Opened 6 months ago

Closed 6 months ago

#17533 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000030e0ab000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030d09f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c093000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b087000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a07b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030906f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000308063000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000307057000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030604b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030503f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000304033000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f5614c80 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 61)


{"app_name":"ChimeraX","timestamp":"2025-05-01 17:53:43.00 +0900","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.4.1 (24E263)","roots_installed":0,"name":"ChimeraX","incident_id":"8BBAD158-B6CA-4621-A39E-B2D0B4FF9A00"}
{
  "uptime" : 210000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,2",
  "coalitionID" : 40545,
  "osVersion" : {
    "train" : "macOS 15.4.1",
    "build" : "24E263",
    "releaseType" : "User"
  },
  "captureTime" : "2025-05-01 17:53:17.9814 +0900",
  "codeSigningMonitor" : 1,
  "incident" : "8BBAD158-B6CA-4621-A39E-B2D0B4FF9A00",
  "pid" : 68471,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-05-01 15:44:12.8808 +0900",
  "procStartAbsTime" : 4918863010114,
  "procExitAbsTime" : 5104730051154,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"C17635AB-2CC7-55FD-94EA-1A09698D8823","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "B5A62B1D-6A4C-80F9-1C84-CE6A9B2C4266",
  "appleIntelligenceStatus" : {"reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"],"state":"unavailable"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "90407F23-A167-4BB9-AAFA-3C9EB19818AB",
  "wakeTime" : 17118,
  "sleepWakeUUID" : "972F2CC3-7E21-4A3D-AD01-596139A7FBC0",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4296753152\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1001b4000-1001b8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":68471},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4296753152\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1001b4000-1001b8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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  "faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Tue Apr 29 15:35:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Fri Apr 18 15:18:01 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Fri Apr 18 13:48:08 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_7FEE_5TGZ_keyresidues.cxs
> format session

Log from Thu Jan 18 17:00:10 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee_5u09_5tgz_superpose.cxs

Log from Wed Jan 10 18:04:34 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee.pdb

7fee.pdb title:  
Crystal structure of protein L [more info...]  
  
Chain information for 7fee.pdb #1  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 67-82 90-305 333-414, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 7fee.pdb #1  
---  
7IC — 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> set bgColor white

> transparency 80 cartoons

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel purple

> color sel byhetero

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> select ::name="CLR"

56 atoms, 62 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="CLR"

56 atoms, 62 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="GOL"

24 atoms, 20 bonds, 4 residues, 1 model selected  

> hide sel target a

> select ::name="HOH"

18 atoms, 18 residues, 1 model selected  

> hide sel target a

> select ::name="OLA"

30 atoms, 26 bonds, 4 residues, 1 model selected  

> hide sel target a

> select ::name="OLC"

50 atoms, 48 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="PEG"

14 atoms, 12 bonds, 2 residues, 1 model selected  

> hide sel target a

[Repeated 1 time(s)]

> select clear

> hide target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> hide sel target a

> show sel target ab

> ui tool show "Side View"

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel : show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5tgz.pdb

5tgz.pdb title:  
Crystal structure of the human cannabinoid receptor CB1 [more info...]  
  
Chain information for 5tgz.pdb #2  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,flavodoxin,cannabinoid receptor 1 | CNR1_HUMAN 99-306 332-414, FLAV_DESVH 1002-1148  
  
Non-standard residues in 5tgz.pdb #2  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
ZDG —
4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl
nitrate  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5tgz.pdb, chain A (#2), sequence
alignment score = 1484.1  
RMSD between 239 pruned atom pairs is 0.879 angstroms; (across all 411 pairs:
17.100)  
  

> transparency 80 cartoons

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel lime

> color sel byhetero

> select clear

> hide target a

> select #1/A:174

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:178

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:177

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel byhetero

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel : select clear

> select #2/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:177

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:174

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> transparency 90 cartoons

> select clear

> select #1/A:361

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:362

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 36 residues  

> ~label sel residues

> select #1/A:379

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select #1/A:383

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select #2/A:267

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 12 residues  

> ~label sel residues

Drag select of 4 atoms, 43 residues, 4 bonds  

> ~label sel residues

> select #1/A:173

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ~label sel residues

Drag select of 5 residues  

> ~label sel residues

> select #2/A:269

7 atoms, 7 bonds, 1 residue, 1 model selected  

> ~label sel residues

Drag select of 18 residues  

> ~label sel residues

> select clear

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5u09.pdb

5u09.pdb title:  
High-resolution crystal structure of the human CB1 cannabinoid receptor [more
info...]  
  
Chain information for 5u09.pdb #3  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 90-301 333-421, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 5u09.pdb #3  
---  
7DY —
N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide  
PEG — di(hydroxyethyl)ether  
SO4 — sulfate ion  
  

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5u09.pdb, chain A (#3), sequence
alignment score = 2477.5  
RMSD between 187 pruned atom pairs is 1.015 angstroms; (across all 478 pairs:
15.275)  
  

> transparency 90 cartoons

> hide target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel orange

> color sel byhetero

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 6 residues  

> show sel target ab

Drag select of 13 residues  

> select clear

Drag select of 11 residues  

> select clear

> select #2/A:171

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:172

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:179

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:178

10 atoms, 10 bonds, 1 residue, 1 model selected  

> transparency 90 cartoons

> select : F177

Nothing selected  

> show target ab

> select : 177

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> select : 174

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> select clear

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select clear

[Repeated 1 time(s)]

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel @ select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee_5u09_5tgz_superpose.cxs

——— End of log from Wed Jan 10 18:04:34 2024 ———

opened ChimeraX session  

> ui tool show "Side View"

> select : 268

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> label sel text "{0.name} {0.number}{0.insertion_code}"

> ~label sel residues

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 379

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 193

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #1/A:268

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #1/A:379

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 363

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 383

18 atoms, 15 bonds, 3 residues, 3 models selected  

> show (#!1 & sel) target ab

> show #!2 models

> hide #!2 models

> show #3 models

> show #!2 models

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 267

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> show (#!1 & sel) target ab

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 196

21 atoms, 18 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 275

36 atoms, 36 bonds, 3 residues, 3 models selected  

> show #!2 models

> show #3 models

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> hide #!2 models

> hide #3 models

> show #!2 models

> show #3 models

> select : 276

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 359

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5xr8.pdb

5xr8.pdb title:  
Crystal structure of the human CB1 In complex with agonist AM841 [more
info...]  
  
