The following bug report has been submitted:
Platform: macOS-15.6.1-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
Current thread 0x00000001f088a0c0 (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, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 121)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "MacBookPro18,3",
"coalitionID" : 146541,
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"build" : "24G90",
"releaseType" : "User"
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"captureTime" : "2026-03-11 22:51:49.8422 -0400",
"codeSigningMonitor" : 1,
"incident" : "3FC770BF-1FB7-49D8-8D42-84710508450C",
"pid" : 77021,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-30 11:51:54.6460 -0400",
"procStartAbsTime" : 12974925176477,
"procExitAbsTime" : 57756813734658,
"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":"0C2BB12E-24B4-5BE2-9EF3-072FD0ADFDC2","thirdParty":true},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA6EEC6E-A890-96AC-901B-4A3BA4995AFD",
"appleIntelligenceStatus" : {"reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"],"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" : "52F873D9-CF35-4D9E-BD7E-324140C9F0A7",
"wakeTime" : 2,
"sleepWakeUUID" : "0EB5212F-4CD5-4ADB-BFBA-10F88FA716D0",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4331274240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1022a0000-1022a4000 [ 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":77021},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4331274240\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1022a0000-1022a4000 [ 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/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs
Log from Mon Sep 29 00:14:22 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/MotB.1_IbpA.cxs
> format session
Log from Thu Sep 25 11:20:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs
> format session
Log from Tue Aug 26 11:16:07 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs
Log from Wed Jul 16 09:52:26 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs
Log from Mon Jun 23 17:09:27 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/AF3yet2solve.cxs
Log from Fri Jun 6 14:27:29 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_0.cif
Chain information for fold_nucleosome_tf_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_1.cif
Chain information for fold_nucleosome_tf_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_2.cif
Chain information for fold_nucleosome_tf_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_3.cif
Chain information for fold_nucleosome_tf_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_4.cif
Chain information for fold_nucleosome_tf_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> show cartoons
Computing secondary structure
[Repeated 4 time(s)]
> show cartoons
> hide atoms
> ui tool show "Color Actions"
> set bgColor white
> color bychain
> open 8vg1 fromDatabase pdb format mmcif
8vg1 title:
Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome [more
info...]
Chain information for 8vg1 #6
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 0-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I | DNA (171-MER) |
J | DNA (171-MER) |
O | Hepatocyte nuclear factor 3-alpha | FOXA1_HUMAN 1-472
T | Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 | MALE_ECOLI -378--13, GATA4_HUMAN 1-442
Non-standard residues in 8vg1 #6
---
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #1-5 to #6
Computing secondary structure
[Repeated 5 time(s)] 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 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F
(#1), sequence alignment score = 3127.7
RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs:
8.007)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F
(#2), sequence alignment score = 3139.7
RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs:
7.604)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F
(#3), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs:
7.070)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F
(#4), sequence alignment score = 3127.7
RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs:
6.895)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F
(#5), sequence alignment score = 3115.7
RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs:
6.506)
> matchmaker #1-5 to #6
Computing secondary structure
[Repeated 5 time(s)] 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 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F
(#1), sequence alignment score = 3127.7
RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs:
8.007)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F
(#2), sequence alignment score = 3139.7
RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs:
7.604)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F
(#3), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs:
7.070)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F
(#4), sequence alignment score = 3127.7
RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs:
6.895)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F
(#5), sequence alignment score = 3115.7
RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs:
6.506)
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #!6 models
> show #!6 models
> hide #!6 atoms
> show #!6 cartoons
> color #!6 bychain
> show #!6 atoms
> show #1 models
> hide #!6 models
> show #1 atoms
> show #!6 models
> hide #1 models
> hide #!6 atoms
[Repeated 1 time(s)]
> show #!6 atoms
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> hide #!6 atoms
> select #6/A
799 atoms, 811 bonds, 97 residues, 1 model selected
Drag select of 5 residues
> select #6/A
799 atoms, 811 bonds, 97 residues, 1 model selected
> show #1 models
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> hide #!6 models
> show #1 cartoons
> hide #1 atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select #6/B
662 atoms, 669 bonds, 83 residues, 1 model selected
> show #1 models
> hide #!6 models
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #1-5 to #6 & sel
Computing secondary structure
[Repeated 5 time(s)] 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 8vg1, chain A (#6) with fold_nucleosome_tf_model_0.cif, chain A
(#1), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.239 angstroms; (across all 97 pairs:
0.239)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_tf_model_1.cif, chain A
(#2), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
0.270)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_tf_model_2.cif, chain A
(#3), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.250 angstroms; (across all 97 pairs:
0.250)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_tf_model_3.cif, chain A
(#4), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.216 angstroms; (across all 97 pairs:
0.216)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_tf_model_4.cif, chain A
(#5), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.240 angstroms; (across all 97 pairs:
0.240)
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select /C
5820 atoms, 5890 bonds, 759 residues, 6 models selected
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select /D
5630 atoms, 5716 bonds, 725 residues, 6 models selected
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
Drag select of 25 residues
> select clear
> select /E
18309 atoms, 18831 bonds, 2487 residues, 6 models selected
> select /F
31577 atoms, 32394 bonds, 4258 residues, 6 models selected
> select #6/E:118
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /G
19955 atoms, 22262 bonds, 1046 residues, 6 models selected
> select /H
19830 atoms, 22186 bonds, 1025 residues, 6 models selected
> select /K
Nothing selected
> select /T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> select /O
856 atoms, 883 bonds, 102 residues, 1 model selected
> hide #!6 models
> select add #1
22023 atoms, 23291 bonds, 2282 residues, 2 models selected
> select add #2
43190 atoms, 45699 bonds, 4462 residues, 3 models selected
> select add #3
64357 atoms, 68107 bonds, 6642 residues, 4 models selected
> select add #4
85524 atoms, 90515 bonds, 8822 residues, 5 models selected
> select add #5
106691 atoms, 112923 bonds, 11002 residues, 6 models selected
> select add #6
120269 atoms, 127441 bonds, 421 pseudobonds, 12173 residues, 8 models selected
> select subtract #6
105835 atoms, 112040 bonds, 10900 residues, 5 models selected
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> delete atoms sel
> delete bonds sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_foxa1_gata4/fold_nucleosome_foxa1_gata4_model_0.cif
Chain information for fold_nucleosome_foxa1_gata4_model_0.cif #1
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
K | .
L | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_foxa1_gata4/fold_nucleosome_foxa1_gata4_model_1.cif
Chain information for fold_nucleosome_foxa1_gata4_model_1.cif #2
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
K | .
L | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_foxa1_gata4/fold_nucleosome_foxa1_gata4_model_2.cif
Chain information for fold_nucleosome_foxa1_gata4_model_2.cif #3
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
K | .
L | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_foxa1_gata4/fold_nucleosome_foxa1_gata4_model_3.cif
Chain information for fold_nucleosome_foxa1_gata4_model_3.cif #4
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
K | .
L | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_foxa1_gata4/fold_nucleosome_foxa1_gata4_model_4.cif
Chain information for fold_nucleosome_foxa1_gata4_model_4.cif #5
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
K | .
L | .
