #8,-0.00087576,-0.99355,0.11335,439.12,-0.94447,0.038071,0.32639,474.41,-0.32861,-0.10677,-0.93841,396.49 > view matrix models > #8,0.93841,-0.2899,0.18799,14.217,-0.32354,-0.54635,0.77254,354.71,-0.12125,-0.78579,-0.6065,430.83 > view matrix models > #8,0.82476,-0.55729,0.095946,132.73,-0.43742,-0.5212,0.73281,386.41,-0.35838,-0.64636,-0.67363,470.98 > select subtract #8 Nothing selected > select #8/1:491@CB 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 25 atoms, 24 bonds, 5 residues, 1 model selected > select up 2548 atoms, 2579 bonds, 388 residues, 1 model selected > select up 2573 atoms, 2603 bonds, 393 residues, 1 model selected > select up 3060 atoms, 3090 bonds, 491 residues, 1 model selected > select up 79757 atoms, 81098 bonds, 10991 residues, 1 model selected > select down 3060 atoms, 3090 bonds, 491 residues, 1 model selected > select down 2573 atoms, 2603 bonds, 393 residues, 1 model selected > select down 2548 atoms, 2579 bonds, 388 residues, 1 model selected > select down 25 atoms, 24 bonds, 5 residues, 1 model selected > select up 2548 atoms, 2579 bonds, 388 residues, 1 model selected > select up 2573 atoms, 2603 bonds, 393 residues, 1 model selected > select up 3060 atoms, 3090 bonds, 491 residues, 1 model selected > hide sel atoms > select #8/2:245@CA 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 65 atoms, 64 bonds, 13 residues, 1 model selected > select up 1588 atoms, 1587 bonds, 319 residues, 1 model selected > hide sel atoms > select #8/4:58@CB 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 90 atoms, 89 bonds, 18 residues, 1 model selected > select up 1475 atoms, 1474 bonds, 297 residues, 1 model selected > hide sel atoms > select #8/6:324@CA 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 30 atoms, 29 bonds, 6 residues, 1 model selected > select up 2197 atoms, 2219 bonds, 335 residues, 1 model selected > hide sel atoms > select #8/0:695@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 73 atoms, 75 bonds, 8 residues, 1 model selected > select up 2172 atoms, 2206 bonds, 295 residues, 1 model selected > hide sel atoms > select #8/0:24@CA 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 75 atoms, 74 bonds, 15 residues, 1 model selected > select up 779 atoms, 782 bonds, 130 residues, 1 model selected > select up 840 atoms, 842 bonds, 142 residues, 1 model selected > select up 2672 atoms, 2699 bonds, 403 residues, 1 model selected > hide sel atoms > select #8/7:525@CA 1 atom, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 3148 atoms, 3207 bonds, 408 residues, 1 model selected > select up 79757 atoms, 81098 bonds, 10991 residues, 1 model selected > select down 3148 atoms, 3207 bonds, 408 residues, 1 model selected > hide sel atoms > select #8/W:364@CA 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 110 atoms, 109 bonds, 22 residues, 1 model selected > select up 1749 atoms, 1770 bonds, 247 residues, 1 model selected > hide sel atoms > select #8/X:138@CB 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 70 atoms, 69 bonds, 14 residues, 1 model selected > select up 293 atoms, 292 bonds, 59 residues, 1 model selected > select up 323 atoms, 321 bonds, 65 residues, 1 model selected > select up 1004 atoms, 1013 bonds, 160 residues, 1 model selected > hide sel atoms > select #8/W:417@C 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 11 residues, 1 model selected > hide sel atoms > select add #8 79757 atoms, 81098 bonds, 322 pseudobonds, 10991 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #8,0.72858,-0.45832,0.50904,11.665,-0.68494,-0.48052,0.54769,524.2,-0.006416,-0.74769,-0.66402,308.68 > select subtract #8 Nothing selected > select add #6 1762 atoms, 1812 bonds, 75 pseudobonds, 207 residues, 4 models selected > select subtract #6 Nothing selected > select add #4 63137 atoms, 64254 bonds, 234 pseudobonds, 7857 residues, 4 models selected > view matrix models > #4,0.21469,-0.22735,-0.94985,539.69,0.44528,0.88836,-0.11199,134.75,0.86927,-0.39891,0.29196,-3.2784,#5,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > select subtract #4 Nothing selected > select add #4 63137 atoms, 64254 bonds, 234 pseudobonds, 7857 residues, 4 models selected > select subtract #4 Nothing selected > close #4 > select add #8 79757 atoms, 81098 bonds, 322 pseudobonds, 10991 residues, 4 models selected > view matrix models > #8,0.95153,-0.30271,-0.054334,179.89,-0.082202,-0.42057,0.90353,383.49,-0.29636,-0.85527,-0.42507,525.85 Peptide pair mapping of Xi evidence file: /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS.csv Unique peptide pairs: 558 out of 1647 Unique peptide pairs with pseudobonds: 217 Pseudobonds are stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,6,8.pb Mapping information is stored in /Users/leonpalaoiii/Library/CloudStorage/Dropbox/Assembly/20230216_SNR20_LargeScale_SAGAMedPIC/combined_20210508_dsbu_ch4plus_v2__yeast_UP000002311_559292_2022_02_Gal4Vp16_P04384__20230421_hjk_murakami_leon_Med_Saga_PIC_DSBU_inj2of10_RTboth_XMAS_1,6,8.tsv > select subtract #8 Nothing selected > select add #6 1762 atoms, 1812 bonds, 88 pseudobonds, 207 residues, 5 models selected > view matrix models > #6,0.84899,-0.24053,-0.47049,284.27,-0.13415,-0.95933,0.24837,387.83,-0.51109,-0.14775,-0.84673,221.31,#7,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.31913,-0.78385,0.53267,302.27,-0.90432,0.42,0.076251,349.45,-0.28349,-0.45737,-0.84288,229.82,#7,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.31913,-0.78385,0.53267,259.94,-0.90432,0.42,0.076251,263.32,-0.28349,-0.45737,-0.84288,235.02,#7,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #6,-0.31913,-0.78385,0.53267,267.11,-0.90432,0.42,0.076251,270.23,-0.28349,-0.45737,-0.84288,245.98,#7,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0 > hide #6.2 models > show #6.2 models > hide #6.1 models > show #6.1 models > view matrix models > #6,-0.52714,-0.77372,0.35141,275.42,-0.78566,0.60132,0.14542,247.04,-0.32383,-0.19943,-0.92486,253.73,#7,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0 > select subtract #6 Nothing selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.5.7 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,2 Processor Name: Dual-Core Intel Core i7 Processor Speed: 3.5 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 509.0.0.0.0 OS Loader Version: 577~129 SMC Version (system): 2.44f6 Software: System Software Overview: System Version: macOS 13.3.1 (22E261) Kernel Version: Darwin 22.4.0 Time since boot: 1 day, 8 hours, 26 minutes Graphics/Displays: Intel Iris Plus Graphics 650: Chipset Model: Intel Iris Plus Graphics 650 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5927 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2717D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 67YGV92JACGL Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.59 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 et-xmlfile: 1.1.0 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 21.3 pandas: 2.0.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 seaborn: 0.12.2 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 tzdata: 2023.3 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect accepted normal Third Party all ChimeraX