Chain information for 5xr8.pdb #4  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,flavodoxin,cannabinoid receptor 1 | CNR1_HUMAN 99-306 356-536, FLAV_DESVH 308-453  
  
Non-standard residues in 5xr8.pdb #4  
---  
8D0 —
(6~{A}~{R},9~{R},10~{A}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-
octan-2-yl)-6,6-dimethyl-6~{A},7,8,9,10,10~{A}-hexahydrobenzo[C]chromen-1-ol  
CLR — cholesterol  
FMN — flavin mononucleotide (riboflavin monophosphate)  
PEG — di(hydroxyethyl)ether  
  

> select add #2

3558 atoms, 3625 bonds, 457 residues, 4 models selected  

> hide #!2 models

> hide #3 models

> ui tool show Matchmaker

> matchmaker #!4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5xr8.pdb, chain A (#4), sequence
alignment score = 1408.3  
RMSD between 205 pruned atom pairs is 0.935 angstroms; (across all 400 pairs:
16.165)  
  

> hide #!1 models

> hide #4 target a

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> show #!2 models

> show #!1 models

> show #3 models

> hide #!2 models

> hide #3 models

> hide #!1 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #!4 models

> show #!4 models

> show #3 models

> show #!2 models

> show #!1 models

> transparency : 80

Missing or invalid "percent" argument: Expected a number  

> transparency 70 cartoons

> hide #3 models

> hide #!2 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> show #!2 models

> show #3 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show #1-3 target ab

> undo

> show #!4 models

> select clear

> select : 359

32 atoms, 28 bonds, 4 residues, 4 models selected  

> hide #3 models

> hide #!4 models

> show #3 models

> show #!4 models

> hide #!4 models

> hide #3 models

> hide #!2 models

> show #!2 models

> show #3 models

> show #!4 models

> hide #!4 models

> hide #3 models

> color #1 #d789c94c

> color #2 #eaec7f4c

> color #2 #ecd8844c

> color #2 #ecd8844d

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel byhetero

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel hot pink

> color sel magenta

> color sel byhetero

[Repeated 1 time(s)]

> select clear

> color #!1-2 byhetero

> transparency 70 cartoons

> transparency 0 atoms

> transparency 90 cartoons

> transparency 80 cartoons

> selet : 174

Unknown command: selet : 174  

> select : 174

44 atoms, 44 bonds, 4 residues, 4 models selected  

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 170

44 atoms, 44 bonds, 4 residues, 4 models selected  

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> hide #!2 models

> ~label (#!1 & sel) residues

> show #!2 models

> color #2 #52edd933

> color #2 #60d9ed33

> color sel & #!1-2 byhetero

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> transparency 0 atoms

> color sel byhetero

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel light sea green

> color sel byhetero

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> select clear

> show #1-2 target ab

> hide #1-2 target a

> ~label #1-2 residues

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> show (#1-2 & sel) target ab

> hide #2 models

> show #2 models

> hide #2 models

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> show (#1 & sel) target ab

> show #2 models

> label (#1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!1-2 byhetero

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!2 models

> show #!2 models

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show (#!1-2 & sel) target ab

> ~label (#!1-2 & sel) residues

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!2 models

> hide #!1 models

> show #!2 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!2 byhetero

> select : 197

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!2 & sel) target ab

> color sel & #!2 byhetero

> show #!1 models

> select : 197

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!1 models

> label (#!2 & sel) text "{0.name} {0.number}{0.insertion_code}"

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 104

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 123

24 atoms, 20 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!2 byhetero

> show #!1 models

> color sel & #!1-2 byhetero

> select : 104

32 atoms, 28 bonds, 4 residues, 4 models selected  

> color sel & #!1-2 byhetero

> select : 387

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

[Repeated 1 time(s)]

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 103

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 105

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 119

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 380

26 atoms, 23 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 384

33 atoms, 29 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> hide #!2 models

> show #!2 models

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> color sel medium blue

> color sel white

> color sel byhetero

> color sel cornflower blue

> color sel byhetero

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> color #2 #eee78f33

> transparency 0 atoms

> color sel orange

> color sel byhetero

> show #!1 models

> select clear

> select : 386

25 atoms, 21 bonds, 4 residues, 4 models selected  

> hide #!1 models

> show #!1 models

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> transparency 90 cartoons

> select : 119, 123, 104, 387, 103, 105, 119, 380, 384

239 atoms, 216 bonds, 32 residues, 4 models selected  

> hide #!1 models

> color (#!2 & sel) lime

> color sel & #!2 byhetero

> select : 279, 102, 356, 197

172 atoms, 173 bonds, 16 residues, 4 models selected  

> color (#!2 & sel) cornflower blue

> color sel & #!2 byhetero

> show #!1 models

> save
> /Users/kimbomin/Dropbox/share_dir/jieun/CB1_project/screening/E460k_result/CB1_7FEE_5TGZ_keyresidues.cxs

——— End of log from Thu Jan 18 17:00:10 2024 ———

opened ChimeraX session  

> select : 170

44 atoms, 44 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #3 models

> show #!4 models

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> show sel target ab

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select add #2

3578 atoms, 3648 bonds, 458 residues, 5 models selected  

> select add #3

7507 atoms, 7584 bonds, 1011 residues, 6 models selected  

> select add #4

10909 atoms, 11067 bonds, 1446 residues, 7 models selected  

> select subtract #4

7499 atoms, 7577 bonds, 1010 residues, 5 models selected  

> select subtract #3

3556 atoms, 3626 bonds, 456 residues, 3 models selected  

> select subtract #2

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> show #!4 models

> select add #4

7470 atoms, 7616 bonds, 956 residues, 4 models selected  

> hide #!1 models

> select subtract #1

3410 atoms, 3490 bonds, 436 residues, 2 models selected  

> color (#!4 & sel) #ffa4aeff

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!3 models

> show #!2 models

> hide #!3 models

> select add #2

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> color (#!2 & sel) #abc5eeff

> color (#!2 & sel) #95a7f2ff

> color (#!2 & sel) #7177f2ff

> show #!3 models

> select add #3

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> hide #!2 models

> color (#!3 & sel) cornflower blue

> color sel byhetero

> show #!2 models

> select add #2

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> hide #!3 models

> select subtract #3

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> color sel byhetero

> transparency 80 cartoons

> show #!1 models

> select add #1

7602 atoms, 7737 bonds, 975 residues, 4 models selected  

> show #!3 models

> select add #3

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> show #!4 models

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select clear

> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"

657 atoms, 560 bonds, 131 residues, 4 models selected  

> hide sel target a

> ui tool show "Side View"

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> hide #!4 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> hide #!1 models

> ~label (#!2 & sel) residues

> show #!1 models

> select clear

Drag select of 3 atoms, 11 residues, 3 bonds  

> select #1/A:388

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #2/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #1/A:388

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select clear

> open
> "/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
> 2025-04-18 오후 1.39.43.png"

Failed opening file
/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
2025-04-18 오후 1.39.43.png:  
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)  

> open /Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif

Summary of feedback from opening
/Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif  
---  
note | Fetching CCD A1AIW from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/A1AIW/A1AIW.cif  
  
9b54.cif title:  
Biased agonist bound CB1-Gi structure [more info...]  
  
Chain information for 9b54.cif #5  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71  
R | Cannabinoid receptor 1 | CNR1_HUMAN -6-472  
S | scFv16 |   
  
Non-standard residues in 9b54.cif #5  
---  
A1AIW — methyl
N-{6-(4-carbamimidamidobutoxy)-1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-
L-valinate  
  

> select add #5

8512 atoms, 8689 bonds, 6 pseudobonds, 1111 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!5 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 9b54.cif, chain R (#5), sequence
alignment score = 1173.5  
RMSD between 164 pruned atom pairs is 1.217 angstroms; (across all 265 pairs:
4.059)  
  

> select clear

> view

> ui tool show "Side View"

> transparency 80 cartoons

> select : 170

67 atoms, 65 bonds, 7 residues, 5 models selected  

> show sel & #!1-2,5 atoms

> style sel & #!1-2,5 stick

Changed 45 atom styles  

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> show sel & #!1-2,4-5 atoms

> style sel & #!1-2,4-5 stick

Changed 50 atom styles  

> color sel & #!1-2,4-5 byhetero

> select #1/A:356

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:355

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 2 atoms, 23 residues, 1 bonds  

