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Opened 9 hours ago
#19990 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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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{
"uptime" : 2400000,
"procRole" : "Background",
"version" : 2,
"userID" : 1816534185,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 146541,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"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},
"parentProc" : "launchd",
"parentPid" : 1,
"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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"path" : "\/usr\/lib\/system\/libxpc.dylib",
"name" : "libxpc.dylib"
}
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"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
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System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Boot Volume File System Type: apfs
Memory Module: LPDDR5, Hynix
USB Device: USB31Bus
USB Device: 4-Port USB 3.0 Hub
USB Device: USB 10/100/1000 LAN
USB Device: 4-Port USB 2.0 Hub
USB Device: Keyboard Hub
USB Device: DELL Laser Mouse
USB Device: Apple Keyboard
USB Device: Logitech USB Headset
USB Device: USB31Bus
USB Device: USB31Bus
Display: DELL U2718Q, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition), Main, MirrorOff, Online
Model: MacBookPro18,3, BootROM 11881.140.96, proc 10:8:2 processors, 32 GB, SMC
Graphics: Apple M1 Pro, Apple M1 Pro, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4387), wl0: Mar 23 2025 19:56:28 version 20.130.17.0.8.7.197 FWID 01-764e34b7
IO80211_driverkit-1485.7 "IO80211_driverkit-1485.7" Jul 15 2025 20:46:41
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== 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
> matchmaker #8 to #14 & 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 9fm6, chain E (#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)
> select #14/E#8/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> matchmaker #8 & sel to #14 & 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 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
E (#8), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> select clear
> select #14
22743 atoms, 23408 bonds, 7 pseudobonds, 2884 residues, 2 models selected
> show sel cartoons
> undo
[Repeated 1 time(s)]
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.unit.png"
> width 800 height 565 supersample 4 transparentBackground true
> hide #8 models
> select #14
22743 atoms, 23408 bonds, 7 pseudobonds, 2884 residues, 2 models selected
> show sel cartoons
> color sel bychain
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> rainbow sel
> undo
> select clear
> show #8 models
> hide #!14 models
> select #8
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> show sel cartoons
> color sel bychain
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> rainbow sel
> select clear
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> 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 #9
---
Chain | Description
A B C D E F G | .
> hide #!14 models
> show #9 cartoons
Computing secondary structure
> hide #9 atoms
> show #!14 models
> show #8 models
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> matchmaker #9 to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with
fold_aerolysin_wt_9fm6_model_0.cif, chain A (#9), sequence alignment score =
2272.4
RMSD between 424 pruned atom pairs is 0.245 angstroms; (across all 424 pairs:
0.245)
> hide #8 models
> hide #!14 models
> select #9/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> show #8 models
> hide #8 models
> rainbow sel
> show #!14 models
> undo
> hide #9 models
> select #9/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 clear
> show #9 models
> show #8 models
> hide #9 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #9 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> show #8 models
> hide #9 models
> hide #!14 models
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> show #9 models
> hide #9 models
> show #!14 models
> hide #8 models
> show #9 models
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.46445,-0.79953,-0.38084,163.55,-0.1926,-0.32855,0.92464,178.17,-0.8644,0.5028,-0.0013961,187.23
> view matrix models
> #9,-0.43901,-0.71339,-0.54622,158.66,0.21806,-0.67435,0.70548,145.23,-0.87162,0.1906,0.4516,196.26
> view matrix models
> #9,-0.4878,-0.22692,-0.84295,177.56,-0.14029,-0.9327,0.33226,70.026,-0.86161,0.28033,0.42314,202.97
> view matrix models
> #9,-0.48207,-0.25635,-0.83779,175.43,-0.05356,-0.94583,0.32023,71.895,-0.8745,0.19924,0.44222,196.14
> view matrix models
> #9,-0.47677,-0.19158,-0.8579,180.22,-0.087854,-0.96069,0.26336,63.801,-0.87462,0.20093,0.4412,196.2
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.47677,-0.19158,-0.8579,168.63,-0.087854,-0.96069,0.26336,65.177,-0.87462,0.20093,0.4412,196.79
> view matrix models
> #9,-0.47677,-0.19158,-0.8579,159.22,-0.087854,-0.96069,0.26336,66.148,-0.87462,0.20093,0.4412,210.7
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "move picked models"
> hide #9 models
> view matrix models #14,1,0,0,-8.678,0,1,0,5.1742,0,0,1,-33.825
> show #9 models
> hide #!14 models
> show #!14 models
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.31221,-0.22529,-0.92291,161.06,-0.040688,-0.96741,0.24992,67.842,-0.94914,0.11558,0.29287,169.98
> view matrix models
> #9,-0.27389,0.026902,-0.96138,208.98,-0.14067,-0.98998,0.012374,26.513,-0.95142,0.13863,0.27493,172.15
> view matrix models
> #9,-0.27566,0.018044,-0.96109,207.13,-0.13736,-0.9903,0.020806,27.74,-0.95139,0.13775,0.27547,172.04
> view matrix models
> #9,-0.25847,0.014987,-0.9659,207.64,-0.13281,-0.99094,0.020164,27.981,-0.95685,0.13349,0.25812,168.7
> view matrix models
> #9,-0.25597,0.027767,-0.96629,210.3,-0.13736,-0.99049,0.0079238,26.22,-0.95688,0.13475,0.25735,168.85
> select clear
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> view matrix models
> #9,-0.33257,0.047672,-0.94187,209.58,-0.16132,-0.98688,0.007013,24.506,-0.92918,0.15428,0.3359,184.33
> view matrix models
> #9,-0.36676,0.027073,-0.92992,203.7,-0.046556,-0.99886,-0.010718,31.198,-0.92915,0.039362,0.3676,165.81
> view matrix models
> #9,-0.39529,0.031452,-0.91802,203.17,-0.055674,-0.9984,-0.010233,30.465,-0.91687,0.047064,0.39641,171.79
> ui mousemode right "translate selected atoms"
> show #8 models
> hide #!14 models
> select clear
> hide #9 models
> show #!14 models
> show #9 models
> hide #9 models
> hide #8 models
> show #9 models
> select clear
> select #14/E:209-288
618 atoms, 631 bonds, 80 residues, 1 model selected
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #8 to #14 & 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 9fm6, chain E (#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)
> select add #9
26587 atoms, 27354 bonds, 1 pseudobond, 3380 residues, 3 models selected
> show #8 models
> select subtract #9
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> select clear
> select #14/E#8/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #8 & sel to #14 & 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 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
E (#8), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> hide #9 models
> select clear
> hide #8 models
> select clear
[Repeated 1 time(s)]
> show #8 models
> hide #!14 models
> show #9 models
> select #14/E#9/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> matchmaker #9 & sel to #14 & 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 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
E (#9), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.33584,0.18461,0.92365,338.65,0.21649,0.93922,-0.26644,340.25,-0.9167,0.28944,0.27546,142.37
> view matrix models
> #9,0.33894,0.21011,0.91705,343.19,0.21958,0.93015,-0.29427,339.6,-0.91482,0.30111,0.26913,144.55
> view matrix models
> #9,0.38644,0.19886,0.90062,343.55,0.21939,0.92863,-0.29919,339.46,-0.89584,0.31321,0.31523,146.06
> view matrix models
> #9,0.38577,0.19903,0.90087,343.54,0.2194,0.92865,-0.29912,339.47,-0.89613,0.31304,0.31458,146.03
> view matrix models
> #9,0.38662,0.20248,0.89974,344.18,0.20679,0.93173,-0.29854,339.49,-0.89876,0.30148,0.31835,143.91
> select clear
> show #!14 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #9 models
> ui mousemode right "rotate selected models"
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> view matrix models
> #9,0.54495,0.14749,0.8254,342.97,0.1938,0.9356,-0.29513,339.55,-0.81577,0.32079,0.48127,145.94
> view matrix models
> #9,0.57833,0.1368,0.80425,343.01,0.17749,0.94112,-0.28772,339.66,-0.79626,0.30914,0.52,143.71
> hide #8 models
> show #8 models
> select clear
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.33945,-0.19129,-0.92097,299.46,0.018945,-0.9803,0.19663,0.97332,-0.94043,0.049297,0.33638,99.879
> view matrix models
> #9,-0.2355,-0.20469,-0.95008,301.93,0.041259,-0.97879,0.20065,1.9587,-0.971,0.0080519,0.23895,94.44
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> select clear
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.40302,-0.19785,-0.89355,295.32,0.044691,-0.97944,0.19672,2.0829,-0.9141,0.039349,0.40358,97.424
> view matrix models
> #9,-0.40723,-0.20807,-0.88931,293.39,-0.064428,-0.96473,0.25522,-1.1123,-0.91105,0.16123,0.37947,117.95
> view matrix models
> #9,-0.44183,-0.20119,-0.87425,292.83,-0.063787,-0.96501,0.25432,-1.1107,-0.89483,0.16813,0.41354,118.8
> view matrix models
> #9,-0.44244,-0.21887,-0.86968,289.82,-0.038117,-0.9643,0.26207,-0.23275,-0.89599,0.1491,0.4183,115.54
> select clear
> show #!14 models
> hide #8 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_wt_9fm6/fold_aerolysin_wt_9fm6_model_3.cif
> /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_1.cif #10
---
Chain | Description
A B C D E F G | .
Chain information for fold_aerolysin_wt_9fm6_model_2.cif #11
---
Chain | Description
A B C D E F G | .
Chain information for fold_aerolysin_wt_9fm6_model_3.cif #13
---
Chain | Description
A B C D E F G | .
Chain information for fold_aerolysin_wt_9fm6_model_4.cif #15
---
Chain | Description
A B C D E F G | .
