![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#8903 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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 "/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 0x000070001cbe1000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
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 0x000070001bbde000 (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 114 in worker
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 0x000070001abdb000 (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 114 in worker
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 0x0000700019bd8000 (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 114 in worker
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 0x0000700018bd5000 (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 114 in worker
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
Current thread 0x00007ff850ba1340 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-04-26 15:29:42.00 -0400","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E261)","roots_installed":0,"name":"ChimeraX","incident_id":"7F4F6F06-BE60-445F-9333-7EBADA0A8061"}
{
"uptime" : 51000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,2",
"coalitionID" : 6590,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E261",
"releaseType" : "User"
},
"captureTime" : "2023-04-26 15:29:19.5715 -0400",
"incident" : "7F4F6F06-BE60-445F-9333-7EBADA0A8061",
"pid" : 17425,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-04-26 12:36:59.4636 -0400",
"procStartAbsTime" : 41126452884268,
"procExitAbsTime" : 51466518721690,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F95D7A5F-EDDF-58C9-A6F5-BD0E7F2A4389","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "39F29B35-0655-1081-2964-457402475F27",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 21272,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "FE8634BD-CB51-4B12-93AE-BC35A5A88122",
"sip" : "enabled",
"vmRegionInfo" : "0x4f67c87d2888 is not in any region. Bytes after previous region: 87301273360521 Bytes before following region: 18245952395128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 153cb1000-15f1a1000 [180.9M] r--\/rwx SM=COW ...t_id=73c06ba5\n---> GAP OF 0x5ffea0e5f000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00004f67c87d2888","rawCodes":[1,87307163871368],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00004f67c87d2888"},
"vmregioninfo" : "0x4f67c87d2888 is not in any region. Bytes after previous region: 87301273360521 Bytes before following region: 18245952395128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 153cb1000-15f1a1000 [180.9M] r--\/rwx SM=COW ...t_id=73c06ba5\n---> GAP OF 0x5ffea0e5f000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== 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
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