> show sel atoms

> undo

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide #!2 models

> hide #!1 models

> hide #!5 models

Drag select of 4 residues  

> show sel atoms

> undo

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> show #!2 models

> show #!1 models

> show #!5 models

> show #!3 models

> hide sel atoms

> undo

> select ~sel

23453 atoms, 23850 bonds, 6 pseudobonds, 3075 residues, 10 models selected  

> hide sel atoms

> select clear

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> show sel atoms

> select : 170

67 atoms, 65 bonds, 7 residues, 5 models selected  

> show sel target ab

> select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Fri Apr 18 13:48:08 2025 ———

opened ChimeraX session  

> select : 155

73 atoms, 72 bonds, 7 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 73 atom styles  

> color sel byhetero

> hide #!2-5 target m

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2-5 target m

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> select #5/A

1659 atoms, 1688 bonds, 2 pseudobonds, 218 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> color (#!5 & sel) forest green

> select #5/B

2573 atoms, 2620 bonds, 338 residues, 1 model selected  

> hide sel target a

> delete atoms sel

> delete bonds sel

> select #5/C

438 atoms, 444 bonds, 57 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/R

2091 atoms, 2141 bonds, 3 pseudobonds, 266 residues, 2 models selected  

> select #1/A

4060 atoms, 4126 bonds, 520 residues, 1 model selected  

> select #5/S

1751 atoms, 1796 bonds, 1 pseudobond, 232 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> hide #!1 models

> hide #!3 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!2 models

> show #!3 models

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> hide #!1 models

> hide #!5 models

> style sel & #!2-3 sphere

Changed 28 atom styles  

> select : 170

55 atoms, 55 bonds, 5 residues, 5 models selected  

> style sel & #!2-3 sphere

Changed 22 atom styles  

> style sel & #!2-3 stick

Changed 22 atom styles  

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> style sel & #!2-3 stick

Changed 28 atom styles  

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show #2-3 target ab

> undo

> show #!1 models

> show #!4 models

> show #!5 models

> hide #!1 models

> hide #!4 models

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show sel atoms

> select H

35 atoms, 1 residue, 1 model selected  

> hide sel target a

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> ~label (#!2-3 & sel) residues

> select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Fri Apr 18 15:18:01 2025 ———

opened ChimeraX session  

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select add #2

7602 atoms, 7737 bonds, 975 residues, 4 models selected  

> select add #3

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select add #5

18705 atoms, 19007 bonds, 5 pseudobonds, 2449 residues, 10 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> show sel & #!2-3,5 atoms

> style sel & #!2-3,5 stick

Changed 81 atom styles  

> color sel & #!2-3,5 byhetero

> select clear

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> label (#!2-3,5 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> select add #1

4166 atoms, 4223 bonds, 532 residues, 6 models selected  

> select add #2

7681 atoms, 7809 bonds, 984 residues, 7 models selected  

> select add #3

11597 atoms, 11735 bonds, 1535 residues, 8 models selected  

> select add #4

14982 atoms, 15203 bonds, 1968 residues, 9 models selected  

> select add #5

18705 atoms, 19007 bonds, 5 pseudobonds, 2449 residues, 11 models selected  

> select subtract #5

14955 atoms, 15178 bonds, 1965 residues, 9 models selected  

> select subtract #4

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select subtract #3

11012 atoms, 11227 bonds, 1411 residues, 6 models selected  

> select subtract #2

7470 atoms, 7616 bonds, 956 residues, 4 models selected  

> select subtract #4

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #2

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> select add #3

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select add #4

10895 atoms, 11052 bonds, 1445 residues, 6 models selected  

> select add #5

14645 atoms, 14881 bonds, 5 pseudobonds, 1929 residues, 9 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> ~label (#!2-3,5 & sel) residues

> hide #!2 models

> hide #!3 models

> hide #!5 models

> select add #5

3856 atoms, 3926 bonds, 5 pseudobonds, 496 residues, 6 models selected  

> select add #4

7241 atoms, 7394 bonds, 5 pseudobonds, 929 residues, 8 models selected  

> select subtract #5

3491 atoms, 3565 bonds, 445 residues, 6 models selected  

> select subtract #4

81 atoms, 75 bonds, 9 residues, 3 models selected  

> select add #3

3997 atoms, 4001 bonds, 560 residues, 4 models selected  

> select add #2

7512 atoms, 7587 bonds, 1012 residues, 5 models selected  

> select add #1

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select subtract #1

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> select add #2

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> select subtract #3

Nothing selected  

> show #!1 models

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show sel & #!1 atoms

> style sel & #!1 stick

Changed 27 atom styles  

> color sel & #!1 byhetero

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> show sel & #!4 atoms

> style sel & #!4 stick

Changed 25 atom styles  

> color sel & #!4 byhetero

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> select : 174

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 55 atom styles  

> color sel byhetero

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!4 models

> show #!5 models

> select : 123

30 atoms, 25 bonds, 5 residues, 5 models selected  

> show sel target ab

> style sel stick

Changed 30 atom styles  

> color sel byhetero

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show #3,5 target ab

> undo

> show #!2 models

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> hide sel target a

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> color sel orange

> color sel byhetero

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select : 123,119,381,384,174

218 atoms, 202 bonds, 25 residues, 5 models selected  

> hide #!5 models

> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!5 models

> select clear

> select ::name="CYS"

390 atoms, 329 bonds, 65 residues, 5 models selected  

> select #3/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:102

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show #!2 models

> select ::name="CYS"

390 atoms, 329 bonds, 65 residues, 5 models selected  

> show sel & #!2-3,5 atoms

> undo

> hide #!5 models

> select #3/A:102

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select #3/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select : 383

32 atoms, 27 bonds, 5 residues, 5 models selected  

> select : 392

33 atoms, 28 bonds, 5 residues, 5 models selected  

> show sel & #!2-3 cartoons

> show sel & #!2-3 atoms

> color sel & #!2-3 byhetero

[Repeated 1 time(s)]

> hide sel & #!2-3 atoms

> select : 390

28 atoms, 23 bonds, 5 residues, 5 models selected  

> show (#!2-3 & sel) target ab

> select #2/A:173

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select : 383

32 atoms, 27 bonds, 5 residues, 5 models selected  

> show sel & #!3,5 atoms

> color sel & #!3,5 byhetero

> style sel & #!3,5 stick

Changed 12 atom styles  

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Tue Apr 29 15:35:07 2025 ———

opened ChimeraX session  

> show #!1 models

> show #!2 models

> show #!4 models

> select clear

> hide atoms

> ~label #1-5 residues

> select : 200,356

127 atoms, 129 bonds, 11 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 127 atom styles  

> color sel byhetero

> hide #2-3#!4-5 target m

> hide #1 models

> show #2 models

> label (#2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

> show #1 models

> show #3 models

> show #!4 models

> show #!5 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> show #!4 models

> select ::name="TRP"

504 atoms, 540 bonds, 36 residues, 5 models selected  

> show sel & #!4-5 atoms

> undo

> select clear

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> show #1 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> open /Users/kimbomin/Library/CloudStorage/Dropbox/Mac/Downloads/7fee.pdb

7fee.pdb title:  
Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound
cannabinoid receptor 1 [more info...]  
  