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #1-5 to #6 & sel
Computing secondary structure
[Repeated 10 time(s)] 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 8vg1, chain A (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
chain A (#1), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.265 angstroms; (across all 97 pairs:
0.265)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_foxa1_gata4_model_1.cif,
chain A (#2), sequence alignment score = 627.8
RMSD between 96 pruned atom pairs is 0.277 angstroms; (across all 97 pairs:
0.454)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_foxa1_gata4_model_2.cif,
chain A (#3), sequence alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.243 angstroms; (across all 97 pairs:
0.243)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_foxa1_gata4_model_3.cif,
chain A (#4), sequence alignment score = 627.8
RMSD between 96 pruned atom pairs is 0.238 angstroms; (across all 97 pairs:
0.406)
Matchmaker 8vg1, chain A (#6) with fold_nucleosome_foxa1_gata4_model_4.cif,
chain A (#5), sequence alignment score = 627.8
RMSD between 95 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
0.537)
> show sel & #1-5 cartoons
> hide sel & #1-5 atoms
> select clear
> show #1-5 cartoons
> hide #1-5 atoms
> show #!6 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #1 models
> show #1 models
> hide #!6 models
> color #1 bychain
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> color #1-5 bychain
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #!6 models
> color #1#!6 bychain
> hide #1 models
> show #1 models
> hide #!6 models
> show #2 models
> hide #1 models
> show #3 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #!6 models
> hide #5 models
> hide #!6 models
> show #1 models
> select /H
5630 atoms, 5716 bonds, 725 residues, 6 models selected
> select /I
21011 atoms, 21942 bonds, 2561 residues, 6 models selected
> select /J
34425 atoms, 35667 bonds, 4346 residues, 6 models selected
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> select clear
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> select /C
5820 atoms, 5890 bonds, 759 residues, 6 models selected
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> hide #1 models
> show #!6 models
> select /I
21011 atoms, 21942 bonds, 2561 residues, 6 models selected
> select /I
21011 atoms, 21942 bonds, 2561 residues, 6 models selected
> show #1 models
> select #1/I#2/I#3/I#4/I#5/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> hide #1 models
> ui tool show "Color Actions"
> show #1 models
> set bgColor sky blue
> set bgColor white
> color sel pale turquoise target acs
> color sel light blue target acs
> color sel light sky blue target acs
> color sel light blue target acs
> color sel powder blue target acs
> color sel light blue target acs
> select clear
> hide #1 models
> show #1 models
> select #1/I#2/I#3/I#4/I#5/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel sky blue target acs
> select clear
> hide #1 models
> show #1 models
> select #1/I#2/I#3/I#4/I#5/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel light sky blue target acs
> select clear
> hide #1 models
> select #1/I#2/I#3/I#4/I#5/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> show #1 models
> color sel medium turquoise target acs
> color sel medium aquamarine target acs
> color sel dark turquoise target acs
> color sel turquoise target acs
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #1/J#2/J#3/J#4/J#5/J
30915 atoms, 31725 bonds, 4175 residues, 5 models selected
> color sel cornflower blue target acs
> show #1 models
> hide #!6 models
> select clear
> show #!6 models
> hide #1 models
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel gray target acs
> select clear
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel tan target acs
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel lavender target acs
> color sel silver target acs
> color sel pink target acs
> select clear
> show #1 models
> hide #!6 models
> select #1/I#2/I#3/K#4/K#5/K
18437 atoms, 20018 bonds, 1514 residues, 5 models selected
> select #1/K#2/K#3/K#4/K#5/K
19055 atoms, 21350 bonds, 930 residues, 5 models selected
> color sel pink target acs
> select #1/L#2/L#3/L#4/L#5/L
19085 atoms, 21430 bonds, 930 residues, 5 models selected
> color sel tan target acs
> select clear
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/L#1/K#1/I#1/J
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> hide sel cartoons
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> select clear
> show #1 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FoxA1_GATA4.cxs"
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> hide #!6 models
> show #!6 models
> hide #2 models
> show #1 models
> hide #1 models
> select #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> show #1 models
> ui tool show Matchmaker
> matchmaker #!6 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 fold_nucleosome_foxa1_gata4_model_0.cif, chain J (#1) with 8vg1,
chain T (#6), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.548 angstroms; (across all 53 pairs:
7.623)
> matchmaker #!6 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] 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 fold_nucleosome_foxa1_gata4_model_0.cif, chain A (#1) with 8vg1,
chain E (#6), sequence alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
0.283)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FoxA1_GATA4.cxs"
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1.png" width 800 height
> 519 supersample 4 transparentBackground true
> show #1 models
> hide #!6 models
> select #1/L#1/K#1/I#1/J
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> show sel cartoons
> select clear
> hide #1 cartoons
> select #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> show sel cartoons
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> select clear
> show #1#!6 atoms
> hide #1#!6 atoms
> show #1#!6 cartoons
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1.AF3.png" width 600
> height 562 supersample 3 transparentBackground true
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1.AF3.png" width 600
> height 562 supersample 4 transparentBackground true
> select #1/L#1/K#1/I#1/J
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> hide sel cartoons
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_A-H.AF3.png" width
> 600 height 562 supersample 4 transparentBackground true
> show #!6 models
> hide #!6 models
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show #!6 models
> hide #1 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1.png" width 600 height
> 562 supersample 4 transparentBackground true
> show #1 models
> select #1/L#1/K#1/I#1/J
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> hide sel cartoons
> hide #!6 models
> show #!6 models
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> select #6/I#6/J
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> hide sel cartoons
> select #6/O/#6/T
Expected an objects specifier or a keyword
> select #6/O#6/T
1271 atoms, 1303 bonds, 4 pseudobonds, 156 residues, 2 models selected
> hide sel cartoons
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_A-H.vs.AF3_A-H.png"
> width 600 height 562 supersample 4 transparentBackground true
> show sel cartoons
> select #1/L#1/K#1/I#1/J
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> show sel cartoons
> hide #!6 models
> select clear
> show #!6 models
> hide #1 models
> show #!6 cartoons
> show #1 models
> hide #!6 models
> select :269-312
3391 atoms, 3446 bonds, 485 residues, 6 models selected
> show #!6 models
> hide #1 models
> select :174-246
9388 atoms, 9916 bonds, 946 residues, 6 models selected
Drag select of 2 residues
Drag select of 5 residues
> select :211-224
1336 atoms, 1359 bonds, 154 residues, 6 models selected
> select #6/J:152
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:151
19 atoms, 20 bonds, 1 residue, 1 model selected
> show #1 models
> hide #!6 models
Drag select of 3 residues
> show #!6 models
> hide #1 models
> select :211-224
1336 atoms, 1359 bonds, 154 residues, 6 models selected
> show #1 models
> hide #!6 models
Drag select of 4 residues
> show #!6 models
> hide #1 models
> select :281-309
2271 atoms, 2302 bonds, 319 residues, 6 models selected
> show #1 models
> hide #!6 models
> select :281-309
2271 atoms, 2302 bonds, 319 residues, 6 models selected
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_huntontin_6x9o/fold_huntontin_6x9o_model_0.cif
Chain information for fold_huntontin_6x9o_model_0.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_huntontin_6x9o/fold_huntontin_6x9o_model_1.cif
Chain information for fold_huntontin_6x9o_model_1.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_huntontin_6x9o/fold_huntontin_6x9o_model_2.cif
Chain information for fold_huntontin_6x9o_model_2.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_huntontin_6x9o/fold_huntontin_6x9o_model_3.cif
Chain information for fold_huntontin_6x9o_model_3.cif #10
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_huntontin_6x9o/fold_huntontin_6x9o_model_4.cif
Chain information for fold_huntontin_6x9o_model_4.cif #11
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> hide #1 models
> open 6x9o fromDatabase pdb format mmcif
Summary of feedback from opening 6x9o fetched from pdb
---
note | Fetching compressed mmCIF 6x9o from http://files.rcsb.org/download/6x9o.cif
6x9o title:
High resolution cryoEM structure of huntingtin in complex with HAP40 [more
info...]