> ui tool show Matchmaker
> matchmaker #10-11,13,15 to #14
Computing secondary structure
[Repeated 7 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_1.cif, chain
A (#10), 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 (#11), 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 (#13), 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 (#15), sequence alignment score = 2070.5
RMSD between 237 pruned atom pairs is 0.727 angstroms; (across all 412 pairs:
31.238)
> hide #9 models
> hide #10 models
> hide #13 models
> hide #!14 models
> show #13 models
> show #10 models
> show #9 models
> hide #9 models
> show #9 models
> show #8 models
> show #!12 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #9 models
> hide #13 models
> show #13 models
> hide #!12 models
> delete atoms #10-11,13,15
> delete bonds #10-11,13,15
> show #8 models
> show #!14 models
> hide #8 models
> show #!14 atoms
> show #8 models
> hide #8 models
> show #9 models
> hide #!14 models
> show #9 atoms
> show #!14 models
> hide #9 models
> show #9 models
> show #8 models
> hide #9 models
> hide #!14 models
> show #8 atoms
> show #9 models
> hide #9 models
> show #9 models
> hide #8-9 atoms
> show #!14 models
> hide #9 models
> hide #8 models
> show #9 models
> hide #9#!14 atoms
> select #14/E:209-288
618 atoms, 631 bonds, 80 residues, 1 model selected
> ui tool show "Color Actions"
> select #14/E:209-288
618 atoms, 631 bonds, 80 residues, 1 model selected
> select :209-288
21819 atoms, 22292 bonds, 1 pseudobond, 2842 residues, 12 models selected
> select /E:209-288
1854 atoms, 1893 bonds, 240 residues, 3 models selected
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #8 models
> lighting simple
> lighting full
> lighting gentle
> lighting full
> lighting soft
> lighting default
> select clear
> show #8 models
> ui tool show Matchmaker
> matchmaker #8 to #14
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)
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #9 models
> hide #9 models
> show #!14 models
> hide #8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.png
> width 600 height 614 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.png
> width 600 height 614 supersample 4 transparentBackground true
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!14 models
> hide #8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.side.png
> width 600 height 614 supersample 4 transparentBackground true
> select /E
16121 atoms, 16490 bonds, 1 pseudobond, 2037 residues, 10 models selected
> select ~sel & ##selected
192837 atoms, 201894 bonds, 427 pseudobonds, 21431 residues, 12 models
selected
> hide sel & #!14 cartoons
> show #8 models
> hide #8 models
> hide #!14 models
> show #9 models
> select clear
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> select clear
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.side-2.png
> width 600 height 614 supersample 4 transparentBackground true
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> ui mousemode right "rotate selected models"
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.top-2.png
> width 600 height 614 supersample 4 transparentBackground true
> select #9
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> select #9/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select ~sel & ##selected
20004 atoms, 20580 bonds, 2544 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show #8 models
> show #!14 models
> 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 cartoons
> select #8/E#14/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> matchmaker #8 & sel to #14 & 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 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
E (#8), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> select clear
> hide #9 models
> show #9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> hide #9 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.png
> width 600 height 614 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.unit.png
> width 600 height 614 supersample 4 transparentBackground true
> show #9 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one-2.png
> width 600 height 614 supersample 4 transparentBackground true
> select #8/E#14/E#9/E:209-288
7201 atoms, 7405 bonds, 1 pseudobond, 916 residues, 4 models selected
> select clear
> hide #9 models
> hide #8 models
> show #8 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 #8 models
> select #14/E:179-190
93 atoms, 95 bonds, 12 residues, 1 model selected
> color sel medium slate blue target acs
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> rainbow sel
> select #14/E:180-190
85 atoms, 87 bonds, 11 residues, 1 model selected
> select #14/E:180-189
78 atoms, 80 bonds, 10 residues, 1 model selected
> color sel medium slate blue target acs
> select clear
> show #8 models
> select #8/E:180-189
78 atoms, 80 bonds, 10 residues, 1 model selected
> color sel medium slate blue target acs
> select clear
> select #8/E:180-189
78 atoms, 80 bonds, 10 residues, 1 model selected
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> select #8/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel medium slate blue target acs
> select #14/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel medium slate blue target acs
> 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
> select #8/E:230-270
320 atoms, 326 bonds, 41 residues, 1 model selected
> color sel medium slate blue target acs
> select clear
> select #8/E:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime target acs
> select clear
> show #!14 models
> select #14/E:230-270
320 atoms, 326 bonds, 41 residues, 1 model selected
> color sel medium slate blue target acs
> hide #8 models
> select clear
> show #7 models
> hide #7 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> select #14/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel magenta target acs
> color sel hot pink target acs
> color sel magenta target acs
> color sel dark gray target acs
> color sel dim gray target acs
> color sel magenta target acs
> select clear
> select #8/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel magenta target acs
> show #8 models
> hide #!14 models
> select clear
> show #!14 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 #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> show #!14 atoms
> hide #!14 atoms
> show #!14 atoms
> hide #!14 atoms
> show #!14 atoms
> hide #!14 atoms
> show #8 models
> hide #8 models
> show #!14 atoms
> hide #!14 atoms
> show #!14 atoms
> hide #!14 atoms
> show #!14 atoms
> hide #!14 atoms
> show #9 models
> hide #9 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
> select #14/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet target acs
> color sel plum target acs
> select clear
> select #14/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel violet target acs
> select clear
> select #8/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> show #8 models
> color sel violet target acs
> select clear
> hide #!14 models
> show #!14 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
> width 600 height 614 supersample 4 transparentBackground true
> 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
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side.png
> width 600 height 614 supersample 3 transparentBackground true
> show #9 models
> hide #8 models
> show #8 models
> hide #8 models
> select #/E:180-194
Expected an objects specifier or a keyword
> select #9/E:180-194
119 atoms, 121 bonds, 15 residues, 1 model selected
> color sel violet target acs
> show #!14 models
> select #9/E:230-270
320 atoms, 326 bonds, 41 residues, 1 model selected
> color sel medium slate blue target acs
> select clear
> show #8 models
> hide #!14 models
> hide #9 models
> show #9 models
> hide #8 models
> show #9 atoms
> hide #9 atoms
> show #9 atoms
> hide #9 atoms
> show #!14 models
> hide #9 models
> show #!14 atoms
> show #9 models
> show #9#!14 atoms
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #9 atoms
[Repeated 1 time(s)]
> show #9 atoms
> hide #9 atoms
> matchmaker #8 to #14
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)
> show #8 models
> hide #9 models
> show #9 models
> hide #9 models
> show #8 atoms
> hide #8 atoms
> show #8 atoms
> hide #8 atoms
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side-2.png
> width 600 height 614 supersample 4 transparentBackground true
> select #9/E#14/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> select #8/E#14/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> rainbow sel & #8
> select #9/E:230-270#14/E:230-270
640 atoms, 652 bonds, 82 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium slate blue target acs
> select #8/E:230-270#14/E:230-270
640 atoms, 652 bonds, 82 residues, 2 models selected
> color sel medium slate blue target acs
> select clear
> show #!14 models
> hide #8#!14 atoms
> show #8#!14 cartoons
> hide #8 models
> 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 & #!14 cartoons
> show #8 models
> select #9/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select #9/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select ~sel & ##selected
20004 atoms, 20580 bonds, 2544 residues, 1 model selected
> hide sel cartoons
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> rainbow sel
> select #8/E:230-270#14/E:230-270
640 atoms, 652 bonds, 82 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium slate blue target acs
> select clear
[Repeated 1 time(s)]
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> show #7 models
> hide #7 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 #8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #8 models
> hide #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6-AF3.one.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!14 models
> 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
> matchmaker #8 to #14 & 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 9fm6, chain E (#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)
> select /E
16121 atoms, 16490 bonds, 1 pseudobond, 2037 residues, 10 models selected
> matchmaker #8 & sel to #14 & 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 9fm6, chain E (#14) with fold_aerolysin_wt_9fm6_model_0.cif, chain
E (#8), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> view matrix models
> #6,-0.93309,0.34317,0.1076,228.65,-0.35255,-0.81364,-0.46228,428.09,-0.071098,-0.46928,0.88018,97.064,#1,0.10137,-0.47898,-0.87195,135.58,-0.7169,-0.64285,0.26979,167.95,-0.68976,0.59776,-0.40855,143,#2,0.66978,0.72663,-0.15297,163.19,-0.19254,0.3689,0.90931,169.03,0.71716,-0.57959,0.38699,161.31,#3,0.92751,-0.35868,0.10525,145.16,0.37372,0.89551,-0.24166,167.73,-0.0075712,0.26347,0.96464,148.17,#4,0.97266,-0.085236,0.21601,146.04,-0.20296,0.13997,0.96913,171.62,-0.11284,-0.98648,0.11885,149.2,#5,0.9921,0.11709,0.045065,165.23,-0.067586,0.80137,-0.59434,161.78,-0.10571,0.5866,0.80295,144.96,#8,0.46652,0.56007,0.6846,142.53,0.29416,-0.82817,0.47708,160.76,0.83417,-0.021183,-0.55111,132.7,#14,0.9112,-0.40973,0.042858,51.919,0.38133,0.87822,0.28866,-88.748,-0.15591,-0.24668,0.95647,30.601,#9,-0.42594,0.20206,-0.8819,332.53,-0.46082,-0.88728,0.019271,63.445,-0.7786,0.41461,0.47104,128.26
> view matrix models
> #6,-0.73769,0.37453,-0.56173,291.79,0.036448,-0.80872,-0.58707,378.2,-0.67416,-0.45355,0.58293,239.92,#1,0.34863,-0.86979,-0.34918,137.08,-0.59863,-0.4933,0.63111,168.23,-0.72118,-0.010996,-0.69266,137.85,#2,0.022216,0.98699,-0.15925,146.88,-0.5277,0.14687,0.83664,156.32,0.84914,0.06545,0.5241,167.18,#3,0.78662,-0.24152,-0.56825,141.09,-0.00395,0.91834,-0.39578,163.72,0.61743,0.31357,0.72142,146.91,#4,0.76181,0.57501,0.29836,141.95,-0.53471,0.29814,0.7907,166.8,0.36571,-0.76189,0.53459,149.49,#5,0.80121,-0.10149,-0.58972,156.97,-0.41891,0.6086,-0.67388,151.19,0.4273,0.78696,0.4451,153.19,#8,-0.099169,0.25866,0.96086,147.15,-0.021814,-0.96596,0.25778,160.48,0.99483,0.0046033,0.10144,131.18,#14,0.86755,0.031287,-0.49637,88.033,0.029869,0.99294,0.11479,-19.983,0.49645,-0.11441,0.86049,-80.548,#9,0.059707,-0.29406,-0.95392,272.68,-0.15391,-0.94691,0.28226,0.70996,-0.98628,0.12997,-0.1018,196.79
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> select ~sel & ##selected
192837 atoms, 201894 bonds, 427 pseudobonds, 21431 residues, 12 models
selected
> show sel & #8#!14 cartoons
> hide #8 models
> mlp sel & #!14
Map values for surface "9fm6_A SES surface": minimum -28.49, mean -5.274,
maximum 23.57
Map values for surface "9fm6_B SES surface": minimum -28.44, mean -5.228,
maximum 23.49
Map values for surface "9fm6_C SES surface": minimum -30.11, mean -5.256,
maximum 23.45
Map values for surface "9fm6_D SES surface": minimum -30.01, mean -5.292,
maximum 23.07
Map values for surface "9fm6_F SES surface": minimum -27.85, mean -5.245,
maximum 23.29
Map values for surface "9fm6_G SES surface": minimum -28.1, mean -5.267,
maximum 23.18
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> mlp #!14
Map values for surface "9fm6_A SES surface": minimum -28.49, mean -5.274,
maximum 23.57
Map values for surface "9fm6_B SES surface": minimum -28.44, mean -5.228,
maximum 23.49
Map values for surface "9fm6_C SES surface": minimum -30.11, mean -5.256,
maximum 23.45
Map values for surface "9fm6_D SES surface": minimum -30.01, mean -5.292,
maximum 23.07
Map values for surface "9fm6_E SES surface": minimum -28.89, mean -5.236,
maximum 22.96
Map values for surface "9fm6_F SES surface": minimum -27.85, mean -5.245,
maximum 23.29
Map values for surface "9fm6_G SES surface": minimum -28.1, mean -5.267,
maximum 23.18
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!14
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 9fm6_A SES surface #14.2: minimum, -19.39, mean -1.41,
maximum 9.89
Coulombic values for 9fm6_B SES surface #14.3: minimum, -18.64, mean -1.42,
maximum 9.90
Coulombic values for 9fm6_C SES surface #14.4: minimum, -19.09, mean -1.41,
maximum 9.79
Coulombic values for 9fm6_D SES surface #14.5: minimum, -19.53, mean -1.54,
maximum 11.33
Coulombic values for 9fm6_E SES surface #14.8: minimum, -19.66, mean -1.68,
maximum 11.91
Coulombic values for 9fm6_F SES surface #14.6: minimum, -19.14, mean -1.55,
maximum 9.44
Coulombic values for 9fm6_G SES surface #14.7: minimum, -18.97, mean -1.42,
maximum 10.20
To also show corresponding color key, enter the above coulombic command and
add key true
> show #9 models
> hide #!14 models
> show #8 models
> hide #9 models
> coulombic #8
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_A SES surface #8.1:
minimum, -16.74, mean -1.45, maximum 9.96
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_B SES surface #8.2:
minimum, -22.14, mean -1.45, maximum 9.94
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_C SES surface #8.3:
minimum, -17.79, mean -1.41, maximum 9.97
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_D SES surface #8.4:
minimum, -20.47, mean -1.44, maximum 9.74
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_E SES surface #8.5:
minimum, -15.80, mean -1.43, maximum 9.90
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_F SES surface #8.6:
minimum, -16.14, mean -1.45, maximum 9.61
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_G SES surface #8.7:
minimum, -15.60, mean -1.42, maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!8
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_A SES surface #8.1:
minimum, -16.74, mean -1.45, maximum 9.96
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_B SES surface #8.2:
minimum, -22.14, mean -1.45, maximum 9.94
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_C SES surface #8.3:
minimum, -17.79, mean -1.41, maximum 9.97
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_D SES surface #8.4:
minimum, -20.47, mean -1.44, maximum 9.74
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_E SES surface #8.5:
minimum, -15.80, mean -1.43, maximum 9.90
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_F SES surface #8.6:
minimum, -16.14, mean -1.45, maximum 9.61
Coulombic values for fold_aerolysin_wt_9fm6_model_0.cif_G SES surface #8.7:
minimum, -15.60, mean -1.42, maximum 10.22
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!8 surfaces
> open 1PRE fromDatabase pdb format mmcif
Summary of feedback from opening 1PRE fetched from pdb
---
note | Fetching compressed mmCIF 1pre from http://files.rcsb.org/download/1pre.cif
1pre title:
Proaerolysin [more info...]