Chain information for 7fee.pdb #6  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 67-82 90-305 333-414, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 7fee.pdb #6  
---  
7IC — 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> hide #!4 models

> hide #!5 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> select : 200,356

152 atoms, 155 bonds, 13 residues, 6 models selected  

> show sel & #1,6 atoms

> style sel & #1,6 stick

Changed 50 atom styles  

> hide #1 models

> show #1 models

> hide #1 models

> close #6

> show #1 models

> show #!2 models

> show #3 models

> show #!4 models

> show #!5 models

> select clear

> select #4/A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #5/A:200

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show (#!5 & sel) target ab

> hide (#!5 & sel) target a

> select clear

> hide cartoons

> show cartoons

> transparency 90 cartoons

> transparency 85cartoons

Missing or invalid "percent" argument: Expected a number  

> transparency 85 cartoons

> hide #1 models

> show #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!5 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #!2 models

> show #3 models

> show #!4 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 55 atom styles  

> color sel byhetero

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #1 models

> show #!2 models

> show #3 models

> show #!5 models

> show #!4 models

> ui tool show "Side View"

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show sel target ab

> select H

35 atoms, 1 residue, 1 model selected  

> hide sel target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="FMN"

62 atoms, 66 bonds, 2 residues, 2 models selected  

> show sel target ab

> hide sel target a

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> hide #1 models

> hide #!5 models

> color sel byhetero

> show #!2 models

> ui tool show "Side View"

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> hide (#!2,4 & sel) target a

> show #3 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #1 models

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #!5 models

> hide #1 models

> hide #!4 models

> show #!4 models

> show #!2 models

> show #3 models

> hide #3 models

> hide #!2 models

> hide (#!4-5 & sel) target a

> select clear

> show #1 models

> hide #1 models

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Target_analysis_papers/6kqi.pdb

6kqi.pdb title:  
Structure of an allosteric modulator bound to the CB1 cannabinoid receptor
[more info...]  
  
Chain information for 6kqi.pdb #6  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase,cannabinoid receptor 1 | CNR1_HUMAN 94-301 333-413, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 6kqi.pdb #6  
---  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
9GL —
5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Target_analysis_papers/7v3z.pdb

7v3z.pdb title:  
Structure of cannabinoid receptor type 1(CB1) [more info...]  
  
Chain information for 7v3z.pdb #7  
---  
Chain | Description | UniProt  
A | fusion protein of cannabinoid receptor 1 and flavodoxin | CNR1_HUMAN 102-306 458-536, FLAV_DESVH 308-453  
  
Non-standard residues in 7v3z.pdb #7  
---  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
FMN — flavin mononucleotide (riboflavin monophosphate)  
  

> ui tool show Matchmaker

> matchmaker #!6 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 6kqi.pdb, chain A (#6), sequence
alignment score = 2396.8  
RMSD between 252 pruned atom pairs is 0.770 angstroms; (across all 473 pairs:
16.637)  
  

> ui tool show "Side View"

> ui tool show Matchmaker

> matchmaker #!7 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 7v3z.pdb, chain A (#7), sequence
alignment score = 1391.6  
RMSD between 192 pruned atom pairs is 0.870 angstroms; (across all 406 pairs:
16.696)  
  

> transparency 85 cartoons

> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="9GL"::name="A1AIW"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"

961 atoms, 868 bonds, 145 residues, 7 models selected  

> hide (#!4-7 & sel) target a

> hide sel & #!4-7 atoms

> select clear

> hide #!4-7 atoms

> select add #6

3828 atoms, 3903 bonds, 1 pseudobond, 483 residues, 3 models selected  

> hide #!5 models

> hide #!4 models

> hide #!7 models

> color (#!6 & sel) orange red

> select clear

> show #!7 models

> show #1 models

> show #!4 models

> show #!5 models

> select : 200, 356

171 atoms, 173 bonds, 15 residues, 7 models selected  

> show sel & #1#!4-7 atoms

> style sel & #1#!4-7 stick

Changed 121 atom styles  

> color sel & #1#!4-7 byhetero

> select clear

> hide #1 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> select ::name="TRP"

700 atoms, 750 bonds, 50 residues, 7 models selected  

> show #1 models

> hide #1 models

> select clear

> select #7/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> hide #!6 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!6 models

> hide #!6 models

> show #1 models

> show #!6 models

> show #!5 models

> hide #!6 models

> hide #!5 models

> hide #!7 models

> hide #!2 models

> hide #1 models

> show #!5 models

> select add #5

3764 atoms, 3844 bonds, 5 pseudobonds, 485 residues, 3 models selected  

> select add #7

7148 atoms, 7308 bonds, 6 pseudobonds, 918 residues, 6 models selected  

> select subtract #7

3750 atoms, 3829 bonds, 5 pseudobonds, 484 residues, 3 models selected  

> color (#!5 & sel) orange

> color sel byhetero

> select clear

> show #!4 models

> select #4/A:477

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/R:355

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> show #!7 models

> show #1 models

> hide #!5 models

> hide #!7 models

> hide #!4 models

> select ::name="HOH"

90 atoms, 90 residues, 4 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> select ::name="OLA"

114 atoms, 103 bonds, 11 residues, 3 models selected  

> delete atoms (#1#!6 & sel)

> delete bonds (#1#!6 & sel)

> select ::name="OLC"

96 atoms, 91 bonds, 5 residues, 3 models selected  

> delete atoms (#1#!6 & sel)

> delete bonds (#1#!6 & sel)

> select ::name="9GL"

29 atoms, 32 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> show #!4 models

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show #1,4,6 target ab

> undo

> show #!2 models

> show #3 models

> show #!5 models

> show #!7 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #5/A

1659 atoms, 1688 bonds, 2 pseudobonds, 218 residues, 2 models selected  

> color (#!5 & sel) forest green

> select clear

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> hide #!2 models

> hide #3 models

> hide #!7 models

> hide #!5 models

> hide #1 models

> hide #!4 models

> show #!4 models

> show #1 models

> hide #1 models

> show #!2 models

> show #3 models

> hide #!6 models

> show #!7 models

> show #!5 models

> hide #!5 models

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

> show #1 models

> hide #1 models

> show #1 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #1 models

> show #!5 models

> show #!7 models

> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="9GL"::name="A1AIW"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"

788 atoms, 725 bonds, 115 residues, 7 models selected  

> hide (#3#!2,4-5,7 & sel) target a

> select #2/A:349

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:155

11 atoms, 11 bonds, 1 residue, 1 model selected  

> hide sel target a

> select clear

> transparency 85 cartoons

> transparency 95 cartoons

> transparency 90 cartoons

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> hide #!7 models

> transparency 50 cartoons

> hide #!5 models

> show #!4 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!5 models


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Thu May 1 17:26:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Tue Apr 29 15:35:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Fri Apr 18 15:18:01 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

Log from Fri Apr 18 13:48:08 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_7FEE_5TGZ_keyresidues.cxs
> format session

Log from Thu Jan 18 17:00:10 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee_5u09_5tgz_superpose.cxs

Log from Wed Jan 10 18:04:34 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee.pdb

7fee.pdb title:  
Crystal structure of protein L [more info...]  
  