Chain information for 6x9o #12
---
Chain | Description | UniProt
A | Huntingtin | HD_HUMAN 1-3144
B | 40-kDa huntingtin-associated protein | HAP40_HUMAN 1-371
> ui tool show Matchmaker
> matchmaker #7-11 to #12
Computing secondary structure
[Repeated 5 time(s)] 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 6x9o, chain A (#12) with fold_huntontin_6x9o_model_0.cif, chain A
(#7), sequence alignment score = 14480.3
RMSD between 1954 pruned atom pairs is 0.819 angstroms; (across all 2425
pairs: 1.628)
Matchmaker 6x9o, chain A (#12) with fold_huntontin_6x9o_model_1.cif, chain A
(#8), sequence alignment score = 14461.7
RMSD between 1967 pruned atom pairs is 0.793 angstroms; (across all 2425
pairs: 1.634)
Matchmaker 6x9o, chain A (#12) with fold_huntontin_6x9o_model_2.cif, chain A
(#9), sequence alignment score = 14478.5
RMSD between 1888 pruned atom pairs is 0.788 angstroms; (across all 2425
pairs: 1.754)
Matchmaker 6x9o, chain A (#12) with fold_huntontin_6x9o_model_3.cif, chain A
(#10), sequence alignment score = 14483.9
RMSD between 1978 pruned atom pairs is 0.803 angstroms; (across all 2425
pairs: 1.620)
Matchmaker 6x9o, chain A (#12) with fold_huntontin_6x9o_model_4.cif, chain A
(#11), sequence alignment score = 14478.5
RMSD between 1906 pruned atom pairs is 0.787 angstroms; (across all 2425
pairs: 1.768)
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #7 models
> show #7 models
> show #8 models
> hide #7 models
> show #9 models
> hide #8 models
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> hide #11 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> select :406-667
21406 atoms, 21868 bonds, 1 pseudobond, 2989 residues, 13 models selected
> color (#7#!12 & sel) yellow
> select clear
> hide #7 models
> show #7 models
> hide #7 models
> rainbow #!12
> show #7 models
> hide #7 models
> color #!12 bychain
> show #7 models
> color #7#!12 bychain
> hide #7 models
> select :#12/A
Expected an objects specifier or a keyword
> select #12/A
19063 atoms, 19440 bonds, 18 pseudobonds, 2425 residues, 2 models selected
> select clear
> select #12/A
19063 atoms, 19440 bonds, 18 pseudobonds, 2425 residues, 2 models selected
> select clear
> select #12/B
1836 atoms, 1868 bonds, 2 pseudobonds, 244 residues, 2 models selected
> select ~sel & ##selected
19063 atoms, 19440 bonds, 18 pseudobonds, 2425 residues, 2 models selected
> rainbow sel
> select clear
> show #7 models
> hide #7 models
> show #8 models
> hide #!12 models
> show #9 models
> show #10 models
> show #11 models
> delete atoms #8-11
> delete bonds #8-11
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_0.cif
Chain information for fold_aerolysin_wt_9fm6_model_0.cif #8
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_1.cif
Chain information for fold_aerolysin_wt_9fm6_model_1.cif #9
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_2.cif
Chain information for fold_aerolysin_wt_9fm6_model_2.cif #10
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_3.cif
Chain information for fold_aerolysin_wt_9fm6_model_3.cif #11
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_4.cif
Chain information for fold_aerolysin_wt_9fm6_model_4.cif #13
---
Chain | Description
A B C D E F G | .
> open 9FM6 fromDatabase pdb format mmcif
Summary of feedback from opening 9FM6 fetched from pdb
---
note | Fetching compressed mmCIF 9fm6 from http://files.rcsb.org/download/9fm6.cif
9fm6 title:
Aerolysin Wildtype in styrene-maleic acid lipid particles [more info...]
Chain information for 9fm6 #14
---
Chain | Description | UniProt
A B C D E F G | Aerolysin | AERA_AERHY 1-424
> show #8-11,13#!14 cartoons
Computing secondary structure
[Repeated 4 time(s)]
> hide #8-11,13#!14 atoms
> matchmaker #8-11,13 to #14
Computing secondary structure
[Repeated 5 time(s)] 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 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
A (#8), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.651 angstroms; (across all 412 pairs:
31.465)
Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_1.cif, chain
A (#9), sequence alignment score = 2074.7
RMSD between 240 pruned atom pairs is 0.637 angstroms; (across all 412 pairs:
31.072)
Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_2.cif, chain
A (#10), sequence alignment score = 2077.7
RMSD between 238 pruned atom pairs is 0.626 angstroms; (across all 412 pairs:
31.112)
Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_3.cif, chain
A (#11), sequence alignment score = 2077.7
RMSD between 239 pruned atom pairs is 0.770 angstroms; (across all 412 pairs:
30.864)
Matchmaker 9fm6, chain A (#14) with fold_aerolysin_wt_9fm6_model_4.cif, chain
A (#13), sequence alignment score = 2070.5
RMSD between 237 pruned atom pairs is 0.727 angstroms; (across all 412 pairs:
31.238)
> hide #13 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #9 models
> show #10 models
> show #11 models
> show #13 models
> hide #13 models
> hide #11 models
> hide #10 models
> hide #9 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #8 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.png" width 600 height
> 562 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> show #9 models
> hide #9 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.png" width 600
> height 562 supersample 4 transparentBackground true
> show #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.vs.AF3.png" width 600
> height 562 supersample 4 transparentBackground true
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.vs.AF3.side.png"
> width 600 height 562 supersample 4 transparentBackground true
> hide #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.side.png" width
> 600 height 562 supersample 4 transparentBackground true
> show #!14 models
> hide #8 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.side.png" width 600
> height 562 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> hide #8 models
> show #9 models
> show #10 models
> show #11 models
> show #13 models
> delete atoms #9-11,13
> delete bonds #9-11,13
> show #7 models
> show #!14 models
> show #8 models
> hide #7 models
> hide #8 models
> select #14/F
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> rainbow sel
> select clear
> show #7 models
> hide #7 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> select #12/F
Nothing selected
> rainbow #8
> color #8 bychain
> select #12/F
Nothing selected
> select #8/F
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> rainbow sel
> select clear
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> color #!14 bychain
> show #8 models
> color #8#!14 bychain
> select #8/E#14?E
Expected an objects specifier or a keyword
> select #8/E#14/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> rainbow sel
> select clear
> hide #8 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.png" width 600 height
> 562 supersample 4 transparentBackground true
> show #7 models
> hide #7 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.png" width 600
> height 562 supersample 4 transparentBackground true
> show #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.vs.AF3.png" width 600
> height 562 supersample 4 transparentBackground true
> hide #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.side.png" width
> 600 height 562 supersample 4 transparentBackground true
> show #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.side.png" width
> 600 height 562 supersample 4 transparentBackground true
> hide #8 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.side.png" width 600
> height 562 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.side.png" width
> 600 height 562 supersample 4 transparentBackground true
> select ~sel & ##selected
Nothing selected
> select #8/E#14/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> select ~sel & ##selected
39498 atoms, 40644 bonds, 6 pseudobonds, 5016 residues, 3 models selected
> hide sel & #8 cartoons
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6-AF3.one.png" width
> 600 height 562 supersample 4 transparentBackground true
> show #!14 models
> hide #8 models
> hide sel & #!14 cartoons
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/9FM6.one.png" width 600
> height 562 supersample 4 transparentBackground true
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FoxA1_GATA4.cxs"
——— End of log from Fri Jun 6 14:27:29 2025 ———
opened ChimeraX session
> show #1 models
> hide #1 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> select #8/:208-289
Expected an objects specifier or a keyword
> select #8:208-289
4410 atoms, 4501 bonds, 574 residues, 1 model selected
> select #8/E:208-289
630 atoms, 643 bonds, 82 residues, 1 model selected
> color sel magenta
> show #!14 models
> select #14/E:208-289
630 atoms, 643 bonds, 82 residues, 1 model selected
> color sel magenta
> select #14/E:208-289#8/E:208-289
1260 atoms, 1286 bonds, 164 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium purple target acs