Chain information for 1pre #10
---
Chain | Description | UniProt
A B | PROAEROLYSIN | AERA_AERHY 1-470
> select ~sel & ##selected
Nothing selected
> select down
Nothing 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
> show #!14 models
> show #7 models
> hide #7 models
> hide sel surfaces
> matchmaker #!10 to #14 & 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 9fm6, chain E (#14) with 1pre, chain B (#10), sequence alignment
score = 2033.3
RMSD between 136 pruned atom pairs is 0.493 angstroms; (across all 411 pairs:
35.144)
> hide #!8 models
> hide #!14 models
> color #!10 bychain
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> matchmaker #!10 to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
(#10), sequence alignment score = 2199.2
RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
17.434)
> show #!8 models
> hide #!8 models
> select #10/A
3541 atoms, 3622 bonds, 2 pseudobonds, 467 residues, 2 models selected
> hide sel cartoons
> show #!8 models
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select ~sel & ##selected
20004 atoms, 20580 bonds, 2544 residues, 1 model selected
> hide sel cartoons
> select #10
7089 atoms, 7255 bonds, 3 pseudobonds, 933 residues, 3 models selected
> color sel dark gray target acs
> select clear
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select #8/E#10/B
6882 atoms, 7063 bonds, 1 pseudobond, 890 residues, 3 models selected
> matchmaker #!10 & sel to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
(#10), sequence alignment score = 2199.2
RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
17.434)
> select clear
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> show #!14 models
> hide #!8 models
> select #14/E
3249 atoms, 3344 bonds, 1 pseudobond, 412 residues, 2 models selected
> select ~sel & ##selected
19494 atoms, 20064 bonds, 6 pseudobonds, 2472 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> show #!8 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!14 models
> show #!14 models
> hide #!10 models
> show #!10 models
> hide #!14 models
> show #!14 models
> hide #!10 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.vs.AF3.one.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!10 models
> hide #!14 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/1PRE.vs.AF3.one.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!14 models
> hide #!10 models
> hide #!8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FM6.one.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!8 models
> select #14/E#8/E
6583 atoms, 6774 bonds, 1 pseudobond, 836 residues, 3 models selected
> matchmaker #!10 & sel to #8 & sel
No molecules/chains to match specified
> matchmaker #!14 & sel to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 9fm6, chain E
(#14), sequence alignment score = 2066.9
RMSD between 239 pruned atom pairs is 0.647 angstroms; (across all 412 pairs:
31.537)
> show #!10 models
> hide #!14 models
> matchmaker #!10 & sel to #8 & sel
No molecules/chains to match specified
> select #8/E#10/B
6882 atoms, 7063 bonds, 1 pseudobond, 890 residues, 3 models selected
> matchmaker #!10 & sel to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 1pre, chain B
(#10), sequence alignment score = 2199.2
RMSD between 256 pruned atom pairs is 0.714 angstroms; (across all 423 pairs:
17.434)
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #9 models
> hide #9 models
> show #!14 models
> select #8#10
30427 atoms, 31265 bonds, 3 pseudobonds, 3901 residues, 4 models selected
> show sel & #!8 cartoons
> select #8#14
46081 atoms, 47418 bonds, 7 pseudobonds, 5852 residues, 3 models selected
> show sel cartoons
> hide #!8 models
> show #!8 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> select clear
> open 5JZH fromDatabase pdb format mmcif
Summary of feedback from opening 5JZH fetched from pdb
---
note | Fetching compressed mmCIF 5jzh from http://files.rcsb.org/download/5jzh.cif
5jzh title:
Cryo-EM structure of aerolysin prepore [more info...]
Chain information for 5jzh #11
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | Aerolysin | AERA_AERHY 1-424
5jzh mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #11#!8 atoms
> show #11#!8 cartoons
> matchmaker #11 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 5jzh, chain A
(#11), sequence alignment score = 2122.9
RMSD between 396 pruned atom pairs is 0.870 angstroms; (across all 424 pairs:
1.173)
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> matchmaker #11 to #8 & 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_aerolysin_wt_9fm6_model_0.cif, chain E (#8) with 5jzh, chain A
(#11), sequence alignment score = 2122.9
RMSD between 365 pruned atom pairs is 0.790 angstroms; (across all 424 pairs:
1.323)
> matchmaker #11 to #14
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 9fm6, chain A (#14) with 5jzh, chain A (#11), sequence alignment
score = 1957.6
RMSD between 240 pruned atom pairs is 0.671 angstroms; (across all 412 pairs:
30.764)
> show #!14 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!14 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #11/A/B/C/D/E
32425 atoms, 32910 bonds, 2120 residues, 1 model selected
> select ~sel & ##selected
58365 atoms, 59238 bonds, 3816 residues, 1 model selected
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> select ~sel
309759 atoms, 321009 bonds, 451 pseudobonds, 33583 residues, 20 models
selected
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> select ~sel & ##selected
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> hide sel cartoons
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!14 models
> show #!10 models
> hide #!10 models
> hide #!14 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> matchmaker #11 & sel 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 5jzh, chain A
(#11), sequence alignment score = 2122.9
RMSD between 396 pruned atom pairs is 0.870 angstroms; (across all 424 pairs:
1.173)
> select clear
> hide #!8 models
> color #11 bychain
> show #!8 models
> hide #11 models
> show #11 models
> hide #!8 models
> show #!8 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel tan target acs
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> hide #11 models
> show #11 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel sky blue target acs
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel cornflower blue target acs
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel royal blue target acs
> color sel powder blue target acs
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel pale violet red target acs
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel pink target acs
> color sel plum target acs
> color sel peach puff target acs
> color sel pink target acs
> color sel light pink target acs
> select clear
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel bychain
> select clear
[Repeated 1 time(s)]
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel tan target acs
> select clear
> hide #11 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel sky blue target acs
> select add #8
68733 atoms, 70084 bonds, 5936 residues, 2 models selected
> select add #11
114128 atoms, 116158 bonds, 8904 residues, 9 models selected
> select subtract #11
23338 atoms, 24010 bonds, 2968 residues, 8 models selected
> color sel sky blue target acs
> select clear
> show #!10 models
> hide #!10 models
> show #11 models
> hide #!8 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel tan target acs
> select clear
> show #!8 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> hide #!8 models
> hide #11 models
> show #!8 models
> select add #8
68733 atoms, 70084 bonds, 5936 residues, 2 models selected
> select add #11
114128 atoms, 116158 bonds, 8904 residues, 9 models selected
> select subtract #11
23338 atoms, 24010 bonds, 2968 residues, 8 models selected
> color sel plum target acs
> select clear
> show #11 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> color sel dodger blue target acs
> color sel cornflower blue target acs
> select clear
> hide #11 models
> select add #8
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> color sel tan target acs
> select clear
> show #11 models
> hide #!8 models
> hide #11 models
> show #!8 models
> select add #8
23338 atoms, 24010 bonds, 2968 residues, 1 model selected
> color sel lime target acs
> select clear
> show #11 models
> hide #11 models
> color #!8 bychain
> select #8/A
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> rainbow sel
> select clear
> color #!8 bychain
> select #8/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> rainbow sel
> show #11 models
> hide #!8 models
> show #!8 models
> hide #11 models
> show #11 models
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/5JZHvsAF3.top.png
> width 600 height 614 supersample 4 transparentBackground true
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/5JZHvsAF3.side.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!14 models
> hide #11 models
> hide #!8 models
> show #11 models
> hide #!14 models
> open 9FMX fromDatabase pdb format mmcif
Summary of feedback from opening 9FMX fetched from pdb
---
note | Fetching compressed mmCIF 9fmx from http://files.rcsb.org/download/9fmx.cif
9fmx title:
Aerolysin Y221G - prepore [more info...]
Chain information for 9fmx #13
---
Chain | Description | UniProt
A B C D E F G H I J K L M N | Aerolysin | AERA_AERHY 1-470
> show #11,13 cartoons
> hide #11,13 atoms
> hide #11 models
> matchmaker #!14 & sel to #11
No molecules/chains to match specified
> matchmaker #!14 to #11
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 5jzh, chain A (#11) with 9fm6, chain A (#14), sequence alignment
score = 1957.6
RMSD between 240 pruned atom pairs is 0.671 angstroms; (across all 412 pairs:
30.764)
> matchmaker #13 to #11
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 5jzh, chain A (#11) with 9fmx, chain A (#13), sequence alignment
score = 2135.5
RMSD between 418 pruned atom pairs is 0.578 angstroms; (across all 424 pairs:
0.683)
> show #!14 models
> select #13/H#13/I#13/J#13/L#13/M#13/N#13/K
45388 atoms, 46067 bonds, 2968 residues, 1 model selected
> hide sel cartoons
> hide #!14 models
> show #7 models
> hide #7 models
> show #!8 models
> select #13/H#13/I#13/J#13/L#13/M#13/N#13/K
45388 atoms, 46067 bonds, 2968 residues, 1 model selected
> select ~sel & ##selected
45388 atoms, 46067 bonds, 2968 residues, 1 model selected
> matchmaker #13 & sel 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
(#13), sequence alignment score = 2181.4
RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
0.985)
> select clear
> select #13:221
98 atoms, 84 bonds, 14 residues, 1 model selected
> show #!14 models
> hide #!8 models
> select #13:221#14:221
182 atoms, 168 bonds, 21 residues, 2 models selected
> show sel atoms
> hide sel atoms
> hide #13 models
> show #13 models
> hide #!14 models
> show #!14 models
> hide #13 models
> show #13 models
> select #13:/D
Expected an objects specifier or a keyword
> select #13/D
6484 atoms, 6581 bonds, 424 residues, 1 model selected
> hide #!14 models
> rainbow sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_0.cif
Chain information for fold_aerolysin_9fmx_model_0.cif #15
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_1.cif
Chain information for fold_aerolysin_9fmx_model_1.cif #16
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_2.cif
Chain information for fold_aerolysin_9fmx_model_2.cif #17
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_3.cif
Chain information for fold_aerolysin_9fmx_model_3.cif #18
---
Chain | Description
A B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_aerolysin_9fmx/fold_aerolysin_9fmx_model_4.cif
Chain information for fold_aerolysin_9fmx_model_4.cif #19
---
Chain | Description
A B C D E F G | .