Chain information for 7fee.pdb #1  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 67-82 90-305 333-414, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 7fee.pdb #1  
---  
7IC — 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> set bgColor white

> transparency 80 cartoons

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel purple

> color sel byhetero

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> select ::name="CLR"

56 atoms, 62 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="CLR"

56 atoms, 62 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="GOL"

24 atoms, 20 bonds, 4 residues, 1 model selected  

> hide sel target a

> select ::name="HOH"

18 atoms, 18 residues, 1 model selected  

> hide sel target a

> select ::name="OLA"

30 atoms, 26 bonds, 4 residues, 1 model selected  

> hide sel target a

> select ::name="OLC"

50 atoms, 48 bonds, 2 residues, 1 model selected  

> hide sel target a

> select ::name="PEG"

14 atoms, 12 bonds, 2 residues, 1 model selected  

> hide sel target a

[Repeated 1 time(s)]

> select clear

> hide target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> hide sel target a

> show sel target ab

> ui tool show "Side View"

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel :< 4

186 atoms, 185 bonds, 18 residues, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5tgz.pdb

5tgz.pdb title:  
Crystal structure of the human cannabinoid receptor CB1 [more info...]  
  
Chain information for 5tgz.pdb #2  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,flavodoxin,cannabinoid receptor 1 | CNR1_HUMAN 99-306 332-414, FLAV_DESVH 1002-1148  
  
Non-standard residues in 5tgz.pdb #2  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
ZDG —
4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl
nitrate  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5tgz.pdb, chain A (#2), sequence
alignment score = 1484.1  
RMSD between 239 pruned atom pairs is 0.879 angstroms; (across all 411 pairs:
17.100)  
  

> transparency 80 cartoons

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel lime

> color sel byhetero

> select clear

> hide target a

> select #1/A:174

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:178

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:177

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel byhetero

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel :< 5

494 atoms, 490 bonds, 50 residues, 2 models selected  

> select clear

> select #2/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:177

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:174

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #2/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> transparency 90 cartoons

> select clear

> select #1/A:361

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:362

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 36 residues  

> ~label sel residues

> select #1/A:379

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select #1/A:383

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select #2/A:267

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 12 residues  

> ~label sel residues

Drag select of 4 atoms, 43 residues, 4 bonds  

> ~label sel residues

> select #1/A:173

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ~label sel residues

Drag select of 5 residues  

> ~label sel residues

> select #2/A:269

7 atoms, 7 bonds, 1 residue, 1 model selected  

> ~label sel residues

Drag select of 18 residues  

> ~label sel residues

> select clear

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5u09.pdb

5u09.pdb title:  
High-resolution crystal structure of the human CB1 cannabinoid receptor [more
info...]  
  
Chain information for 5u09.pdb #3  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 90-301 333-421, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 5u09.pdb #3  
---  
7DY —
N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide  
PEG — di(hydroxyethyl)ether  
SO4 — sulfate ion  
  

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5u09.pdb, chain A (#3), sequence
alignment score = 2477.5  
RMSD between 187 pruned atom pairs is 1.015 angstroms; (across all 478 pairs:
15.275)  
  

> transparency 90 cartoons

> hide target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel orange

> color sel byhetero

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 6 residues  

> show sel target ab

Drag select of 13 residues  

> select clear

Drag select of 11 residues  

> select clear

> select #2/A:171

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:172

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

> select #2/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:170

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:179

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:178

10 atoms, 10 bonds, 1 residue, 1 model selected  

> transparency 90 cartoons

> select : F177

Nothing selected  

> show target ab

> select : 177

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> select : 174

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> select clear

> select #1/A:189

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select clear

[Repeated 1 time(s)]

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @< 5

364 atoms, 309 bonds, 75 residues, 3 models selected  

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @< 4

194 atoms, 141 bonds, 56 residues, 3 models selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @< 4

237 atoms, 179 bonds, 63 residues, 3 models selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @< 5

397 atoms, 323 bonds, 94 residues, 3 models selected  

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @< 4

194 atoms, 141 bonds, 56 residues, 3 models selected  

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> select sel @< 3

90 atoms, 75 bonds, 20 residues, 3 models selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @< 6

616 atoms, 543 bonds, 128 residues, 3 models selected  

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> select sel @< 7

860 atoms, 784 bonds, 163 residues, 3 models selected  

> select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel @< 5

420 atoms, 353 bonds, 89 residues, 3 models selected  

> select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> select sel @< 7

864 atoms, 788 bonds, 168 residues, 3 models selected  

> select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/7fee_5u09_5tgz_superpose.cxs

——— End of log from Wed Jan 10 18:04:34 2024 ———

opened ChimeraX session  

> ui tool show "Side View"

> select : 268

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> label sel text "{0.name} {0.number}{0.insertion_code}"

> ~label sel residues

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 379

33 atoms, 33 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 193

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #1/A:268

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #1/A:379

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 363

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 383

18 atoms, 15 bonds, 3 residues, 3 models selected  

> show (#!1 & sel) target ab

> show #!2 models

> hide #!2 models

> show #3 models

> show #!2 models

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 267

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> show (#!1 & sel) target ab

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 196

21 atoms, 18 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 275

36 atoms, 36 bonds, 3 residues, 3 models selected  

> show #!2 models

> show #3 models

> show sel target ab

> hide #3 models

> hide #!2 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> hide #!2 models

> hide #3 models

> show #!2 models

> show #3 models

> select : 276

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> select : 359

24 atoms, 21 bonds, 3 residues, 3 models selected  

> show sel target ab

> hide #!2 models

> hide #3 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> show #3 models

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun/CB1_project/Target_analysis_papers/5xr8.pdb

5xr8.pdb title:  
Crystal structure of the human CB1 In complex with agonist AM841 [more
info...]  
  
Chain information for 5xr8.pdb #4  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,flavodoxin,cannabinoid receptor 1 | CNR1_HUMAN 99-306 356-536, FLAV_DESVH 308-453  
  
Non-standard residues in 5xr8.pdb #4  
---  
8D0 —
(6~{A}~{R},9~{R},10~{A}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-
octan-2-yl)-6,6-dimethyl-6~{A},7,8,9,10,10~{A}-hexahydrobenzo[C]chromen-1-ol  
CLR — cholesterol  
FMN — flavin mononucleotide (riboflavin monophosphate)  
PEG — di(hydroxyethyl)ether  
  

> select add #2

3558 atoms, 3625 bonds, 457 residues, 4 models selected  

> hide #!2 models

> hide #3 models

> ui tool show Matchmaker

> matchmaker #!4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 5xr8.pdb, chain A (#4), sequence
alignment score = 1408.3  
RMSD between 205 pruned atom pairs is 0.935 angstroms; (across all 400 pairs:
16.165)  
  

> hide #!1 models

> hide #4 target a

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> show #!2 models

> show #!1 models

> show #3 models

> hide #!2 models

> hide #3 models

> hide #!1 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel byhetero

> select clear

> hide #!4 models

> show #!4 models

> show #3 models

> show #!2 models

> show #!1 models

> transparency : 80

Missing or invalid "percent" argument: Expected a number  

> transparency 70 cartoons

> hide #3 models

> hide #!2 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> show #!2 models

> show #3 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show #1-3 target ab

> undo

> show #!4 models

> select clear

> select : 359

32 atoms, 28 bonds, 4 residues, 4 models selected  

> hide #3 models

> hide #!4 models

> show #3 models

> show #!4 models

> hide #!4 models

> hide #3 models

> hide #!2 models

> show #!2 models

> show #3 models

> show #!4 models

> hide #!4 models

> hide #3 models

> color #1 #d789c94c

> color #2 #eaec7f4c

> color #2 #ecd8844c

> color #2 #ecd8844d

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel byhetero

> select clear

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> color sel hot pink

> color sel magenta

> color sel byhetero

[Repeated 1 time(s)]