> select clear
> rainbow #8#!14
> select #14/E:208-289#8/E:210-290
1255 atoms, 1281 bonds, 163 residues, 2 models selected
> select #14/E:208-289#8/E:209-288
1248 atoms, 1274 bonds, 162 residues, 2 models selected
> select #14/E:209-288#8/E:209-288
1236 atoms, 1262 bonds, 160 residues, 2 models selected
> color sel medium purple target acs
> select clear
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> ui tool show Matchmaker
[deleted to fit within ticket limits]
> select #3/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/B:124
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add #3/A:148
35 atoms, 35 bonds, 3 residues, 2 models selected
> select add #3/A:184
43 atoms, 42 bonds, 4 residues, 3 models selected
> select add #3/A:101@CA
44 atoms, 42 bonds, 5 residues, 3 models selected
> select add #3/A:102@CB
45 atoms, 43 bonds, 6 residues, 3 models selected
> select subtract #3/A:102
44 atoms, 43 bonds, 5 residues, 3 models selected
> select add #3/A:102
52 atoms, 50 bonds, 6 residues, 3 models selected
> select subtract #3/A:101
51 atoms, 49 bonds, 5 residues, 3 models selected
> select add #3/A:101
59 atoms, 56 bonds, 6 residues, 3 models selected
> select add #3/A:100
73 atoms, 71 bonds, 7 residues, 3 models selected
> select add #3/A:99
81 atoms, 78 bonds, 8 residues, 3 models selected
> select add #3/A:183
91 atoms, 88 bonds, 9 residues, 3 models selected
> select add #3/A:143
97 atoms, 93 bonds, 10 residues, 3 models selected
> select add #3/A:98
104 atoms, 100 bonds, 11 residues, 3 models selected
> select add #3/A:19
110 atoms, 105 bonds, 12 residues, 3 models selected
> select add #3/A:18
118 atoms, 112 bonds, 13 residues, 3 models selected
> select add #3/A:17
124 atoms, 117 bonds, 14 residues, 3 models selected
> select add #3/A:16
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:9
136 atoms, 127 bonds, 16 residues, 3 models selected
> select subtract #3/A:9
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:8
138 atoms, 129 bonds, 16 residues, 3 models selected
> select subtract #3/A:8
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10@CB
132 atoms, 123 bonds, 16 residues, 3 models selected
> select subtract #3/A:10@CB
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10
141 atoms, 133 bonds, 16 residues, 3 models selected
> select add #3/B:57
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 148 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select subtract #3/B:52
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CB
158 atoms, 147 bonds, 19 residues, 3 models selected
> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #3/B:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> label height 3
> label height 2
> label height 1
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> show #5 models
> hide #!3 models
> select #5/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #5/B:124
23 atoms, 23 bonds, 2 residues, 1 model selected
> select add #5/A:100
37 atoms, 39 bonds, 3 residues, 1 model selected
> select add #5/A:101
45 atoms, 45 bonds, 4 residues, 1 model selected
> select add #5/A:16
52 atoms, 51 bonds, 5 residues, 1 model selected
> select add #5/A:10
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:11
69 atoms, 68 bonds, 7 residues, 1 model selected
> select subtract #5/A:11
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:12
73 atoms, 72 bonds, 7 residues, 1 model selected
> select add #5/B:60
87 atoms, 87 bonds, 8 residues, 1 model selected
> select add #5/B:57
95 atoms, 94 bonds, 9 residues, 1 model selected
> select add #5/B:58
102 atoms, 100 bonds, 10 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #5/B:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #4 models
> hide #4 models
> show #!3 models
> hide #!5 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!3 models
> hide sel atoms
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> hide #!5 models
> show #7 models
> hide #7 models
> show #11 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> 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 add #11/A:101
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/A:143
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #11/A:19
20 atoms, 18 bonds, 3 residues, 1 model selected
> select add #11/A:18
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #11/A:17
34 atoms, 30 bonds, 5 residues, 1 model selected
> select add #11/A:10
44 atoms, 40 bonds, 6 residues, 1 model selected
> select add #11/A:100
58 atoms, 55 bonds, 7 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!5 models
> hide #!11 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> ~label #5 residues
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #15 models
> hide #5 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select ::name="CBD"
204 atoms, 224 bonds, 4 residues, 1 model selected
> color sel pale turquoise
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/3w78.AzrC.CBD.FMN.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> select clear
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #15 models
> undo
> hide #!16 models
> show #!16 models
> hide #15 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> show #!6 models
> hide #!16 models
> show #1 models
> hide #!6 models
> show #!16 models
> hide #1 models
> show #!6 models
> hide #!16 models
> show #!16 models
> hide #!6 models
> show #1 models
> hide #!16 models
> show #!16 models
> hide #1 models
> show #!3 models
> hide #!16 models
> show #!16 models
> hide #!3 models
> select #16/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> show #5 models
> hide #5 models
> show #!17 models
> hide #!16 models
> show #1 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #1 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!6 models
> hide #!17 models
> show #15 models
> hide #!3 models
> show #!16 models
> hide #15 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!16 models
> show #!3 models
> show #1 models
> hide #1 models
> show #7 models
> hide #7 models
> hide #!6 models
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> hide #1 models
> show #7 models
> show #1 models
> hide #7 models
> show #7 models
> hide #1 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> view matrix models
> #16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786
> hide #8 models
> show #12 models
> hide #12 models
> show #9 models
> show #10 models
> hide #9 models
> show #!3 models
> hide #10 models
> select #3/A:104
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> view matrix models
> #3,0.23414,-0.80222,0.54921,11.186,0.21867,-0.50698,-0.83376,-19.133,0.94729,0.31531,0.056721,3.3647
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> open 2Bzs fromDatabase pdb format mmcif
Summary of feedback from opening 2Bzs fetched from pdb
---
notes | Fetching compressed mmCIF 2bzs from http://files.rcsb.org/download/2bzs.cif
Fetching CCD CB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/CB1/CB1.cif
2bzs title:
Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed
by the crystal structure of their complex. [more info...]
Chain information for 2bzs #19
---
Chain | Description | UniProt
A B | NRH DEHYDROGENASE [QUINONE] 2 | NQO2_HUMAN 1-230
Non-standard residues in 2bzs #19
---
CB1 — 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954; Tretazicar)
FAD — flavin-adenine dinucleotide
ZN — zinc ion
> hide #!3 models
> color #!19 bychain
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> show #!3 models
> hide #!3 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #!19 to #3 & sel
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2bzs, chain B
(#19), sequence alignment score = 223.4
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 198 pairs:
5.647)
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #1 models
> hide #!19 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #1 to #3 & sel
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
> show #!19 models
> hide #1 models
> show #1 models
> hide #!3 models
> hide #!19 models
> show #!19 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #4 models
> hide #4 models
> show #1 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> color sel bychain
> select clear
> hide #1 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!19 models
> show #!19 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select clear
> open 2VPw fromDatabase pdb format mmcif
Summary of feedback from opening 2VPw fetched from pdb
---
notes | Fetching compressed mmCIF 2vpw from http://files.rcsb.org/download/2vpw.cif
Fetching CCD MGD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MGD/MGD.cif
Fetching CCD MO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MO/MO.cif
Fetching CCD MQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/MQ7/MQ7.cif
2vpw title:
Polysulfide reductase with bound menaquinone [more info...]