> hide #13 models
> select add #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> select subtract #13
Nothing selected
> show #15-19 cartoons
Computing secondary structure
[Repeated 4 time(s)]
> show #15-19 cartoons
> hide #15-19 atoms
> select #13/D
6484 atoms, 6581 bonds, 424 residues, 1 model selected
> matchmaker #15-19 to #13 & 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 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_0.cif, chain A
(#15), sequence alignment score = 2333.5
RMSD between 255 pruned atom pairs is 0.655 angstroms; (across all 424 pairs:
17.845)
Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_1.cif, chain A
(#16), sequence alignment score = 2336.5
RMSD between 257 pruned atom pairs is 0.672 angstroms; (across all 424 pairs:
17.898)
Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_2.cif, chain A
(#17), sequence alignment score = 2336.5
RMSD between 258 pruned atom pairs is 0.687 angstroms; (across all 424 pairs:
17.841)
Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_3.cif, chain A
(#18), sequence alignment score = 2336.5
RMSD between 255 pruned atom pairs is 0.654 angstroms; (across all 424 pairs:
17.922)
Matchmaker 9fmx, chain D (#13) with fold_aerolysin_9fmx_model_4.cif, chain A
(#19), sequence alignment score = 2322.7
RMSD between 254 pruned atom pairs is 0.752 angstroms; (across all 424 pairs:
17.875)
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> show #!10 models
> hide #!10 models
> show #16 models
> show #17 models
> show #18 models
> hide #15 models
> hide #17 models
> hide #18 models
> show #15 models
> hide #16 models
> show #16 models
> show #17 models
> hide #15 models
> hide #16 models
> show #18 models
> hide #17 models
> show #19 models
> hide #18 models
> show #15 models
> hide #19 models
> show #!10 models
> select #15/A
3680 atoms, 3778 bonds, 472 residues, 1 model selected
> rainbow sel
> select #15/F:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> hide #!10 models
> color #15 bychain
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMX.AF3.png
> width 600 height 614 supersample 4 transparentBackground true
> show #!10 models
> select #15/A
3680 atoms, 3778 bonds, 472 residues, 1 model selected
> select ~sel & ##selected
22080 atoms, 22668 bonds, 2832 residues, 1 model selected
> hide sel cartoons
> select #15/A
3680 atoms, 3778 bonds, 472 residues, 1 model selected
> matchmaker #15 to #10
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 1pre, chain B (#10) with fold_aerolysin_9fmx_model_0.cif, chain A
(#15), sequence alignment score = 2407.9
RMSD between 448 pruned atom pairs is 0.805 angstroms; (across all 451 pairs:
0.831)
> select clear
[Repeated 1 time(s)]
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/1PRE.vs.9FMX_A.AF3.png
> width 600 height 614 supersample 4 transparentBackground true
[Repeated 1 time(s)]
> hide #15 models
> hide #!10 models
> show #13 models
> show #11 models
> select #11/A/B/C/D/E/F/G
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> select ~sel & ##selected
45395 atoms, 46074 bonds, 2968 residues, 1 model selected
> hide sel cartoons
> hide #13 models
> show #13 models
> hide #11 models
> show #11 models
> hide #11 models
> color #13 bychain
> select #9/E
3334 atoms, 3430 bonds, 424 residues, 1 model selected
> select #13/E
6484 atoms, 6581 bonds, 424 residues, 1 model selected
> rainbow sel
> select clear
Drag select of 25 residues
Drag select of 2 residues
> select #13/E:214
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!8 models
> hide #13 models
> show #13 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> matchmaker #13 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
(#13), sequence alignment score = 2181.4
RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
0.985)
> matchmaker #13 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
(#13), sequence alignment score = 2181.4
RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
0.985)
> hide #13 models
> show #13 models
> hide #!8 models
> select #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> color sel thistle target acs
> color sel pink target acs
> color sel plum target acs
> select clear
> show #!8 models
> select #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> color sel gray target acs
> select clear
> select #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> color sel burly wood target acs
> select clear
> hide #!8 models
> show #!8 models
> hide #13 models
> show #13 models
> select #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> color sel gainsboro target acs
> color sel light cyan target acs
> color sel pale green target acs
> select clear
> select #13
90776 atoms, 92134 bonds, 5936 residues, 1 model selected
> select clear
> hide #13 models
> show #13 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMXvsAF3.png
> width 600 height 614 supersample 4 transparentBackground true
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/9FMXvsAF3.side.png
> width 600 height 614 supersample 4 transparentBackground true
> matchmaker #13 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
(#13), sequence alignment score = 2181.4
RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
0.985)
> matchmaker #13 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_aerolysin_wt_9fm6_model_0.cif, chain A (#8) with 9fmx, chain A
(#13), sequence alignment score = 2181.4
RMSD between 414 pruned atom pairs is 0.825 angstroms; (across all 424 pairs:
0.985)
> show #!10 models
> hide #!8 models
> hide #13 models
> rainbow #!10
> show #!14 models
> hide #!10 models
> show #13 models
> hide #!14 models
> show #!8 models
> hide #!8 models
> show #11 models
> hide #11 models
> show #11 models
> hide #13 models
> show #13 models
> hide #11 models
> show #!14 models
> hide #13 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!14 models
> show #!14 models
> show #13 models
> hide #!14 models
> hide #!8 models
> show #15 models
> hide #13 models
> show #16 models
> hide #15 models
> show #17 models
> hide #16 models
> show #18 models
> hide #17 models
> show #19 models
> hide #18 models
> show #!14 models
> hide #19 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs
——— End of log from Mon Jun 23 17:09:27 2025 ———
opened ChimeraX session
> hide #!14 models
> show #!6 models
> open 3aze fromDatabase pdb format mmcif
Summary of feedback from opening 3aze fetched from pdb
---
notes | Fetching compressed mmCIF 3aze from http://files.rcsb.org/download/3aze.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
3aze title:
Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation
[more info...]
Chain information for 3aze #20
---
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 J | 146-MER DNA |
Non-standard residues in 3aze #20
---
CL — chloride ion
MN — manganese (II) ion
> show #!6,20 cartoons
> hide #!6,20 atoms
> ui tool show Matchmaker
> select #6/A
799 atoms, 811 bonds, 97 residues, 1 model selected
> matchmaker #!20 to #6 & 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 8vg1, chain A (#6) with 3aze, chain A (#20), sequence alignment
score = 623.8
RMSD between 96 pruned atom pairs is 0.318 angstroms; (across all 96 pairs:
0.318)
> 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 #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> matchmaker #!20 to #6 & 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 8vg1, chain A (#6) with 3aze, chain A (#20), sequence alignment
score = 623.8
RMSD between 96 pruned atom pairs is 0.318 angstroms; (across all 96 pairs:
0.318)
> select #6
14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected
> matchmaker #!20 to #6 & 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 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
score = 625.6
RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
0.414)
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #1 models
> hide #!20 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 #1 models
> hide #5 models
> show #!6 models
> hide #1 models
> select #6/B/F
1324 atoms, 1338 bonds, 166 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> color sel pale violet red
> color sel burly wood
> color sel rosy brown
> color sel light pink
> color sel thistle
> select #6/C/G
1740 atoms, 1762 bonds, 225 residues, 1 model selected
> color sel sky blue
> color sel deep sky blue
> color sel powder blue
> color sel light steel blue
> color sel sky blue
> color sel light sky blue
> color sel deep sky blue
> color sel sky blue
> select #6/C/G
1740 atoms, 1762 bonds, 225 residues, 1 model selected
> color sel medium slate blue
> color sel medium purple
> color sel thistle
> color sel gray
> color sel silver
> color sel light steel blue
> color sel sky blue
> select #6/D/H
1490 atoms, 1512 bonds, 190 residues, 1 model selected
> color sel dark sea green
> select #6/A/E
1598 atoms, 1622 bonds, 194 residues, 1 model selected
> color sel light coral
> select #6/B/F
1324 atoms, 1338 bonds, 166 residues, 1 model selected
> color sel tan
> color sel khaki
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel silver
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel light steel blue
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel deep sky blue
> color sel royal blue
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> select clear
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> color sel hot pink
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel aquamarine
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel light pink
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel wheat
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel olive drab
> color sel forest green
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel dodger blue
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel medium purple
> select clear
> select #6/D
745 atoms, 756 bonds, 95 residues, 1 model selected
> color sel pale green
> select clear
> select #6/C
840 atoms, 850 bonds, 109 residues, 1 model selected
> color sel pale turquoise
> select clear
> select #6/A
799 atoms, 811 bonds, 97 residues, 1 model selected
> color sel light pink
> color sel light coral
> select clear
> select #6/B
662 atoms, 669 bonds, 83 residues, 1 model selected
> color sel pale goldenrod
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel lavender
[Repeated 1 time(s)]
> color sel thistle
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel royal blue
> select clear
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> color sel medium violet red
> select clear
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel light steel blue
> color sel pale turquoise
> color sel powder blue
> select clear
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel pale turquoise
> select clear
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel light steel blue
> select clear
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #7 models
> hide #7 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
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel medium violet red
> show #!6 models
> color sel thistle
> select clear
> hide #!6 models
> select #1/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> color sel medium violet red
> select clear
> select #1/I/J
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> hide sel cartoons
> show #7 models
> hide #7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #1/A:1-38
274 atoms, 275 bonds, 38 residues, 1 model selected
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
2280 atoms, 2296 bonds, 304 residues, 1 model selected
> hide #1 models
> show #1 models
> color sel ivory
> select clear
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
2280 atoms, 2296 bonds, 304 residues, 1 model selected
> hide sel cartoons
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #7 models
> hide #7 models
> show #!6 models
> hide #!6 models
> select #1/L
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> color sel deep sky blue
> select #1/K
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> show #!6 models
> hide #!6 models
> color sel violet
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> rainbow sel
> select clear
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> undo
[Repeated 6 time(s)]
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> rainbow sel
> select clear
> undo
[Repeated 2 time(s)]
> show #1 models
> select clear
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
2280 atoms, 2296 bonds, 304 residues, 1 model selected
> show #!6 cartoons
> show #1 models
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
2280 atoms, 2296 bonds, 304 residues, 1 model selected
> select clear
> hide #1 models
> show #1 models
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-38
2280 atoms, 2296 bonds, 304 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/A:1-38/B:1-38/C:1-38/D:1-38/E:1-38/F:1-38/G:1-38/H:1-30
2207 atoms, 2222 bonds, 296 residues, 1 model selected
> select #1/A:1-30/B:1-30/C:1-30/D:1-30/E:1-30/F:1-30/G:1-30/H:1-30
1762 atoms, 1770 bonds, 240 residues, 1 model selected
> hide sel cartoons
> select clear
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> hide #1 models
> show #1 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 #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> select #6/T30
Nothing selected
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel royal blue
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel medium blue
> select clear
> hide #1 models
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel dark turquoise
> color sel dark cyan
> select clear
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel deep sky blue
> color sel dodger blue
> color sel blue
> select clear
> show #1 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
> show #1 models
> hide #!6 models
> select
> #1/A:120-126/B:120-126/C:120-126/D:120-126/E:120-126/F:120-126/G:120-126/H:120-126
346 atoms, 348 bonds, 42 residues, 1 model selected
> select
> #1/A:120-126/B:120-126/C:120-126/D:120-126/E:120-126/F:120-126/G:120-126/H:120-130
346 atoms, 348 bonds, 42 residues, 1 model selected
> select
> #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
472 atoms, 474 bonds, 58 residues, 1 model selected
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> color sel white
> select clear
[Repeated 1 time(s)]
> hide #!6 models
> select clear
> show #!6 models
> hide #!6 models
> select #1/I/J
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/I/J
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show #!6 models
> hide #1 models
> show #1 models
> select #1/I/J
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/J
6183 atoms, 6345 bonds, 835 residues, 1 model selected
> color sel blue
> select clear
> hide #!6 models
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.png" width 740
> height 627 supersample 4 transparentBackground true
> select #1/J
6183 atoms, 6345 bonds, 835 residues, 1 model selected
> hide sel cartoons
> select #1/J/J
6183 atoms, 6345 bonds, 835 residues, 1 model selected
> select #1/J/I
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> hide sel cartoons
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.noTFs.png"
> width 740 height 627 supersample 4 transparentBackground true
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/J/I
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> show sel cartoons
> select #1/J:1-268/J:321-900/I:1-167/I:270-478
8445 atoms, 8673 bonds, 1159 residues, 1 model selected
> hide sel cartoons
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.png" width 740
> height 627 supersample 4 transparentBackground true
> show #!6 models
> hide #!6 models
> select