> select clear

> color #!1-2 byhetero

> transparency 70 cartoons

> transparency 0 atoms

> transparency 90 cartoons

> transparency 80 cartoons

> selet : 174

Unknown command: selet : 174  

> select : 174

44 atoms, 44 bonds, 4 residues, 4 models selected  

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 170

44 atoms, 44 bonds, 4 residues, 4 models selected  

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> hide #!2 models

> ~label (#!1 & sel) residues

> show #!2 models

> color #2 #52edd933

> color #2 #60d9ed33

> color sel & #!1-2 byhetero

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> transparency 0 atoms

> color sel byhetero

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel light sea green

> color sel byhetero

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> select clear

> show #1-2 target ab

> hide #1-2 target a

> ~label #1-2 residues

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> show (#1-2 & sel) target ab

> hide #2 models

> show #2 models

> hide #2 models

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> show (#1 & sel) target ab

> show #2 models

> label (#1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!1-2 byhetero

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!2 models

> show #!2 models

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> hide (#!1-2 & sel) target a

> ~label (#!1-2 & sel) residues

> select : 279

56 atoms, 60 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show (#!1-2 & sel) target ab

> ~label (#!1-2 & sel) residues

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!2 models

> hide #!1 models

> show #!2 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!2 byhetero

> select : 197

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!2 & sel) target ab

> color sel & #!2 byhetero

> show #!1 models

> select : 197

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!1 models

> label (#!2 & sel) text "{0.name} {0.number}{0.insertion_code}"

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 104

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 123

24 atoms, 20 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> color sel & #!2 byhetero

> show #!1 models

> color sel & #!1-2 byhetero

> select : 104

32 atoms, 28 bonds, 4 residues, 4 models selected  

> color sel & #!1-2 byhetero

> select : 387

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

[Repeated 1 time(s)]

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 103

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 105

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 119

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 380

26 atoms, 23 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> select : 384

33 atoms, 29 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> color sel & #!1-2 byhetero

> hide #!1 models

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!1 models

> hide #!2 models

> show #!2 models

> select clear

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> color sel blue

> color sel byhetero

> color sel medium blue

> color sel white

> color sel byhetero

> color sel cornflower blue

> color sel byhetero

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> color #2 #eee78f33

> transparency 0 atoms

> color sel orange

> color sel byhetero

> show #!1 models

> select clear

> select : 386

25 atoms, 21 bonds, 4 residues, 4 models selected  

> hide #!1 models

> show #!1 models

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> transparency 90 cartoons

> select : 119, 123, 104, 387, 103, 105, 119, 380, 384

239 atoms, 216 bonds, 32 residues, 4 models selected  

> hide #!1 models

> color (#!2 & sel) lime

> color sel & #!2 byhetero

> select : 279, 102, 356, 197

172 atoms, 173 bonds, 16 residues, 4 models selected  

> color (#!2 & sel) cornflower blue

> color sel & #!2 byhetero

> show #!1 models

> save
> /Users/kimbomin/Dropbox/share_dir/jieun/CB1_project/screening/E460k_result/CB1_7FEE_5TGZ_keyresidues.cxs

——— End of log from Thu Jan 18 17:00:10 2024 ———

opened ChimeraX session  

> select : 170

44 atoms, 44 bonds, 4 residues, 4 models selected  

> show (#!1-2 & sel) target ab

> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #3 models

> show #!4 models

> show sel target ab

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> show sel target ab

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select add #2

3578 atoms, 3648 bonds, 458 residues, 5 models selected  

> select add #3

7507 atoms, 7584 bonds, 1011 residues, 6 models selected  

> select add #4

10909 atoms, 11067 bonds, 1446 residues, 7 models selected  

> select subtract #4

7499 atoms, 7577 bonds, 1010 residues, 5 models selected  

> select subtract #3

3556 atoms, 3626 bonds, 456 residues, 3 models selected  

> select subtract #2

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> show #!4 models

> select add #4

7470 atoms, 7616 bonds, 956 residues, 4 models selected  

> hide #!1 models

> select subtract #1

3410 atoms, 3490 bonds, 436 residues, 2 models selected  

> color (#!4 & sel) #ffa4aeff

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!3 models

> show #!2 models

> hide #!3 models

> select add #2

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> color (#!2 & sel) #abc5eeff

> color (#!2 & sel) #95a7f2ff

> color (#!2 & sel) #7177f2ff

> show #!3 models

> select add #3

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> hide #!2 models

> color (#!3 & sel) cornflower blue

> color sel byhetero

> show #!2 models

> select add #2

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> hide #!3 models

> select subtract #3

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> color sel byhetero

> transparency 80 cartoons

> show #!1 models

> select add #1

7602 atoms, 7737 bonds, 975 residues, 4 models selected  

> show #!3 models

> select add #3

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> show #!4 models

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select clear

> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"

657 atoms, 560 bonds, 131 residues, 4 models selected  

> hide sel target a

> ui tool show "Side View"

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> select : 356

50 atoms, 52 bonds, 4 residues, 4 models selected  

> hide #!4 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2 models

> hide #!1 models

> ~label (#!2 & sel) residues

> show #!1 models

> select clear

Drag select of 3 atoms, 11 residues, 3 bonds  

> select #1/A:388

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #2/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #1/A:388

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select clear

> open
> "/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
> 2025-04-18 오후 1.39.43.png"

Failed opening file
/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
2025-04-18 오후 1.39.43.png:  
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)  

> open /Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif

Summary of feedback from opening
/Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif  
---  
note | Fetching CCD A1AIW from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/A1AIW/A1AIW.cif  
  
9b54.cif title:  
Biased agonist bound CB1-Gi structure [more info...]  
  
Chain information for 9b54.cif #5  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71  
R | Cannabinoid receptor 1 | CNR1_HUMAN -6-472  
S | scFv16 |   
  
Non-standard residues in 9b54.cif #5  
---  
A1AIW — methyl
N-{6-(4-carbamimidamidobutoxy)-1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-
L-valinate  
  

> select add #5

8512 atoms, 8689 bonds, 6 pseudobonds, 1111 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!5 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 9b54.cif, chain R (#5), sequence
alignment score = 1173.5  
RMSD between 164 pruned atom pairs is 1.217 angstroms; (across all 265 pairs:
4.059)  
  

> select clear

> view

> ui tool show "Side View"

> transparency 80 cartoons

> select : 170

67 atoms, 65 bonds, 7 residues, 5 models selected  

> show sel & #!1-2,5 atoms

> style sel & #!1-2,5 stick

Changed 45 atom styles  

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> show sel & #!1-2,4-5 atoms

> style sel & #!1-2,4-5 stick

Changed 50 atom styles  

> color sel & #!1-2,4-5 byhetero

> select #1/A:356

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:355

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 2 atoms, 23 residues, 1 bonds  

> show sel atoms

> undo

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide #!2 models

> hide #!1 models

> hide #!5 models

Drag select of 4 residues  

> show sel atoms

> undo

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> show #!2 models

> show #!1 models

> show #!5 models

> show #!3 models

> hide sel atoms

> undo

> select ~sel

23453 atoms, 23850 bonds, 6 pseudobonds, 3075 residues, 10 models selected  

> hide sel atoms

> select clear

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> show sel atoms

> select : 170

67 atoms, 65 bonds, 7 residues, 5 models selected  

> show sel target ab

> select clear

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Fri Apr 18 13:48:08 2025 ———

opened ChimeraX session  

> select : 155

73 atoms, 72 bonds, 7 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 73 atom styles  