Chain information for 2vpw #20
---
Chain | Description | UniProt
A E | THIOSULFATE REDUCTASE | Q72LA4_THET2 1-765
B F | NRFC PROTEIN | Q72LA5_THET2 1-195
C G | HYPOTHETICAL MEMBRANE SPANNING PROTEIN | Q72LA6_THET2 0-252 1-253
Non-standard residues in 2vpw #20
---
MGD —
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)
MO — molybdenum atom
MQ7 — menaquinone-7
SF4 — iron/sulfur cluster
> hide #!19 models
> hide #1 models
> hide #!20 surfaces
> hide #!20 atoms
> show #!20 cartoons
> matchmaker #!20 to #3 & sel
No 'to' model specified
> matchmaker #!20 to #3
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2vpw, chain E
(#20), sequence alignment score = 78
RMSD between 8 pruned atom pairs is 1.398 angstroms; (across all 148 pairs:
20.313)
> show #!3 models
> hide #!3 models
> select /A
51617 atoms, 51746 bonds, 16 pseudobonds, 7421 residues, 24 models selected
> rainbow sel & #!20
> select ::name="MQ7"
30 atoms, 32 bonds, 2 residues, 1 model selected
> show sel surfaces
> open 7NZ1 fromDatabase pdb format mmcif
Summary of feedback from opening 7NZ1 fetched from pdb
---
notes | Fetching compressed mmCIF 7nz1 from http://files.rcsb.org/download/7nz1.cif
Fetching CCD CSX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CSX/CSX.cif
7nz1 title:
Respiratory complex I from Escherichia coli - focused refinement of
cytoplasmic arm [more info...]
Chain information for 7nz1 #21
---
Chain | Description | UniProt
B | NADH-quinone oxidoreductase subunit B |
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180
Non-standard residues in 7nz1 #21
---
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
SF4 — iron/sulfur cluster
> hide sel atoms
> show sel cartoons
> hide #!20 models
> show #!21 cartoons
> hide #!21 atoms
> view matrix models
> #20,-0.20963,0.97025,0.12114,-159.27,0.41872,0.20104,-0.88558,-19.075,-0.88359,-0.13493,-0.44841,140.58
> color #!21 bychain
> matchmaker #!21 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 fold_azor_monomer_model_0.cif, chain A (#1) with 7nz1, chain G
(#21), sequence alignment score = 86.3
RMSD between 22 pruned atom pairs is 0.859 angstroms; (across all 180 pairs:
20.357)
> show #1 models
> select #21/G
7630 atoms, 7235 bonds, 24 pseudobonds, 1469 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!21 models
> show #!21 models
> hide #1 models
> matchmaker #!21 to #8
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 fold_mqo_model_0.cif, chain A (#8) with 7nz1, chain G (#21),
sequence alignment score = 63.6
RMSD between 5 pruned atom pairs is 1.257 angstroms; (across all 362 pairs:
31.062)
> show #8 models
> hide #!21 models
> hide #8 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif
Chain information for fold_tcr_ankkflltv_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_1.cif #23
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_2.cif #24
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_3.cif #25
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_4.cif #26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #23-26 to #22
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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_1.cif, chain B (#23), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.184 angstroms; (across all 111 pairs:
0.184)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_2.cif, chain B (#24), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.232 angstroms; (across all 111 pairs:
0.232)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_3.cif, chain B (#25), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.364 angstroms; (across all 111 pairs:
0.364)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_4.cif, chain B (#26), sequence alignment score =
573.8
RMSD between 110 pruned atom pairs is 0.269 angstroms; (across all 111 pairs:
0.332)
> view matrix models
> #21,0.56571,0.78878,0.24042,-111.9,-0.81332,0.5818,0.0049461,-39.828,-0.13598,-0.19834,0.97066,-77.181
Drag select of 9 atoms, 113 residues, 8 bonds
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif
Chain information for fold_tcr_demefteae_model_0.cif #27
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_1.cif #28
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_2.cif #29
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_3.cif #30
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_4.cif #31
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #27-31 to #22
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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_0.cif, chain B (#27), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.323 angstroms; (across all 111 pairs:
0.323)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_1.cif, chain B (#28), sequence alignment score =
570.2
RMSD between 111 pruned atom pairs is 0.204 angstroms; (across all 111 pairs:
0.204)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_2.cif, chain B (#29), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.345 angstroms; (across all 111 pairs:
0.345)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_3.cif, chain B (#30), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.287 angstroms; (across all 111 pairs:
0.287)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_4.cif, chain B (#31), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.349 angstroms; (across all 111 pairs:
0.349)
> select clear
> delete atoms #22-31
> delete bonds #22-31
> show #!13 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_aiykksqhm/fold_tcr_aiykksqhm_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_aiykksqhm/fold_tcr_aiykksqhm_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_aiykksqhm/fold_tcr_aiykksqhm_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_aiykksqhm/fold_tcr_aiykksqhm_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_aiykksqhm/fold_tcr_aiykksqhm_model_4.cif
Chain information for fold_tcr_aiykksqhm_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_aiykksqhm_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_aiykksqhm_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_aiykksqhm_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_aiykksqhm_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-5 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 fold_tcr_aiykksqhm_model_0.cif, chain A (#1) with
fold_tcr_aiykksqhm_model_1.cif, chain A (#2), sequence alignment score = 564.3
RMSD between 105 pruned atom pairs is 0.187 angstroms; (across all 109 pairs:
0.852)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_aiykksqhm_model_2.cif, chain B (#3), sequence alignment score = 573.8
RMSD between 109 pruned atom pairs is 0.297 angstroms; (across all 111 pairs:
1.233)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_aiykksqhm_model_3.cif, chain B (#4), sequence alignment score = 581
RMSD between 109 pruned atom pairs is 0.230 angstroms; (across all 111 pairs:
1.219)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_aiykksqhm_model_4.cif, chain B (#5), sequence alignment score = 573.8
RMSD between 109 pruned atom pairs is 0.277 angstroms; (across all 111 pairs:
0.970)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #1 models
> delete atoms #2-5
> delete bonds #2-5
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
Chain information for fold_tcr_ankkflltv_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
Chain information for fold_tcr_ankkflltv_model_1.cif #3
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
Chain information for fold_tcr_ankkflltv_model_2.cif #4
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
Chain information for fold_tcr_ankkflltv_model_3.cif #5
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif
Chain information for fold_tcr_ankkflltv_model_4.cif #6
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #2-6 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ankkflltv_model_0.cif, chain B (#2), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.241 angstroms; (across all 111 pairs:
0.241)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ankkflltv_model_1.cif, chain B (#3), sequence alignment score = 573.8
RMSD between 111 pruned atom pairs is 0.277 angstroms; (across all 111 pairs:
0.277)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ankkflltv_model_2.cif, chain B (#4), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.231 angstroms; (across all 111 pairs:
0.231)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ankkflltv_model_3.cif, chain B (#5), sequence alignment score = 573.8
RMSD between 110 pruned atom pairs is 0.346 angstroms; (across all 111 pairs:
0.399)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ankkflltv_model_4.cif, chain B (#6), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.297 angstroms; (across all 111 pairs:
0.297)
> hide #3 models
> hide #2 models
> hide #5 models
> hide #6 models
> show #2 models
> hide #4 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> hide #2 models
> delete atoms #3-6
> delete bonds #3-6
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