> #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
472 atoms, 474 bonds, 58 residues, 1 model selected
> show #!6 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 #!6 models
> show #!6 models
> hide #!6 models
> select
> #1/A:120-130/B:120-130/C:120-130/D:120-130/E:120-130/F:1120-130/G:120-130/H:120-130
472 atoms, 474 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select #1/I/J/K/L
17313 atoms, 18505 bonds, 1685 residues, 1 model selected
> hide sel cartoons
> show #!6 models
> select #6/I/J/O/T
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
> select clear
> select #1/A:38
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> 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 #6/D
745 atoms, 756 bonds, 95 residues, 1 model selected
> color sel pale green
> color sel thistle
> color sel honeydew
> color sel azure
> color sel honeydew
> select clear
> select #6/D
745 atoms, 756 bonds, 95 residues, 1 model selected
> color sel pale green
> select #6/H
745 atoms, 756 bonds, 95 residues, 1 model selected
> color sel medium sea green
> select clear
> select #6/G
900 atoms, 912 bonds, 116 residues, 1 model selected
> color sel dark turquoise
> select clear
> select #6/E
799 atoms, 811 bonds, 97 residues, 1 model selected
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #1/B
800 atoms, 808 bonds, 103 residues, 1 model selected
> color sel saddle brown
> select clear
> 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
> select #6/E
799 atoms, 811 bonds, 97 residues, 1 model selected
> color sel tomato
> select clear
> show #1 models
> hide #!6 models
> select #1/E
1081 atoms, 1095 bonds, 136 residues, 1 model selected
> color sel dark goldenrod
> show #!6 models
> select clear
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 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 #!6 models
> show #!6 models
> hide #!6 models
> select #1/C:10-26
131 atoms, 131 bonds, 17 residues, 1 model selected
> show sel cartoons
> select #1/C:10-40
248 atoms, 251 bonds, 31 residues, 1 model selected
> show sel cartoons
> color sel pale green
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select #1/C
996 atoms, 1008 bonds, 130 residues, 1 model selected
> select #6/C
840 atoms, 850 bonds, 109 residues, 1 model selected
> color sel sky blue
> color sel light sky blue
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/D:31-39
79 atoms, 79 bonds, 9 residues, 1 model selected
> color sel tan
> select clear
> show #!6 models
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.vs.AF3.histones.png"
> width 740 height 627 supersample 4 transparentBackground true
> select #6
14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected
> hide #1 models
> show sel cartoons
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1-2.png" width 740
> height 627 supersample 3
> show #1 models
> hide #!6 models
> select #1
25021 atoms, 26311 bonds, 2675 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/J:1-268/J:321-900/I:1-167/I:270-478
8445 atoms, 8673 bonds, 1159 residues, 1 model selected
> hide sel cartoons
> show #!6 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> hide #!6 models
> show #!6 models
> select #6/O#1/I:168-269
1712 atoms, 1766 bonds, 204 residues, 2 models selected
> matchmaker #1 & sel to #6 & 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 8vg1, chain O (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
chain I (#1), sequence alignment score = 540.2
RMSD between 85 pruned atom pairs is 0.884 angstroms; (across all 102 pairs:
1.802)
> hide #!6 models
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> ui tool show "Side View"
> hide #1 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> transparency (#!6 & sel) 70
> select clear
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> select #6/I/J
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 7011 atom styles
> select clear
> select #6/I/J
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> select clear
> select #6/I/J
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> color sel bynucleotide
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> undo
[Repeated 5 time(s)]
> hide #!6 atoms
> nucleotides #!6 atoms
> style nucleic & #!6 stick
Changed 7011 atom styles
> show #!6 atoms
> hide #!6 atoms
> select #6/I/J
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 7011 atom styles
> show sel atoms
> color sel bynucleotide
> select clear
> transparency #6 60
> transparency #6 30
> transparency #6 40
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.s.png" width
> 740 height 627 supersample 4 transparentBackground true
> hide #!6 surfaces
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 740
> height 627 supersample 4 transparentBackground true
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 740
> height 627 supersample 4 transparentBackground true
> show #1 models
> hide #!6 models
> select #1/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> color sel dark orchid
> color sel medium violet red
> color sel deep pink
> color sel medium orchid
[Repeated 1 time(s)]
> select clear
> show #!6 models
> hide #!6 models
> select #1/L/K
7628 atoms, 8556 bonds, 372 residues, 1 model selected
> color sel bynucleotide
> show #!6 models
> hide #!6 models
> select #1/L/K
7628 atoms, 8556 bonds, 372 residues, 1 model selected
> color sel bynucleotide
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 7628 atom styles
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.AF3.png" width
> 740 height 627 supersample 4 transparentBackground true
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.vs.AF3.png"
> width 740 height 627 supersample 4 transparentBackground true
> hide #1 models
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> show #1 models
> select #6/T#1/J
6598 atoms, 6765 bonds, 4 pseudobonds, 889 residues, 3 models selected
> matchmaker #1 & sel to #6 & 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 8vg1, chain T (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
chain J (#1), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.548 angstroms; (across all 53 pairs:
7.623)
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> color sel thistle
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel lavender
> color sel pale turquoise
> select #6/J/I
7011 atoms, 7864 bonds, 417 pseudobonds, 342 residues, 2 models selected
> style sel stick
Changed 7011 atom styles
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 7011 atom styles
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.GATA3.png" width 740
> height 627 supersample 4 transparentBackground true
> show #1 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select clear
> show #1 models
> hide #!6 models
> select #1/L
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel plum
> select #1/K
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> color sel deep sky blue
> select #1/L:158
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/L
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel violet
> select clear
> select #1/L/K
7628 atoms, 8556 bonds, 372 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> color sel deep pink
> select clear
> show #!6 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.GATA3.AF3.png" width
> 740 height 627 supersample 4 transparentBackground true
> hide #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> delete atoms #2-5
> delete bonds #2-5
> show #15 models
> show #16 models
> hide #15 models
> show #17 models
> show #18 models
> show #19 models
> delete atoms #16-19
> delete bonds #16-19
> show #!14 models
> show #15 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/GATA4_8vg1.aerolysin_9FMM6.cxs"
——— End of log from Wed Jul 16 09:52:26 2025 ———
opened ChimeraX session
> hide #!14 models
> hide #15 models
> show #!6 models
> show #1 models
> show #7 models
> hide #7 models
> show #!20 models
> show #!12 models
> show #11 models
> hide #11 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
> hide #1 models
> hide #!6 models
> hide #!12 models
> hide #!20 models
> show #7 models
> hide #7 models
> show #!8 models
> show #9 models
> show #!10 models
> show #11 models
> show #!12 models
> show #7 models
> show #13 models
> show #!14 models
> show #15 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> delete atoms #7-15
> delete bonds #7-15
> show #1 models
> show #!6 models
> show #!20 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
——— End of log from Tue Aug 26 11:16:07 2025 ———
opened ChimeraX session
> hide #1 models
> hide #!20 models
> hide #!6 models
> show #!20 models
> hide #!20 models
> show #!6 models
> show #1 models
> hide #!6 models
> select #1/J
6183 atoms, 6345 bonds, 835 residues, 1 model selected
> show sel cartoons
> show #!6 models
> hide #1 models
> view matrix models
> #1,-0.92427,0.28609,-0.25274,96.671,-0.20231,0.19434,0.95984,231.94,0.32372,0.93829,-0.12175,145.04
> view matrix models
> #1,-0.92427,0.28609,-0.25274,107.63,-0.20231,0.19434,0.95984,235.09,0.32372,0.93829,-0.12175,125.75
> hide #!6 atoms
> select ::name="CYS"
186 atoms, 155 bonds, 31 residues, 3 models selected
> show sel & #!6 atoms
> style sel & #!6 ball
Changed 66 atom styles
> color (#!6 & sel) yellow
> select clear
> show #1 models
> hide #!6 models
> select #1/J:269-320
384 atoms, 389 bonds, 52 residues, 1 model selected
> color sel cyan
> select ::name="CYS"
186 atoms, 155 bonds, 31 residues, 3 models selected
> show sel & #1 atoms
> style sel & #1 ball
Changed 96 atom styles
> color (#1 & sel) yellow
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/J:269-320
384 atoms, 389 bonds, 52 residues, 1 model selected
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/J:394
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> hide sel atoms
> select #1/J:1-393
3055 atoms, 3132 bonds, 393 residues, 1 model selected
> select #1/J:1-393
3055 atoms, 3132 bonds, 393 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/J:1-393
3055 atoms, 3132 bonds, 393 residues, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> show #!6 models
> hide #1 models
> select Zn
1 atom, 1 residue, 1 model selected
> show sel atoms
> color sel dark gray
> select clear
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif #2
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif #3
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif #4
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif #5
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif #7
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif #8
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif #9
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif #10
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif #11
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4_zn_8vg1/fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif
Chain information for fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif #12
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif
Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif #13
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif
Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif #14
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif
Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif #15
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif
Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif #16
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_nucleosome_foxa1_gata4nombp_zn/fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif
Chain information for fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif #17
---
Chain | Description
A E | .
B F | .
C G | .
D H | .
I | .
J | .
L | .
M | .
> ui tool show Matchmaker
> matchmaker #1-5,7-17#!20 to #6
Computing secondary structure
[Repeated 29 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_foxa1_gata4_model_0.cif,
chain J (#1), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.548 angstroms; (across all 53 pairs:
7.623)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
alignment score = 3151.7
RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
7.477)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain J (#3), sequence
alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.604 angstroms; (across all 53 pairs:
7.758)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain J (#4), sequence
alignment score = 3139.7
RMSD between 45 pruned atom pairs is 0.494 angstroms; (across all 53 pairs:
7.946)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain J (#5), sequence
alignment score = 3109.7
RMSD between 44 pruned atom pairs is 0.520 angstroms; (across all 53 pairs:
6.394)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain J (#7), sequence
alignment score = 3139.7
RMSD between 44 pruned atom pairs is 0.558 angstroms; (across all 53 pairs:
7.840)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#8), sequence
alignment score = 3151.7
RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
7.477)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain J (#9), sequence
alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.604 angstroms; (across all 53 pairs:
7.758)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain J (#10), sequence
alignment score = 3139.7
RMSD between 45 pruned atom pairs is 0.494 angstroms; (across all 53 pairs:
7.946)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain J (#11), sequence
alignment score = 3109.7
RMSD between 44 pruned atom pairs is 0.520 angstroms; (across all 53 pairs:
6.394)
Matchmaker 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain J (#12), sequence
alignment score = 3139.7
RMSD between 44 pruned atom pairs is 0.558 angstroms; (across all 53 pairs:
7.840)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 1915.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
alignment score = 1927.2
RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs:
1.776)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
alignment score = 1924.2
RMSD between 78 pruned atom pairs is 0.751 angstroms; (across all 102 pairs:
2.144)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
alignment score = 1901.4
RMSD between 80 pruned atom pairs is 0.855 angstroms; (across all 102 pairs:
3.778)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
alignment score = 1909.2
RMSD between 82 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.994)
Matchmaker 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
score = 625.6
RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
0.414)
> hide #2-5,7-17#!6 surfaces
> hide #2-5,7-17#!6 atoms
> show #2-5,7-17#!6 cartoons
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #!6 models
> show #7 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> delete atoms #8-12
> delete bonds #8-12
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_0.cif
Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_0.cif #8
---
Chain | Description
A | .
B | .
D | .
E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_1.cif
Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_1.cif #9
---
Chain | Description
A | .
B | .
D | .
E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_2.cif
Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_2.cif #10
---
Chain | Description
A | .
B | .
D | .
E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_3.cif
Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_3.cif #11
---
Chain | Description
A | .
B | .
D | .
E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/CASP16/yet2solve/AF3/fold_dna_foxa1_gata4_zn_8vg1/fold_dna_foxa1_gata4_zn_8vg1_model_4.cif
Chain information for fold_dna_foxa1_gata4_zn_8vg1_model_4.cif #12
---
Chain | Description
A | .
B | .
D | .
E | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #8-12 to #6
Computing secondary structure
[Repeated 4 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_dna_foxa1_gata4_zn_8vg1_model_0.cif,
chain B (#8), sequence alignment score = 3142.7
RMSD between 44 pruned atom pairs is 0.526 angstroms; (across all 53 pairs:
8.378)
Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_1.cif,
chain B (#9), sequence alignment score = 3139.7
RMSD between 44 pruned atom pairs is 0.562 angstroms; (across all 53 pairs:
8.220)
Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_2.cif,
chain B (#10), sequence alignment score = 3142.7
RMSD between 44 pruned atom pairs is 0.525 angstroms; (across all 53 pairs:
8.352)
Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_3.cif,
chain B (#11), sequence alignment score = 3142.7
RMSD between 44 pruned atom pairs is 0.484 angstroms; (across all 53 pairs:
8.451)
Matchmaker 8vg1, chain T (#6) with fold_dna_foxa1_gata4_zn_8vg1_model_4.cif,
chain B (#12), sequence alignment score = 3142.7
RMSD between 44 pruned atom pairs is 0.546 angstroms; (across all 53 pairs:
8.252)
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> color #8 bychain
> undo
> show #9 models
> hide #9 models
> show #9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> color #11 bychain
> show #12 models
> hide #11 models
> color #12 bychain
> show #!6 models
> hide #12 models
> select #6/J:129
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:130
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #6/J:129
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #6/J:127
63 atoms, 68 bonds, 3 residues, 1 model selected
> select add #6/J:128
85 atoms, 92 bonds, 4 residues, 1 model selected
> show #8 models
> hide #!6 models
> select #8/D:127-130/E:127-130
167 atoms, 186 bonds, 8 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> view matrix models
> #8,-0.46108,0.5647,0.68448,84.162,0.54831,-0.42517,0.72012,195.51,0.69768,0.70735,-0.11359,198.18
> show #!6 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/I
Alignment identifier is 6/I
> sequence chain #6/J
Alignment identifier is 6/J
> select #6/J:129
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/J:130
41 atoms, 44 bonds, 2 residues, 1 model selected
Drag select of 69 residues
> select #6/I:55
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/I:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel bynucleotide
> select clear
> show #!8 models
> hide #!6 models
> select #8/D:55-58/E:55-58
165 atoms, 183 bonds, 8 residues, 1 model selected
> select #8/D:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> select #6/I:74-75
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #6/I:74-85
242 atoms, 270 bonds, 12 residues, 1 model selected
> hide #!8 models
> show #!8 models
> show #!6 models
> hide #!8 models
> view matrix models
> #6,-0.73769,0.37453,-0.56173,264.58,0.036448,-0.80872,-0.58707,415.46,-0.67416,-0.45355,0.58293,241.01
> select #6/I:74
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/I:74-85
242 atoms, 270 bonds, 12 residues, 1 model selected
> select #6/I:29-30
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #6/I:29-41
269 atoms, 301 bonds, 13 residues, 1 model selected
> show #!8 models
> hide #!6 models
> select #8/B
6183 atoms, 6345 bonds, 835 residues, 1 model selected
> rainbow sel
> select clear
> show #9 models
> hide #!8 models
> select #8/D:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> select #9/D:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> show #10 models
> show #11 models
> show #12 models
> delete atoms sel
> delete bonds sel
> delete atoms #9-12
> delete bonds #9-12
> show #13 models
> hide #13 models
> show #2 models
> select #2/D:55-58
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/L:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 84 atom styles
> select ::name="CYS"
1218 atoms, 1015 bonds, 203 residues, 14 models selected
> view matrix models
> #6,-0.73769,0.37453,-0.56173,269.6,0.036448,-0.80872,-0.58707,432.04,-0.67416,-0.45355,0.58293,254.02,#1,-0.92427,0.28609,-0.25274,101.56,-0.20231,0.19434,0.95984,246.06,0.32372,0.93829,-0.12175,156.74,#20,0.14776,-0.82411,0.54682,108.45,-0.98901,-0.12627,0.076949,151.2,0.0056323,-0.55218,-0.83371,190.92,#2,0.024733,0.99955,-0.016702,116.88,0.86184,-0.012853,0.50702,233.63,0.50658,-0.026935,-0.86177,141.05,#3,-0.83981,0.54288,-0.0021306,112.92,0.53652,0.83055,0.14943,240.58,0.082892,0.12435,-0.98877,143.99,#4,-0.63125,0.75845,-0.1621,122.48,0.26879,0.40999,0.87158,218.47,0.72752,0.50661,-0.46267,137.12,#5,0.63307,-0.70266,-0.32479,124.8,-0.16013,0.29162,-0.94304,229.07,0.75735,0.64902,0.072096,143.22,#7,0.62567,0.033784,-0.77936,119.07,0.72551,-0.39233,0.56543,209.05,-0.28666,-0.9192,-0.26998,149.03,#13,0.0038706,-0.86688,-0.49851,188.37,0.53647,-0.4189,0.73261,202.94,-0.84391,-0.27027,0.46343,99.492,#14,-0.26132,0.8822,0.39171,219.83,-0.81884,-0.41748,0.39396,236.82,0.51108,-0.21779,0.83148,168.82,#15,-0.24072,0.6086,-0.75608,210.52,-0.8187,0.29109,0.49497,247.97,0.52133,0.73815,0.42819,157.81,#16,0.85782,0.51132,-0.051848,180.55,-0.18642,0.40358,0.89575,169.72,0.47894,-0.75873,0.44152,125.75,#17,-0.42368,-0.0075666,-0.90578,204.22,-0.89534,-0.14814,0.42003,190.96,-0.13736,0.98894,0.05599,104.17,#8,-0.46108,0.5647,0.68448,89.185,0.54831,-0.42517,0.72012,212.08,0.69768,0.70735,-0.11359,211.19
> select #2/J:610
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/J:631
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #2/J:634
18 atoms, 15 bonds, 3 residues, 1 model selected
> select clear
> select cys
Expected an objects specifier or a keyword
> show #!6 models
> hide #2 models
> select #6/T:274
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/T:292
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #6/T:271
18 atoms, 15 bonds, 3 residues, 2 models selected
> select add #6/T:295
24 atoms, 20 bonds, 4 residues, 2 models selected
> show sel atoms
> select #6/T:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #13 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #16 models
> hide #15 models
> show #!6 models
> hide #16 models
> select #6/A/B/C/D/E/F/G/H
6152 atoms, 6234 bonds, 775 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3-5,7,13-17 to #6 & sel
Computing secondary structure
[Repeated 8 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 E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
0.536)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
0.445)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
0.580)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
0.719)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
0.330)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
0.576)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
0.518)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
0.530)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
alignment score = 628.4
RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
0.994)
> matchmaker #3-5,7,13-17 to #6 & sel
Computing secondary structure
[Repeated 8 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 E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
0.536)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
0.445)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
0.580)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
0.719)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
0.330)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
0.576)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
0.518)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
0.530)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
alignment score = 628.4
RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
0.994)
> view matrix models
> #6,-0.73769,0.37453,-0.56173,278.96,0.036448,-0.80872,-0.58707,433.15,-0.67416,-0.45355,0.58293,242.88
> show #2 models
> hide #!6 models
> hide #2 models
> show #!6 models
> hide #!6 models
> show #13 models
> show #!6 models
> hide #!6 models
> select #13/A/B/C/D/E/F/G/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> select ~sel & ##selected
14259 atoms, 15372 bonds, 1293 residues, 1 model selected
> hide sel cartoons
> view matrix models
> #13,0.35348,0.24328,-0.90325,108.78,-0.42269,-0.81985,-0.38623,247.75,-0.8345,0.51832,-0.18697,212.23
> show #!6 models
> hide #13 models
> select #6/A/B/C/D/E/F/G/H
6152 atoms, 6234 bonds, 775 residues, 1 model selected
> select ~sel & ##selected
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> hide sel cartoons
> show #13 models
> select #6/A/B/C/D/E/F/G/H
6152 atoms, 6234 bonds, 775 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #13 to #6 & 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 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
0.330)
> matchmaker #1-5,7 to #6 & sel
Computing secondary structure
[Repeated 4 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 E (#6) with fold_nucleosome_foxa1_gata4_model_0.cif,
chain A (#1), sequence alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
0.283)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
0.242)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_1.cif, chain A (#3), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.333 angstroms; (across all 97 pairs:
0.536)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_2.cif, chain A (#4), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.280 angstroms; (across all 97 pairs:
0.445)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_3.cif, chain A (#5), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.270 angstroms; (across all 97 pairs:
0.580)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_4.cif, chain A (#7), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.283 angstroms; (across all 97 pairs:
0.719)
> matchmaker #14-17#!20 to #6 & sel
Computing secondary structure
[Repeated 3 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 E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
0.576)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
0.518)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
0.530)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
alignment score = 628.4
RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
0.994)
Matchmaker 8vg1, chain E (#6) with 3aze, chain E (#20), sequence alignment
score = 625.6
RMSD between 96 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
0.414)
> select clear
> show #14 models
> hide #13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #15 models
> show #16 models
> show #17 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #13 models
> hide #14 models
> show #14 models
> select #13#14/I/J
28597 atoms, 29994 bonds, 3203 residues, 2 models selected
> hide sel cartoons
> show #15 models
> show #16 models
> show #17 models
> select #13#14#15#16#17/I/J
94498 atoms, 99528 bonds, 10052 residues, 5 models selected
> select #13#14#15/I/J#16/I/J#17/I/J
63824 atoms, 66804 bonds, 7326 residues, 5 models selected
> hide sel cartoons
> view matrix models
> #13,0.35348,0.24328,-0.90325,123.72,-0.42269,-0.81985,-0.38623,236.68,-0.8345,0.51832,-0.18697,157.55,#14,0.19712,0.42197,-0.88492,137.55,0.12928,-0.90594,-0.4032,235.57,-0.97182,-0.034925,-0.23313,158.82,#15,0.60279,-0.17833,-0.77771,136.5,0.36617,-0.80418,0.46821,238.71,-0.70892,-0.56701,-0.41945,151.78,#16,-0.74187,0.17181,0.64815,134.72,0.59305,-0.28296,0.75381,234.63,0.31291,0.94362,0.10802,161.92,#17,0.44598,-0.29411,-0.84534,122.34,-0.61903,0.5808,-0.52865,242.51,0.64646,0.75906,0.076956,154.59
> show #!6 models
> select #13#14/K/L#15/K/L#16/K/L#17/K/L
37215 atoms, 40258 bonds, 3031 residues, 5 models selected
> hide sel cartoons
> select #13#14/K/L#15/M#16/K/L#17/K/L
37220 atoms, 40274 bonds, 3030 residues, 5 models selected
> hide sel cartoons
> select #13#14/K/L#15/M#16/K/L#17/M/L
41036 atoms, 44560 bonds, 3215 residues, 5 models selected
> hide sel cartoons
> select #13#14/K/L#15/M#16/M/L#17/M/L
44852 atoms, 48846 bonds, 3400 residues, 5 models selected
> hide sel cartoons
> hide #14 models
> hide #!6 models
> show #14 models
> show #!6 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #13 models
> show #13 models
> select #13
21967 atoms, 23178 bonds, 2283 residues, 1 model selected
> show sel cartoons
> select #13/I/J/K/L/M/N
14259 atoms, 15372 bonds, 1293 residues, 1 model selected
> hide sel cartoons
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> ui tool show Matchmaker
> select #13/I/J/K/L/M/N
14259 atoms, 15372 bonds, 1293 residues, 1 model selected
> select ~sel & ##selected
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> matchmaker #13-17 to #6 & sel
No 'to' model specified
> ui tool show Matchmaker
> select #13/A/B/C/D/E/F/G/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> matchmaker #13-17 to #1
Computing secondary structure
[Repeated 4 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 I (#1) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 2350.2
RMSD between 18 pruned atom pairs is 1.472 angstroms; (across all 478 pairs:
37.002)
Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
alignment score = 2302.8
RMSD between 88 pruned atom pairs is 0.556 angstroms; (across all 478 pairs:
31.892)
Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
alignment score = 2288.4
RMSD between 93 pruned atom pairs is 0.653 angstroms; (across all 478 pairs:
33.966)
Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
alignment score = 2262.6
RMSD between 60 pruned atom pairs is 0.381 angstroms; (across all 478 pairs:
51.446)
Matchmaker fold_nucleosome_foxa1_gata4_model_0.cif, chain I (#1) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
alignment score = 2265
RMSD between 5 pruned atom pairs is 1.237 angstroms; (across all 478 pairs:
30.443)
> select #6/A/B/C/D/E/F/G/H
6152 atoms, 6234 bonds, 775 residues, 1 model selected
> matchmaker #13-17 to #6 & sel
Computing secondary structure
[Repeated 4 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 E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain A (#13), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.330 angstroms; (across all 97 pairs:
0.330)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.313 angstroms; (across all 97 pairs:
0.576)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.271 angstroms; (across all 97 pairs:
0.518)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
alignment score = 628.4
RMSD between 96 pruned atom pairs is 0.327 angstroms; (across all 97 pairs:
0.530)
Matchmaker 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
alignment score = 628.4
RMSD between 93 pruned atom pairs is 0.338 angstroms; (across all 97 pairs:
0.994)
> show #14 models
> show #16 models
> hide #13 models
> hide #16 models
> select clear
> select #14/A/B/C/D/E/F/G/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> show sel cartoons
> select clear
> show #13 models
> hide #14 models
> hide #!6 models
> show #!6 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #17 models
> show #16 models
> show #15 models
> show #14 models
> show #13 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> select #6
14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected
> show sel cartoons
> select clear
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #14 models
> show #15 models
> show #16 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #14 models
> hide #15 models
> hide #16 models
> show #!6 models
> select /A
16994 atoms, 17273 bonds, 2169 residues, 14 models selected
> hide #!6 models
> show #!6 models
> select /A
16994 atoms, 17273 bonds, 2169 residues, 14 models selected
> matchmaker #13-17 & sel to #6 & sel
Computing secondary structure
[Repeated 4 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_gata4nombp_zn_model_0.cif, chain A (#13), sequence
alignment score = 627.8
RMSD between 97 pruned atom pairs is 0.335 angstroms; (across all 97 pairs:
0.335)
Matchmaker 8vg1, chain A (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain A (#14), sequence
alignment score = 627.8
RMSD between 96 pruned atom pairs is 0.286 angstroms; (across all 97 pairs:
0.591)
Matchmaker 8vg1, chain A (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain A (#15), sequence
alignment score = 627.8
RMSD between 96 pruned atom pairs is 0.257 angstroms; (across all 97 pairs:
0.549)
Matchmaker 8vg1, chain A (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain A (#16), sequence
alignment score = 627.8
RMSD between 96 pruned atom pairs is 0.292 angstroms; (across all 97 pairs:
0.549)
Matchmaker 8vg1, chain A (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain A (#17), sequence
alignment score = 627.8
RMSD between 93 pruned atom pairs is 0.307 angstroms; (across all 97 pairs:
0.978)
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> color sel & #!6 bychain
> select clear
> color #!6 bychain
> undo
[Repeated 3 time(s)]
> view matrix models
> #6,-0.73769,0.37453,-0.56173,282.99,0.036448,-0.80872,-0.58707,434.38,-0.67416,-0.45355,0.58293,234.8,#1,0.34863,-0.86979,-0.34918,128.28,-0.59863,-0.4933,0.63111,224.41,-0.72118,-0.010996,-0.69266,132.73,#20,0.14776,-0.82411,0.54682,94.626,-0.98901,-0.12627,0.076949,190.8,0.0056323,-0.55218,-0.83371,172.79,#2,-0.78547,-0.55054,0.28274,136.79,-0.049609,0.51138,0.85792,225.98,-0.61691,0.65985,-0.42898,142.62,#3,0.86327,0.50474,-0.0016107,141.97,0.44874,-0.76894,-0.45538,211.84,-0.23109,0.39239,-0.8903,138.27,#4,-0.29416,-0.93822,-0.18224,142.42,-0.72095,0.092643,0.68677,229.03,-0.62746,0.33341,-0.70366,155.96,#5,-0.73977,0.075381,0.66862,129.67,-0.44258,-0.80299,-0.39915,231.15,0.50681,-0.5912,0.6274,149.58,#7,0.13642,-0.011203,0.99059,138.93,-0.88638,-0.44793,0.117,206.62,0.4424,-0.894,-0.071036,150.01,#13,0.5006,-0.78154,0.37228,134.44,0.80193,0.58063,0.1406,208.91,-0.32604,0.22816,0.91741,154.17,#14,0.83547,-0.37468,0.40201,128.15,0.33015,0.92702,0.17787,213.49,-0.43931,-0.015884,0.89819,142.59,#15,0.52676,0.33889,0.77954,135.69,0.1418,0.8692,-0.47369,213.23,-0.8381,0.36006,0.4098,140.7,#16,0.14896,-0.98297,-0.10763,126.11,-0.8605,-0.075231,-0.50386,212.24,0.48718,0.16767,-0.85705,146.16,#17,-0.90964,-0.40837,0.076035,139.24,0.41536,-0.89211,0.17782,204.61,-0.0047835,0.19333,0.98112,152.39,#8,-0.46108,0.5647,0.68448,93.212,0.54831,-0.42517,0.72012,213.31,0.69768,0.70735,-0.11359,203.11
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> ui tool show "Color Actions"
> select /A/E
34318 atoms, 35243 bonds, 4048 residues, 14 models selected
> color sel cornflower blue
> select /B/F
26404 atoms, 26771 bonds, 3429 residues, 14 models selected
> color sel medium turquoise
> color sel yellow green
> color sel olive drab
> color sel dark sea green
> select /C/G
25294 atoms, 25598 bonds, 3299 residues, 14 models selected
> color sel tan
> select /D/H
28252 atoms, 29083 bonds, 1 pseudobond, 3336 residues, 15 models selected
> color sel plum
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #13/I/J
6630 atoms, 6816 bonds, 920 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #13/L/M
7628 atoms, 8556 bonds, 372 residues, 1 model selected
> show sel cartoons
> select clear
> select /I
45018 atoms, 46920 bonds, 4 pseudobonds, 5580 residues, 14 models selected
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!6 models
> color sel dim gray
> select /J
59201 atoms, 61380 bonds, 1 pseudobond, 7539 residues, 14 models selected
> color sel dark gray
> color sel gray
> color sel light gray
> select clear
> hide #!6 models
> select #13/L#14/L#15/L#16/L#17/L
19055 atoms, 21350 bonds, 930 residues, 5 models selected
> color sel dim gray
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
> hide #13 models
> show #13 models
> hide #14 models
> show #14 models
> hide #14 models
> hide #13 models
> show #13 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #13 models
> show #14 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> show #16 models
> show #17 models
> show #13 models
> select /L/M
80097 atoms, 89846 bonds, 3906 residues, 11 models selected
> hide sel & #13-17 cartoons
[Repeated 1 time(s)]
> show sel & #13-17 cartoons
> hide sel & #13-17 cartoons
> show #!6 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> select /#6/I#6/J#6/O#6/T
Expected an objects specifier or a keyword
> select #6/I#6/J#6/O#6/T
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #17 models
> hide #16 models
> hide #14 models
> hide #15 models
> hide #13 models
> select #6/A#6/E
1598 atoms, 1622 bonds, 194 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> show #13 models
> hide #13 models
> color sel medium blue
> show #13 models
> select clear
> hide #13 models
> select #6/C#6/G
1740 atoms, 1762 bonds, 225 residues, 1 model selected
> color sel dark goldenrod
> show #13 models
> select clear
> show #14 models
> show #15 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> show #17 models
> hide #17 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> select #6/D#6/H
1490 atoms, 1512 bonds, 190 residues, 1 model selected
> color sel magenta
> show #13 models
> hide #13 models
> select #6/D#6/H
1490 atoms, 1512 bonds, 190 residues, 1 model selected
> color sel orchid
> show #13 models
> color sel magenta
> select clear
> select #6/B#6/F
1324 atoms, 1338 bonds, 166 residues, 1 model selected
> color sel forest green
> color sel green
> select clear
> hide #13 models
> select #6/I#6/J#6/O#6/T
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> show sel cartoons
> select clear
> select #6/I#6/J#6/O#6/T
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show #13 models
> color sel deep sky blue
> select clear
> hide #13 models
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel medium purple
> color sel deep sky blue
> select clear
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> color sel medium purple
> select clear
> select ::name="CYS"
1218 atoms, 1015 bonds, 203 residues, 14 models selected
> select #6/T:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/T:271
12 atoms, 10 bonds, 2 residues, 2 models selected
> color sel gold
> show sel atoms
> select ::name="CYS"
1218 atoms, 1015 bonds, 203 residues, 14 models selected
> select clear
> select add #6/T:292
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/T:274
12 atoms, 10 bonds, 2 residues, 2 models selected
> color sel gold
> show sel atoms
> select #6/I:56
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6
14434 atoms, 15401 bonds, 421 pseudobonds, 1273 residues, 3 models selected
> show sel atoms
> hide sel atoms
> undo
[Repeated 2 time(s)]
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3/8VG1_nucleosome_FOXA1_GATA4.cxs"
> select ::name="ZN"
12 atoms, 12 residues, 12 models selected
> show sel & #!6 atoms
> color sel dim gray
> select #6/I
3501 atoms, 3922 bonds, 171 residues, 1 model selected
> ui tool show "Color Actions"
> color sel silver
> color sel dark sea green
> color sel dark olive green
> color sel steel blue
> color sel cadet blue
> color sel light slate gray
> color sel slate gray
> color sel light slate gray
> select clear
> select #6/J
3510 atoms, 3942 bonds, 171 residues, 1 model selected
> color sel light steel blue
> color sel light blue
> select clear
> show #13 models
> hide #13 models
> select #6/I#6/J#6/O#6/T
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #1 models
> hide #1 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/AF3_0-4.8VG1_nucleosome.png"
> width 900 height 712 supersample 4 transparentBackground true
> show #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/8VG1.vs.AF3.nucleosome.png"
> width 900 height 712 supersample 4 transparentBackground true
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #14 models
> show #15 models
> hide #14 models
> hide #15 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/8VG1.vs.AF3-0.nucleosome.png"
> width 900 height 712 supersample 4 transparentBackground true
> show sel cartoons
> hide #13 models
> hide sel cartoons
> show #2 models
> hide #2 models
> show sel cartoons
> select #13#14#15#16#17
109835 atoms, 115890 bonds, 11415 residues, 5 models selected
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show sel cartoons
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #13 models
> show #13 models
> hide #!6 models
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> select #13/L#14/L#15/L#16/L#17/L
19055 atoms, 21350 bonds, 930 residues, 5 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> show #!6 models
> hide #!6 models
> select #13/M#14/M#15/M#16/M#17/M
19085 atoms, 21430 bonds, 930 residues, 5 models selected
> select #6/J:134
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/J:134
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel light steel blue
> select #13/M#14/M#15/M#16/M#17/M
19085 atoms, 21430 bonds, 930 residues, 5 models selected
> color sel light steel blue
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> select ::name="CYS"
1218 atoms, 1015 bonds, 203 residues, 14 models selected
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel medium slate blue
> color sel medium purple
> show #!6 models
> hide #13 models
> select #6/o
856 atoms, 883 bonds, 102 residues, 1 model selected
> color sel purple
> color sel medium slate blue
> color sel slate blue
> select clear
> show #13 models
> hide #!6 models
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel violet
> color sel pale violet red
> color sel hot pink
[Repeated 1 time(s)]
> select clear
> show #!6 models
> hide #!6 models
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel aquamarine
> color sel light sky blue
> select clear
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel aquamarine
> color sel light sky blue
> select clear
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel light sky blue
> color sel aquamarine
> select clear
[Repeated 1 time(s)]
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel dark turquoise
> color sel light sky blue
> select clear
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel aquamarine
> select clear
[Repeated 2 time(s)]
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel thistle
> color sel plum
> color sel orchid
> color sel medium orchid
> color sel medium purple
> select clear
> show #!6 models
> hide #!6 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel thistle
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> select clear
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel powder blue
> color sel pale turquoise
> select clear
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> color sel light cyan
> select clear
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel lavender
> select clear
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel thistle
> select clear
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> select #13/I#14/I#15/I#16/I#17/I:168-269
14864 atoms, 15299 bonds, 2014 residues, 5 models selected
> show #!6 models
> hide #13 models
> show #13 models
[Repeated 1 time(s)]
> select #13/I:168-269#14/I:168-269#15/I:168-269#16/I:168-269#17/I:168-269
4280 atoms, 4415 bonds, 510 residues, 5 models selected
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> color sel lavender blush
> select clear
> select #13/I:168-269#14/I:168-269#15/I:168-269#16/I:168-269#17/I:168-269
4280 atoms, 4415 bonds, 510 residues, 5 models selected
> color sel medium purple
> hide #13 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> select #13/J:269-321
414 atoms, 420 bonds, 53 residues, 1 model selected
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> ui tool show "Color Actions"
> color sel dark turquoise
> select clear
> select ::name="CYS"
1218 atoms, 1015 bonds, 203 residues, 14 models selected
> select #13/L:67
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/J:274
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #13/J:294
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #13/J:295
17 atoms, 14 bonds, 3 residues, 1 model selected
> select subtract #13/J:294
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #13/J:271
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #13/J:292
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel gold
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 24 atom styles
> select clear
> select #14/J:269-321
414 atoms, 420 bonds, 53 residues, 1 model selected
> select #14/J:269-321#15/J:269-321#16/J:269-321#17/J:269-321
1656 atoms, 1680 bonds, 212 residues, 4 models selected
> color sel dark turquoise
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> select clear
> show #13 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> hide sel & #13,15 cartoons
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> hide sel & #13,15 cartoons