> color sel byhetero

> hide #!2-5 target m

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!2-5 target m

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> select #5/A

1659 atoms, 1688 bonds, 2 pseudobonds, 218 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> color (#!5 & sel) forest green

> select #5/B

2573 atoms, 2620 bonds, 338 residues, 1 model selected  

> hide sel target a

> delete atoms sel

> delete bonds sel

> select #5/C

438 atoms, 444 bonds, 57 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/R

2091 atoms, 2141 bonds, 3 pseudobonds, 266 residues, 2 models selected  

> select #1/A

4060 atoms, 4126 bonds, 520 residues, 1 model selected  

> select #5/S

1751 atoms, 1796 bonds, 1 pseudobond, 232 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> hide #!1 models

> hide #!3 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!2 models

> show #!3 models

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> hide #!1 models

> hide #!5 models

> style sel & #!2-3 sphere

Changed 28 atom styles  

> select : 170

55 atoms, 55 bonds, 5 residues, 5 models selected  

> style sel & #!2-3 sphere

Changed 22 atom styles  

> style sel & #!2-3 stick

Changed 22 atom styles  

> select : 356

64 atoms, 67 bonds, 5 residues, 5 models selected  

> style sel & #!2-3 stick

Changed 28 atom styles  

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show #2-3 target ab

> undo

> show #!1 models

> show #!4 models

> show #!5 models

> hide #!1 models

> hide #!4 models

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show sel atoms

> select H

35 atoms, 1 residue, 1 model selected  

> hide sel target a

> select : 102

38 atoms, 37 bonds, 4 residues, 4 models selected  

> ~label (#!2-3 & sel) residues

> select clear

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Fri Apr 18 15:18:01 2025 ———

opened ChimeraX session  

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select add #2

7602 atoms, 7737 bonds, 975 residues, 4 models selected  

> select add #3

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select add #5

18705 atoms, 19007 bonds, 5 pseudobonds, 2449 residues, 10 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> show sel & #!2-3,5 atoms

> style sel & #!2-3,5 stick

Changed 81 atom styles  

> color sel & #!2-3,5 byhetero

> select clear

> select add #1

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> label (#!2-3,5 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> select add #1

4166 atoms, 4223 bonds, 532 residues, 6 models selected  

> select add #2

7681 atoms, 7809 bonds, 984 residues, 7 models selected  

> select add #3

11597 atoms, 11735 bonds, 1535 residues, 8 models selected  

> select add #4

14982 atoms, 15203 bonds, 1968 residues, 9 models selected  

> select add #5

18705 atoms, 19007 bonds, 5 pseudobonds, 2449 residues, 11 models selected  

> select subtract #5

14955 atoms, 15178 bonds, 1965 residues, 9 models selected  

> select subtract #4

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select add #4

14955 atoms, 15178 bonds, 1965 residues, 8 models selected  

> select subtract #3

11012 atoms, 11227 bonds, 1411 residues, 6 models selected  

> select subtract #2

7470 atoms, 7616 bonds, 956 residues, 4 models selected  

> select subtract #4

4060 atoms, 4126 bonds, 520 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #2

3542 atoms, 3611 bonds, 455 residues, 2 models selected  

> select add #3

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select add #4

10895 atoms, 11052 bonds, 1445 residues, 6 models selected  

> select add #5

14645 atoms, 14881 bonds, 5 pseudobonds, 1929 residues, 9 models selected  

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> ~label (#!2-3,5 & sel) residues

> hide #!2 models

> hide #!3 models

> hide #!5 models

> select add #5

3856 atoms, 3926 bonds, 5 pseudobonds, 496 residues, 6 models selected  

> select add #4

7241 atoms, 7394 bonds, 5 pseudobonds, 929 residues, 8 models selected  

> select subtract #5

3491 atoms, 3565 bonds, 445 residues, 6 models selected  

> select subtract #4

81 atoms, 75 bonds, 9 residues, 3 models selected  

> select add #3

3997 atoms, 4001 bonds, 560 residues, 4 models selected  

> select add #2

7512 atoms, 7587 bonds, 1012 residues, 5 models selected  

> select add #1

11545 atoms, 11688 bonds, 1529 residues, 6 models selected  

> select subtract #1

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> select add #2

7485 atoms, 7562 bonds, 1009 residues, 4 models selected  

> select subtract #2

3943 atoms, 3951 bonds, 554 residues, 2 models selected  

> select subtract #3

Nothing selected  

> show #!1 models

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show sel & #!1 atoms

> style sel & #!1 stick

Changed 27 atom styles  

> color sel & #!1 byhetero

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select : 119,381,384

133 atoms, 122 bonds, 15 residues, 5 models selected  

> show sel & #!4 atoms

> style sel & #!4 stick

Changed 25 atom styles  

> color sel & #!4 byhetero

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> select : 174

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 55 atom styles  

> color sel byhetero

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!4 models

> show #!5 models

> select : 123

30 atoms, 25 bonds, 5 residues, 5 models selected  

> show sel target ab

> style sel stick

Changed 30 atom styles  

> color sel byhetero

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show #3,5 target ab

> undo

> show #!2 models

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> hide sel target a

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> color sel orange

> color sel byhetero

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select : 123,119,381,384,174

218 atoms, 202 bonds, 25 residues, 5 models selected  

> hide #!5 models

> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> show #!5 models

> select clear

> select ::name="CYS"

390 atoms, 329 bonds, 65 residues, 5 models selected  

> select #3/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:102

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show #!2 models

> select ::name="CYS"

390 atoms, 329 bonds, 65 residues, 5 models selected  

> show sel & #!2-3,5 atoms

> undo

> hide #!5 models

> select #3/A:102

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:104

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:103

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> select #3/A:387

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select : 383

32 atoms, 27 bonds, 5 residues, 5 models selected  

> select : 392

33 atoms, 28 bonds, 5 residues, 5 models selected  

> show sel & #!2-3 cartoons

> show sel & #!2-3 atoms

> color sel & #!2-3 byhetero

[Repeated 1 time(s)]

> hide sel & #!2-3 atoms

> select : 390

28 atoms, 23 bonds, 5 residues, 5 models selected  

> show (#!2-3 & sel) target ab

> select #2/A:173

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select : 383

32 atoms, 27 bonds, 5 residues, 5 models selected  

> show sel & #!3,5 atoms

> color sel & #!3,5 byhetero

> style sel & #!3,5 stick

Changed 12 atom styles  

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Tue Apr 29 15:35:07 2025 ———

opened ChimeraX session  

> show #!1 models

> show #!2 models

> show #!4 models

> select clear

> hide atoms

> ~label #1-5 residues

> select : 200,356

127 atoms, 129 bonds, 11 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 127 atom styles  

> color sel byhetero

> hide #2-3#!4-5 target m

> hide #1 models

> show #2 models

> label (#2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

> show #1 models

> show #3 models

> show #!4 models

> show #!5 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> show #!4 models

> select ::name="TRP"

504 atoms, 540 bonds, 36 residues, 5 models selected  

> show sel & #!4-5 atoms

> undo

> select clear

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> show #1 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> open /Users/kimbomin/Library/CloudStorage/Dropbox/Mac/Downloads/7fee.pdb

7fee.pdb title:  
Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound
cannabinoid receptor 1 [more info...]  
  