Chain information for fold_tcr_demefteae_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
Chain information for fold_tcr_demefteae_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
Chain information for fold_tcr_demefteae_model_2.cif #5
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
Chain information for fold_tcr_demefteae_model_3.cif #6
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif
Chain information for fold_tcr_demefteae_model_4.cif #7
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #3-7 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_demefteae_model_0.cif, chain B (#3), sequence alignment score = 573.8
RMSD between 111 pruned atom pairs is 0.346 angstroms; (across all 111 pairs:
0.346)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_demefteae_model_1.cif, chain B (#4), sequence alignment score = 563
RMSD between 111 pruned atom pairs is 0.280 angstroms; (across all 111 pairs:
0.280)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_demefteae_model_2.cif, chain B (#5), sequence alignment score = 579.8
RMSD between 110 pruned atom pairs is 0.344 angstroms; (across all 111 pairs:
0.396)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_demefteae_model_3.cif, chain B (#6), sequence alignment score = 573.8
RMSD between 111 pruned atom pairs is 0.331 angstroms; (across all 111 pairs:
0.331)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_demefteae_model_4.cif, chain B (#7), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.332 angstroms; (across all 111 pairs:
0.332)
> hide #3 models
> delete atoms #4-7
> delete bonds #4-7
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_fainntksf/fold_tcr_fainntksf_model_0.cif
Chain information for fold_tcr_fainntksf_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_fainntksf/fold_tcr_fainntksf_model_1.cif
Chain information for fold_tcr_fainntksf_model_1.cif #5
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_fainntksf/fold_tcr_fainntksf_model_2.cif
Chain information for fold_tcr_fainntksf_model_2.cif #6
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_fainntksf/fold_tcr_fainntksf_model_3.cif
Chain information for fold_tcr_fainntksf_model_3.cif #7
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_fainntksf/fold_tcr_fainntksf_model_4.cif
Chain information for fold_tcr_fainntksf_model_4.cif #8
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #4-8 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_fainntksf_model_0.cif, chain B (#4), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.245 angstroms; (across all 111 pairs:
0.245)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_fainntksf_model_1.cif, chain B (#5), sequence alignment score = 573.8
RMSD between 109 pruned atom pairs is 0.182 angstroms; (across all 111 pairs:
0.882)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_fainntksf_model_2.cif, chain B (#6), sequence alignment score = 587
RMSD between 110 pruned atom pairs is 0.254 angstroms; (across all 111 pairs:
0.363)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_fainntksf_model_3.cif, chain B (#7), sequence alignment score = 573.8
RMSD between 110 pruned atom pairs is 0.265 angstroms; (across all 111 pairs:
0.354)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_fainntksf_model_4.cif, chain B (#8), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.352 angstroms; (across all 111 pairs:
0.352)
> hide #4 models
> delete atoms #5-8
> delete bonds #5-8
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_model_0.cif
Chain information for fold_tcr_illgfsftl_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_model_1.cif
Chain information for fold_tcr_illgfsftl_model_1.cif #6
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_model_2.cif
Chain information for fold_tcr_illgfsftl_model_2.cif #7
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_model_3.cif
Chain information for fold_tcr_illgfsftl_model_3.cif #8
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_model_4.cif
Chain information for fold_tcr_illgfsftl_model_4.cif #9
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #5-9 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_illgfsftl_model_0.cif, chain B (#5), sequence alignment score = 570.2
RMSD between 111 pruned atom pairs is 0.274 angstroms; (across all 111 pairs:
0.274)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_illgfsftl_model_1.cif, chain B (#6), sequence alignment score = 569
RMSD between 111 pruned atom pairs is 0.254 angstroms; (across all 111 pairs:
0.254)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_illgfsftl_model_2.cif, chain B (#7), sequence alignment score = 573.8
RMSD between 111 pruned atom pairs is 0.262 angstroms; (across all 111 pairs:
0.262)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_illgfsftl_model_3.cif, chain B (#8), sequence alignment score = 573.8
RMSD between 111 pruned atom pairs is 0.229 angstroms; (across all 111 pairs:
0.229)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_illgfsftl_model_4.cif, chain B (#9), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.304 angstroms; (across all 111 pairs:
0.304)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #6 models
> show #7 models
> show #8 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #9 models
> hide #9 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_summary_confidences_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_summary_confidences_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_illgfsftl/fold_tcr_illgfsftl_summary_confidences_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> hide #8 models
> show #8 models
> show #6 models
> show #7 models
> hide #8 models
> show #9 models
> hide #9 models
> show #9 models
> delete atoms #6-7,9
> delete bonds #6-7,9
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_kllqfpihl/fold_tcr_kllqfpihl_model_0.cif
Chain information for fold_tcr_kllqfpihl_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_kllqfpihl/fold_tcr_kllqfpihl_model_1.cif
Chain information for fold_tcr_kllqfpihl_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_kllqfpihl/fold_tcr_kllqfpihl_model_2.cif
Chain information for fold_tcr_kllqfpihl_model_2.cif #9
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_kllqfpihl/fold_tcr_kllqfpihl_model_3.cif
Chain information for fold_tcr_kllqfpihl_model_3.cif #10
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_kllqfpihl/fold_tcr_kllqfpihl_model_4.cif
Chain information for fold_tcr_kllqfpihl_model_4.cif #11
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #6-7,9-11 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_kllqfpihl_model_0.cif, chain B (#6), sequence alignment score = 579.8
RMSD between 109 pruned atom pairs is 0.168 angstroms; (across all 111 pairs:
1.231)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_kllqfpihl_model_1.cif, chain B (#7), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.350 angstroms; (across all 111 pairs:
0.350)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_kllqfpihl_model_2.cif, chain B (#9), sequence alignment score = 579.8
RMSD between 111 pruned atom pairs is 0.229 angstroms; (across all 111 pairs:
0.229)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_kllqfpihl_model_3.cif, chain B (#10), sequence alignment score = 563
RMSD between 105 pruned atom pairs is 0.178 angstroms; (across all 111 pairs:
1.538)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_kllqfpihl_model_4.cif, chain B (#11), sequence alignment score =
573.8
RMSD between 109 pruned atom pairs is 0.256 angstroms; (across all 111 pairs:
1.094)
> hide #6 models
> delete atoms #7,9-11
> delete bonds #7,9-11
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_lvlgfvfml/fold_tcr_lvlgfvfml_model_0.cif
Chain information for fold_tcr_lvlgfvfml_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_lvlgfvfml/fold_tcr_lvlgfvfml_model_1.cif
Chain information for fold_tcr_lvlgfvfml_model_1.cif #9
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_lvlgfvfml/fold_tcr_lvlgfvfml_model_2.cif
Chain information for fold_tcr_lvlgfvfml_model_2.cif #10
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_lvlgfvfml/fold_tcr_lvlgfvfml_model_3.cif
Chain information for fold_tcr_lvlgfvfml_model_3.cif #11
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_lvlgfvfml/fold_tcr_lvlgfvfml_model_4.cif
Chain information for fold_tcr_lvlgfvfml_model_4.cif #12
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #7,9-12 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_lvlgfvfml_model_0.cif, chain B (#7), sequence alignment score = 587
RMSD between 111 pruned atom pairs is 0.304 angstroms; (across all 111 pairs:
0.304)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_lvlgfvfml_model_1.cif, chain B (#9), sequence alignment score = 569
RMSD between 111 pruned atom pairs is 0.192 angstroms; (across all 111 pairs:
0.192)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_lvlgfvfml_model_2.cif, chain B (#10), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.300 angstroms; (across all 111 pairs:
0.300)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_lvlgfvfml_model_3.cif, chain B (#11), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.318 angstroms; (across all 111 pairs:
0.318)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_lvlgfvfml_model_4.cif, chain B (#12), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.231 angstroms; (across all 111 pairs:
0.231)
> hide #7 models
> delete atoms #9-12
> delete bonds #9-12
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_rvyaptstl/fold_tcr_rvyaptstl_model_0.cif
Chain information for fold_tcr_rvyaptstl_model_0.cif #9
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_rvyaptstl/fold_tcr_rvyaptstl_model_1.cif
Chain information for fold_tcr_rvyaptstl_model_1.cif #10
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_rvyaptstl/fold_tcr_rvyaptstl_model_2.cif
Chain information for fold_tcr_rvyaptstl_model_2.cif #11
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_rvyaptstl/fold_tcr_rvyaptstl_model_3.cif
Chain information for fold_tcr_rvyaptstl_model_3.cif #12
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_rvyaptstl/fold_tcr_rvyaptstl_model_4.cif
Chain information for fold_tcr_rvyaptstl_model_4.cif #13
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #9-13 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_rvyaptstl_model_0.cif, chain B (#9), sequence alignment score = 579.8
RMSD between 110 pruned atom pairs is 0.280 angstroms; (across all 111 pairs:
0.344)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_rvyaptstl_model_1.cif, chain B (#10), sequence alignment score = 563
RMSD between 111 pruned atom pairs is 0.306 angstroms; (across all 111 pairs:
0.306)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_rvyaptstl_model_2.cif, chain B (#11), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.194 angstroms; (across all 111 pairs:
0.194)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_rvyaptstl_model_3.cif, chain B (#12), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.291 angstroms; (across all 111 pairs:
0.291)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_rvyaptstl_model_4.cif, chain B (#13), sequence alignment score =
573.8
RMSD between 108 pruned atom pairs is 0.271 angstroms; (across all 111 pairs:
0.474)
> hide #9 models
> hide #10 models
> show #10 models
> show #9 models
> hide #9 models
> hide #10 models
> show #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> show #11 models
> hide #11 models
> show #9 models
> hide #10 models
> show #1 models
> hide #1 models
> show #10 models
> hide #10 models
> show #11 models
> show #12 models
> show #13 models
> hide #9 models
> delete atoms #11-13
> delete bonds #11-13
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ssyrrpvgi/fold_tcr_ssyrrpvgi_model_0.cif
Chain information for fold_tcr_ssyrrpvgi_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ssyrrpvgi/fold_tcr_ssyrrpvgi_model_1.cif
Chain information for fold_tcr_ssyrrpvgi_model_1.cif #12
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ssyrrpvgi/fold_tcr_ssyrrpvgi_model_2.cif
Chain information for fold_tcr_ssyrrpvgi_model_2.cif #13
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ssyrrpvgi/fold_tcr_ssyrrpvgi_model_3.cif
Chain information for fold_tcr_ssyrrpvgi_model_3.cif #14
---
Chain | Description
A | .
B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_ssyrrpvgi/fold_tcr_ssyrrpvgi_model_4.cif
Chain information for fold_tcr_ssyrrpvgi_model_4.cif #15
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> matchmaker #11-15 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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ssyrrpvgi_model_0.cif, chain B (#11), sequence alignment score = 587
RMSD between 111 pruned atom pairs is 0.276 angstroms; (across all 111 pairs:
0.276)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ssyrrpvgi_model_1.cif, chain B (#12), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.268 angstroms; (across all 111 pairs:
0.268)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ssyrrpvgi_model_2.cif, chain B (#13), sequence alignment score =
579.8
RMSD between 110 pruned atom pairs is 0.219 angstroms; (across all 111 pairs:
0.295)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ssyrrpvgi_model_3.cif, chain B (#14), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.309 angstroms; (across all 111 pairs:
0.309)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcr_ssyrrpvgi_model_4.cif, chain B (#15), sequence alignment score =
579.8
RMSD between 111 pruned atom pairs is 0.280 angstroms; (across all 111 pairs:
0.280)
> hide #11 models
> delete atoms #12-15
> delete bonds #12-15
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcrb_lvlgfvfml/fold_tcrb_lvlgfvfml_model_0.cif
Chain information for fold_tcrb_lvlgfvfml_model_0.cif #12
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcrb_lvlgfvfml/fold_tcrb_lvlgfvfml_model_1.cif
Chain information for fold_tcrb_lvlgfvfml_model_1.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcrb_lvlgfvfml/fold_tcrb_lvlgfvfml_model_2.cif
Chain information for fold_tcrb_lvlgfvfml_model_2.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcrb_lvlgfvfml/fold_tcrb_lvlgfvfml_model_3.cif
Chain information for fold_tcrb_lvlgfvfml_model_3.cif #15
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcrb_lvlgfvfml/fold_tcrb_lvlgfvfml_model_4.cif
Chain information for fold_tcrb_lvlgfvfml_model_4.cif #16
---
Chain | Description
A | .
B | .
Computing secondary structure
> select /B
10243 atoms, 10490 bonds, 1266 residues, 16 models selected
> select #1/B
898 atoms, 920 bonds, 111 residues, 1 model selected
> matchmaker #12-16 to #1 & sel
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 fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcrb_lvlgfvfml_model_0.cif, chain A (#12), sequence alignment score =
560.6
RMSD between 106 pruned atom pairs is 0.301 angstroms; (across all 111 pairs:
1.348)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcrb_lvlgfvfml_model_1.cif, chain A (#13), sequence alignment score = 563
RMSD between 108 pruned atom pairs is 0.403 angstroms; (across all 111 pairs:
1.291)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcrb_lvlgfvfml_model_2.cif, chain A (#14), sequence alignment score = 569
RMSD between 107 pruned atom pairs is 0.361 angstroms; (across all 111 pairs:
1.239)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcrb_lvlgfvfml_model_3.cif, chain A (#15), sequence alignment score = 569
RMSD between 109 pruned atom pairs is 0.409 angstroms; (across all 111 pairs:
0.546)
Matchmaker fold_tcr_aiykksqhm_model_0.cif, chain B (#1) with
fold_tcrb_lvlgfvfml_model_4.cif, chain A (#16), sequence alignment score =
573.8
RMSD between 108 pruned atom pairs is 0.413 angstroms; (across all 111 pairs:
1.038)
> hide #12 models
> delete atoms #13-16
> delete bonds #13-16
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> select /A
10083 atoms, 10281 bonds, 1310 residues, 12 models selected
> hide #12 models
> select add #12
10156 atoms, 10355 bonds, 1319 residues, 12 models selected
> select subtract #12
9185 atoms, 9361 bonds, 1199 residues, 11 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel light blue
> color sel light sky blue
> color sel light blue
> color sel powder blue
> select /B
9951 atoms, 10194 bonds, 1230 residues, 12 models selected
> color sel thistle
> select clear
> show #12 models
> select #12/A
898 atoms, 920 bonds, 111 residues, 1 model selected
> color sel thistle
> select clear
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #1 surfaces
> select #11/C
73 atoms, 74 bonds, 9 residues, 1 model selected
> hide #!1 surfaces
> select /A/B
20034 atoms, 20475 bonds, 2540 residues, 12 models selected
> show sel & #!1 surfaces
> select clear
> show #2 models
> hide #!1 models
> show #!1 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> hide #12 models
> select /A/B
20034 atoms, 20475 bonds, 2540 residues, 12 models selected
> show sel & #2-11#!1 surfaces
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide sel & #!1-2 surfaces
> hide #!1 models
> show sel & #!2 surfaces
> select #2/B:50@CB
1 atom, 1 residue, 1 model selected
> select clear
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!1 surfaces
> select #1/C
77 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel surfaces
> select clear
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!4 models
> hide #!1 models
> hide #!4 surfaces
> show #!1 models
> hide #!1,4 surfaces
> show #!1,4 surfaces
> select /C
811 atoms, 821 bonds, 99 residues, 11 models selected
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide sel & #!1 surfaces
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select /C
811 atoms, 821 bonds, 99 residues, 11 models selected
> hide sel & #!1,4 surfaces
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 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 #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!2 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #12 models
> hide #12 models
> show #12 models
> show #!11 models
> hide #!10 models
> select #12/B
73 atoms, 74 bonds, 9 residues, 1 model selected
> color sel blue
> select clear
> select O
4009 atoms, 2639 residues, 12 models selected
> select clear
> select add #12/B:7@O
1 atom, 1 residue, 1 model selected
> select add #12/B:9@O
2 atoms, 2 residues, 1 model selected
> select add #12/B:5@O
3 atoms, 3 residues, 1 model selected
> select add #12/B:3@O
4 atoms, 4 residues, 1 model selected
> select add #12/B:4@O
5 atoms, 5 residues, 1 model selected
> select add #12/B:2@O
6 atoms, 6 residues, 1 model selected
> color sel red
> select clear
> select add #12/B:6@O
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> hide #12 models
> hide #!11 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 surfaces
> show #!1 surfaces
> select #1/C
77 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel surfaces
> select clear
> hide #!1 surfaces
> show #!7 models
> hide #!1 models
> hide #!7 models
> show #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!5,8 surfaces
> show #!1 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> hide #!8 models
> show #!2 models
> hide #!1-2 surfaces
> hide #!2 models
> select #1/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:91
20 atoms, 18 bonds, 2 residues, 2 models selected
> select add #1/A:92
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #1/A:93
36 atoms, 33 bonds, 4 residues, 2 models selected
> select add #1/A:94
41 atoms, 37 bonds, 5 residues, 2 models selected
> select add #1/A:95
50 atoms, 45 bonds, 6 residues, 2 models selected
> select add #1/A:96
54 atoms, 48 bonds, 7 residues, 2 models selected
> select add #1/B:92
59 atoms, 52 bonds, 8 residues, 2 models selected
> select add #1/A:97
67 atoms, 59 bonds, 9 residues, 2 models selected
> select subtract #1/B:92
62 atoms, 55 bonds, 8 residues, 2 models selected
> color sel cornflower blue
> hide sel surfaces
> select #1/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel surfaces
> select clear
> show #!1 surfaces
> select #1/C
77 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel surfaces
> select clear
> hide #!1 surfaces
> select #1/A#1/B
1733 atoms, 1771 bonds, 220 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!1 surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:87-94
60 atoms, 60 bonds, 8 residues, 1 model selected
> select #1/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> select #1/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!2 models
> select #1/A.87
Expected an objects specifier or a keyword
> hide #!2 models
> select #1/A.87
Expected an objects specifier or a keyword
> select #1/A87
Nothing selected
> select #1/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:87-:99
Expected an objects specifier or a keyword
> select #1/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> select /A:87-99
1182 atoms, 1193 bonds, 156 residues, 12 models selected
> color sel cornflower blue
> show #!2 models
> hide #!1 models
> show #!3 models
> hide sel & #!2-3 surfaces
> show sel & #!2-3 surfaces
> select clear
> hide #!2-3 surfaces
> hide #!2 models
> show #!4 models
> hide #!3-4 surfaces
> hide #!3 models
> select #4/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/A:97
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #4/A:91
28 atoms, 25 bonds, 3 residues, 2 models selected
> select add #4/A:92
32 atoms, 28 bonds, 4 residues, 2 models selected
> show #!1 models
> hide #!4 models
> select add #1/A:90
41 atoms, 36 bonds, 5 residues, 3 models selected
> select add #1/A:97
49 atoms, 43 bonds, 6 residues, 4 models selected
> select #1/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select add #1/A:91
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/A:92
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #1/A:93
27 atoms, 25 bonds, 3 residues, 2 models selected
> select add #1/A:94
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add #1/A:95
41 atoms, 37 bonds, 5 residues, 2 models selected
> select add #1/A:96
45 atoms, 40 bonds, 6 residues, 2 models selected
> select add #1/A:97
53 atoms, 47 bonds, 7 residues, 2 models selected
> select #1/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide sel surfaces
> select /A:87-99
1182 atoms, 1193 bonds, 156 residues, 12 models selected
> color sel cornflower blue
> select clear
> hide #!1-11 surfaces
> select #1/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> select /B:91-102
1012 atoms, 1023 bonds, 132 residues, 11 models selected
> color sel pale violet red
> select #12/A:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> color sel pale violet red
> show #12 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!11 models
> hide #!10 models
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #12 models
> show #12 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #12 models
> hide #!11 models
> hide #!2 models
> show #!1 surfaces
> select C
13128 atoms, 10567 bonds, 2639 residues, 12 models selected
> select /C
811 atoms, 821 bonds, 99 residues, 11 models selected
> hide sel & #!1 surfaces
> select #1/B:54@CD2
1 atom, 1 residue, 1 model selected
> select clear
> show #!2 models
> hide #!2 models
> hide #!1 surfaces
> ui tool show "Side View"
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!1 surfaces
> select /C
811 atoms, 821 bonds, 99 residues, 11 models selected
> hide sel & #!1 surfaces
> select clear
> show #!2 models
> hide #!1 models
> show #!2 surfaces
> select /C
811 atoms, 821 bonds, 99 residues, 11 models selected
> hide sel & #!2 surfaces
> select #2/B:57@CA
1 atom, 1 residue, 1 model selected
> select clear
> show #!1 models
> hide #!2 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> peptide.cxs
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> AIYKKSQHM.s.png width 600 height 448 supersample 4 transparentBackground
> true
> hide #!1 surfaces
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> AIYKKSQHM.png width 600 height 448 supersample 4 transparentBackground true
> open 1KJ2 fromDatabase pdb format mmcif
Summary of feedback from opening 1KJ2 fetched from pdb
---
notes | Fetching compressed mmCIF 1kj2 from http://files.rcsb.org/download/1kj2.cif
Fetching CCD GAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
Fetching CCD SIA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/SIA/SIA.cif
1kj2 title:
Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex [more
info...]
Chain information for 1kj2 #13
---
Chain | Description | UniProt
A D | KB5-C20 T-Cell receptor alpha-chain |
B E | KB5-C20 T-Cell receptor beta-chain |
H I | Allogeneic H-2Kb MHC Class I Molecule |
L M | Beta-2 microglobulin | B2MG_MOUSE 1-99
P Q | Naturally processed octapeptide PKB1 | GTB1_MOUSE 1-8
Non-standard residues in 1kj2 #13
---
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SIA — N-acetyl-alpha-neuraminic acid (N-acetylneuraminic acid; sialic acid;
alpha-sialic acid; O-SIALIC ACID)
1kj2 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> show #13#!1 cartoons
> hide #13#!1 atoms
> matchmaker #13 to #1 & sel
No 'to' model specified
> matchmaker #13 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 fold_tcr_aiykksqhm_model_0.cif, chain A (#1) with 1kj2, chain A
(#13), sequence alignment score = 257.5
RMSD between 90 pruned atom pairs is 0.882 angstroms; (across all 108 pairs:
2.210)
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /D/E/I/M
4947 atoms, 5050 bonds, 642 residues, 1 model selected
> hide sel cartoons
> select /D/E/I/M/Q
5017 atoms, 5117 bonds, 653 residues, 1 model selected
> hide sel cartoons
> color sel bychain
> select /P
69 atoms, 67 bonds, 10 residues, 1 model selected
> select /P
69 atoms, 67 bonds, 10 residues, 1 model selected
> color sel magenta
> select clear
> select /P
69 atoms, 67 bonds, 10 residues, 1 model selected
> show sel atoms
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_0.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_1.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_2.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_3.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_4.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_2.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_3.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_4.cif #10
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_1.cif #12
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_2.cif #13
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_3.cif #14
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_4.cif #15
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
[Repeated 13 time(s)]
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
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 Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H00105LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 196 days, 6 hours, 24 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2718Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Reported by Emily Tai