Chain information for 7fee.pdb #6  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase | CNR1_HUMAN 67-82 90-305 333-414, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 7fee.pdb #6  
---  
7IC — 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> hide #!4 models

> hide #!5 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> select : 200,356

152 atoms, 155 bonds, 13 residues, 6 models selected  

> show sel & #1,6 atoms

> style sel & #1,6 stick

Changed 50 atom styles  

> hide #1 models

> show #1 models

> hide #1 models

> close #6

> show #1 models

> show #!2 models

> show #3 models

> show #!4 models

> show #!5 models

> select clear

> select #4/A:356

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #5/A:200

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show (#!5 & sel) target ab

> hide (#!5 & sel) target a

> select clear

> hide cartoons

> show cartoons

> transparency 90 cartoons

> transparency 85cartoons

Missing or invalid "percent" argument: Expected a number  

> transparency 85 cartoons

> hide #1 models

> show #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!5 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #!2 models

> show #3 models

> show #!4 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show sel atoms

> style sel stick

Changed 55 atom styles  

> color sel byhetero

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> hide #!5 models

> show #1 models

> show #!2 models

> show #3 models

> show #!5 models

> show #!4 models

> ui tool show "Side View"

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="ZDG"

33 atoms, 36 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="A1AIW"

73 atoms, 75 bonds, 1 residue, 1 model selected  

> show sel target ab

> select H

35 atoms, 1 residue, 1 model selected  

> hide sel target a

> select ::name="9GF"

27 atoms, 28 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="FMN"

62 atoms, 66 bonds, 2 residues, 2 models selected  

> show sel target ab

> hide sel target a

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide #3 models

> hide #!2 models

> hide #1 models

> hide #!5 models

> color sel byhetero

> show #!2 models

> ui tool show "Side View"

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> hide (#!2,4 & sel) target a

> show #3 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #1 models

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select : 155

55 atoms, 55 bonds, 5 residues, 5 models selected  

> show #!5 models

> hide #1 models

> hide #!4 models

> show #!4 models

> show #!2 models

> show #3 models

> hide #3 models

> hide #!2 models

> hide (#!4-5 & sel) target a

> select clear

> show #1 models

> hide #1 models

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Target_analysis_papers/6kqi.pdb

6kqi.pdb title:  
Structure of an allosteric modulator bound to the CB1 cannabinoid receptor
[more info...]  
  
Chain information for 6kqi.pdb #6  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,GLGA glycogen synthase,cannabinoid receptor 1 | CNR1_HUMAN 94-301 333-413, Q9V2J8_PYRAB 1001-1196  
  
Non-standard residues in 6kqi.pdb #6  
---  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
9GL —
5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
  

> open
> /Users/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Target_analysis_papers/7v3z.pdb

7v3z.pdb title:  
Structure of cannabinoid receptor type 1(CB1) [more info...]  
  
Chain information for 7v3z.pdb #7  
---  
Chain | Description | UniProt  
A | fusion protein of cannabinoid receptor 1 and flavodoxin | CNR1_HUMAN 102-306 458-536, FLAV_DESVH 308-453  
  
Non-standard residues in 7v3z.pdb #7  
---  
9GF —
2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol  
CLR — cholesterol  
FMN — flavin mononucleotide (riboflavin monophosphate)  
  

> ui tool show Matchmaker

> matchmaker #!6 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 6kqi.pdb, chain A (#6), sequence
alignment score = 2396.8  
RMSD between 252 pruned atom pairs is 0.770 angstroms; (across all 473 pairs:
16.637)  
  

> ui tool show "Side View"

> ui tool show Matchmaker

> matchmaker #!7 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7fee.pdb, chain A (#1) with 7v3z.pdb, chain A (#7), sequence
alignment score = 1391.6  
RMSD between 192 pruned atom pairs is 0.870 angstroms; (across all 406 pairs:
16.696)  
  

> transparency 85 cartoons

> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="9GL"::name="A1AIW"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"

961 atoms, 868 bonds, 145 residues, 7 models selected  

> hide (#!4-7 & sel) target a

> hide sel & #!4-7 atoms

[Repeated 2 time(s)]

> select clear

> hide #!4-7 atoms

> select add #6

3828 atoms, 3903 bonds, 1 pseudobond, 483 residues, 3 models selected  

> hide #!5 models

> hide #!4 models

> hide #!7 models

> color (#!6 & sel) orange red

> select clear

> show #!7 models

> show #1 models

> show #!4 models

> show #!5 models

> select : 200, 356

171 atoms, 173 bonds, 15 residues, 7 models selected  

> show sel & #1#!4-7 atoms

> style sel & #1#!4-7 stick

Changed 121 atom styles  

> color sel & #1#!4-7 byhetero

> select clear

> hide #1 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> select ::name="TRP"

700 atoms, 750 bonds, 50 residues, 7 models selected  

> show #1 models

> hide #1 models

> select clear

> select #7/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> hide #!6 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!6 models

> hide #!6 models

> show #1 models

> show #!6 models

> show #!5 models

> hide #!6 models

> hide #!5 models

> hide #!7 models

> hide #!2 models

> hide #1 models

> show #!5 models

> select add #5

3764 atoms, 3844 bonds, 5 pseudobonds, 485 residues, 3 models selected  

> select add #7

7148 atoms, 7308 bonds, 6 pseudobonds, 918 residues, 6 models selected  

> select subtract #7

3750 atoms, 3829 bonds, 5 pseudobonds, 484 residues, 3 models selected  

> color (#!5 & sel) orange

> color sel byhetero

> select clear

> show #!4 models

> select #4/A:477

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/R:355

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/A:478

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> show #!7 models

> show #1 models

> hide #!5 models

> hide #!7 models

> hide #!4 models

> select ::name="HOH"

90 atoms, 90 residues, 4 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> select ::name="OLA"

114 atoms, 103 bonds, 11 residues, 3 models selected  

> delete atoms (#1#!6 & sel)

> delete bonds (#1#!6 & sel)

> select ::name="OLC"

96 atoms, 91 bonds, 5 residues, 3 models selected  

> delete atoms (#1#!6 & sel)

> delete bonds (#1#!6 & sel)

> select ::name="9GL"

29 atoms, 32 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> show #!4 models

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> select ::name="7DY"

36 atoms, 38 bonds, 1 residue, 1 model selected  

> show #1,4,6 target ab

> undo

> show #!2 models

> show #3 models

> show #!5 models

> show #!7 models

> select ::name="8D0"

29 atoms, 31 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #5/A

1659 atoms, 1688 bonds, 2 pseudobonds, 218 residues, 2 models selected  

> color (#!5 & sel) forest green

> select clear

> select ::name="7IC"

26 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> hide #!2 models

> hide #3 models

> hide #!7 models

> hide #!5 models

> hide #1 models

> hide #!4 models

> show #!4 models

> show #1 models

> hide #1 models

> show #!2 models

> show #3 models

> hide #!6 models

> show #!7 models

> show #!5 models

> hide #!5 models

> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs

——— End of log from Thu May 1 17:26:07 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z15Y0001VKH/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 8일 1시간 48분

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR QHD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 6 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 6 months ago

Resolution: → duplicate
Status: assigned → closed
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