> show #!6 models
> hide #13 models
> hide #15 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 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 #13 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #14 models
> hide #15 models
> hide sel & #14 cartoons
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> hide sel & #14 cartoons
> show #15 models
> hide #14 models
> show #14 models
> hide #14 models
> show #16 models
> hide #15 models
> show #17 models
> hide sel & #16-17 cartoons
> select #13/J#14/J#15/J#16/J#17/J
15640 atoms, 16060 bonds, 2210 residues, 5 models selected
> hide sel & #16-17 cartoons
> show #15 models
> show #14 models
> show #13 models
> show #!6 models
> hide #!6 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #!6 models
> select #6/T:298
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel dodger blue
> color sel deep sky blue
> select clear
> show #13 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #13 models
> hide #14 models
> show #15 models
> hide #13 models
> show #16 models
> hide #15 models
> show #17 models
> hide #16 models
> show #!6 models
> hide #17 models
> show #13 models
> hide #!6 models
> hide #13 models
> show #13 models
> show #17 models
> hide #17 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> rainbow #13
> undo
> select #13/J
3128 atoms, 3212 bonds, 442 residues, 1 model selected
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!6 models
> hide #15 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> hide sel atoms
> show #!6 models
> show #!8 models
> hide #!8 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #16 models
> hide #15 models
> show #17 models
> hide #16 models
> show #!6 models
> hide #17 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.DNA.png" width 900
> height 712 supersample 4 transparentBackground true
> show #13 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-0.DNA.png" width
> 900 height 712 supersample 4 transparentBackground true
> show #14 models
> hide #13 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-.DNA.png" width
> 900 height 712 supersample 4 transparentBackground true
> show #15 models
> hide #14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-2.DNA.png" width
> 900 height 712 supersample 4 transparentBackground true
> show #16 models
> hide #15 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-3.DNA.png" width
> 900 height 712 supersample 4 transparentBackground true
> show #17 models
> hide #16 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3-4.DNA.png" width
> 900 height 712 supersample 4 transparentBackground true
> show #!6 models
> hide #17 models
> view matrix models
> #13,0.5006,-0.78154,0.37228,131.9,0.80193,0.58063,0.1406,208.59,-0.32604,0.22816,0.91741,156.99
> view matrix models
> #13,0.5006,-0.78154,0.37228,129.59,0.80193,0.58063,0.1406,208.48,-0.32604,0.22816,0.91741,156.57
> select #6/I:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/I:34
39 atoms, 41 bonds, 2 residues, 1 model selected
> select add #6/I:35
60 atoms, 64 bonds, 3 residues, 1 model selected
> select add #6/I:37
79 atoms, 84 bonds, 4 residues, 1 model selected
> select add #6/I:36
101 atoms, 108 bonds, 5 residues, 1 model selected
> select add #6/I:38
122 atoms, 131 bonds, 6 residues, 1 model selected
> select add #6/I:39
144 atoms, 155 bonds, 7 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/I
Alignment identifier is 6/I
> select #6/I:31
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/I:31-37
143 atoms, 159 bonds, 7 residues, 1 model selected
> color sel bynucleotide
> show sel atoms
> label sel attribute label_one_letter_code
> label height 2
> label height 3
> view matrix models
> #6,-0.73769,0.37453,-0.56173,277.08,0.036448,-0.80872,-0.58707,433.88,-0.67416,-0.45355,0.58293,237.79
> select clear
> select #6/J:156
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #6/J:155
40 atoms, 43 bonds, 2 residues, 1 model selected
> select add #6/J:154
61 atoms, 66 bonds, 3 residues, 1 model selected
> select add #6/J:153
83 atoms, 90 bonds, 4 residues, 1 model selected
> select add #6/J:152
103 atoms, 111 bonds, 5 residues, 1 model selected
> select add #6/J:151
122 atoms, 131 bonds, 6 residues, 1 model selected
> select add #6/J:150
144 atoms, 155 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA3.png" width 900
> height 712 supersample 4 transparentBackground true
[Repeated 1 time(s)]
> show #13 models
> hide #!6 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> show sel & #13 cartoons
> select clear
> select #13/I:31-37#14/I:31-37#15/I:31-37#16/I:31-37#17/I:31-37
235 atoms, 230 bonds, 35 residues, 5 models selected
> select #13/L:31-37#14/L:31-37#15/L:31-37#16/L:31-37#17/L:31-37
715 atoms, 795 bonds, 35 residues, 5 models selected
> rainbow sel & #13
> show #14 models
> hide #13 models
> rainbow sel & #14
> color sel & #14 bynucleotide
> show #13 models
> color sel & #13-14 bynucleotide
> hide #13 models
> hide #14 models
> show #15 models
> color sel & #15 bynucleotide
> show #16 models
> hide #15 models
> color sel & #16 bynucleotide
> show #17 models
> hide #16 models
> color sel & #17 bynucleotide
> show #14 models
> show #15 models
> show #16 models
> select #13/I#14/I#15/I#16/I#17/I
17510 atoms, 18020 bonds, 2390 residues, 5 models selected
> show #13 models
> show sel cartoons
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> select clear
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #16 models
> hide #15 models
> show #17 models
> hide #16 models
> show #!6 models
> hide #17 models
> show #13 models
> hide #!6 models
> show #13 cartoons
> show #!6 models
> hide #13 models
> select #6/J:130
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/I:55
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/I:56
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #6/I:57
63 atoms, 68 bonds, 3 residues, 1 model selected
> select add #6/I:58
84 atoms, 91 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> label sel attribute label_one_letter_code
> label height 3
> show sel atoms
> show #13 models
> hide #!6 models
> color #13 bynucleotide
> undo
> select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
420 atoms, 470 bonds, 20 residues, 5 models selected
> color sel & #13 bynucleotide
> show #14 models
> hide #13 models
> select clear
> show #14 cartoons
> show #15 models
> hide #14 models
> show #15 cartoons
> show #16 models
> hide #15 models
> show #16 cartoons
> show #17 models
> hide #16 models
> show #17 cartoons
> show #16 models
> show #15 models
> show #14 models
> show #13 models
> select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
420 atoms, 470 bonds, 20 residues, 5 models selected
> color sel bynucleotide
> hide #13 models
> show #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #!6 models
> hide #13 models
Drag select of 19 residues
> select #6/H:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/T
415 atoms, 420 bonds, 4 pseudobonds, 54 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show #13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #14 cartoons
[Repeated 1 time(s)]
> select #14
21967 atoms, 23178 bonds, 2283 residues, 1 model selected
> show sel cartoons
> select clear
> show #15 models
> hide #14 models
> show #16 models
> hide #15 models
> show #17 models
> hide #16 models
> show #!6 models
> hide #17 models
> show #13 models
> hide #!6 models
> select #13/J
3128 atoms, 3212 bonds, 442 residues, 1 model selected
> select #13/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> hide sel cartoons
> show #!6 models
> hide #13 models
Drag select of 165 residues
> select clear
> show #2 models
> hide #!6 models
> show #3 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #7 models
> hide #5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #7 models
> show #1 models
> hide #1 models
> show #2 models
> hide #!8 models
> show #!6 models
> hide #2 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #!6 models
> select #13/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> show sel cartoons
> select clear
> show #!6 models
> hide #13 models
> show #13 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> ui tool show Matchmaker
> select #6/O#13/I#14/I#15/I#16/I#17/I
18366 atoms, 18903 bonds, 2492 residues, 6 models selected
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> matchmaker #13-17 & sel to #6 & sel
Computing secondary structure
[Repeated 4 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 O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 1915.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_1.cif, chain I (#14), sequence
alignment score = 1927.2
RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs:
1.776)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_2.cif, chain I (#15), sequence
alignment score = 1924.2
RMSD between 78 pruned atom pairs is 0.751 angstroms; (across all 102 pairs:
2.144)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_3.cif, chain I (#16), sequence
alignment score = 1901.4
RMSD between 80 pruned atom pairs is 0.855 angstroms; (across all 102 pairs:
3.778)
Matchmaker 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_4.cif, chain I (#17), sequence
alignment score = 1909.2
RMSD between 82 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.994)
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #13 models
> show #13 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #14 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select clear
> hide #!6 surfaces
> show #!6 surfaces
> undo
> hide #!6 surfaces
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!6 surfaces
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> select clear
> show #13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #!6 models
> hide #14 models
> show #13 models
> hide #!6 models
> show #14 models
> hide #13 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #14 models
> show #13 models
> hide #!6 models
> show #!6 models
> hide #13 models
> hide #!6 surfaces
> select #6/I:31
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel surfaces
> select clear
> show #!6 surfaces
> show #13 models
> hide #!6 models
> show #13 surfaces
> hide #!13 surfaces
[Repeated 1 time(s)]
> show #!13 surfaces
> hide #!13 surfaces
> show #!13 surfaces
> hide #!13 surfaces
> select #13/L:55-58#14/L:55-58#15/L:55-58#16/L:55-58#17/L:55-58
420 atoms, 470 bonds, 20 residues, 5 models selected
> select #13/I:393
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/J:298
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> show #14 models
> hide #!13 models
> show #14 cartoons
> show #14 surfaces
> hide #!14 surfaces
> show #!14 surfaces
> show #15 models
> hide #!14 models
> hide #15 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_0.cif
Chain information for fold_motb_1_ibpa_model_0.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_1.cif
Chain information for fold_motb_1_ibpa_model_1.cif #10
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_2.cif
Chain information for fold_motb_1_ibpa_model_2.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_3.cif
Chain information for fold_motb_1_ibpa_model_3.cif #12
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1_ibpa/fold_motb_1_ibpa_model_4.cif
Chain information for fold_motb_1_ibpa_model_4.cif #18
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> select /A
21864 atoms, 22273 bonds, 2764 residues, 19 models selected
> ui tool show Matchmaker
> matchmaker #10-12,18 & sel to #9 & sel
Computing secondary structure
[Repeated 4 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_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1_ibpa_model_1.cif, chain A (#10), sequence alignment score = 618.4
RMSD between 86 pruned atom pairs is 0.539 angstroms; (across all 119 pairs:
10.720)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1_ibpa_model_2.cif, chain A (#11), sequence alignment score = 618.4
RMSD between 83 pruned atom pairs is 0.491 angstroms; (across all 119 pairs:
19.970)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1_ibpa_model_3.cif, chain A (#12), sequence alignment score = 607.6
RMSD between 84 pruned atom pairs is 0.273 angstroms; (across all 119 pairs:
19.835)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1_ibpa_model_4.cif, chain A (#18), sequence alignment score = 588.4
RMSD between 87 pruned atom pairs is 0.448 angstroms; (across all 119 pairs:
14.443)
> select clear
> color #9-12,18 bychain
> select /B
21839 atoms, 22208 bonds, 2813 residues, 19 models selected
> rainbow sel & #9-12,18
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #18 models
> show #9 models
> hide #9 models
> show #9 models
> hide #18 models
> show #18 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #18 models
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> select clear
> select /B
21839 atoms, 22208 bonds, 2813 residues, 19 models selected
> show sel & #12 surfaces
> show #18 models
> hide #!12 models
> show sel & #18 surfaces
> hide #!18 models
> show #9 models
> show sel & #9 surfaces
> select /A
21864 atoms, 22273 bonds, 2764 residues, 19 models selected
> show sel & #!9 surfaces
> hide sel & #!9 surfaces
> show sel & #!9 surfaces
[Repeated 1 time(s)]
> hide sel & #!9 surfaces
> view matrix models
> #6,-0.73769,0.37453,-0.56173,264.4,0.036448,-0.80872,-0.58707,432.16,-0.67416,-0.45355,0.58293,229.9,#1,0.34863,-0.86979,-0.34918,115.59,-0.59863,-0.4933,0.63111,222.69,-0.72118,-0.010996,-0.69266,124.84,#20,0.14776,-0.82411,0.54682,81.945,-0.98901,-0.12627,0.076949,189.08,0.0056323,-0.55218,-0.83371,164.9,#2,-0.78547,-0.55054,0.28274,124.11,-0.049609,0.51138,0.85792,224.26,-0.61691,0.65985,-0.42898,134.73,#3,0.86327,0.50474,-0.0016107,129.29,0.44874,-0.76894,-0.45538,210.11,-0.23109,0.39239,-0.8903,130.38,#4,-0.29416,-0.93822,-0.18224,129.74,-0.72095,0.092643,0.68677,227.3,-0.62746,0.33341,-0.70366,148.07,#5,-0.73977,0.075381,0.66862,116.99,-0.44258,-0.80299,-0.39915,229.43,0.50681,-0.5912,0.6274,141.69,#7,0.13642,-0.011203,0.99059,126.25,-0.88638,-0.44793,0.117,204.9,0.4424,-0.894,-0.071036,142.12,#13,0.0038706,-0.86688,-0.49851,155.96,0.53647,-0.4189,0.73261,240.32,-0.84391,-0.27027,0.46343,76.465,#14,-0.26132,0.8822,0.39171,187.41,-0.81884,-0.41748,0.39396,274.2,0.51108,-0.21779,0.83148,145.79,#15,-0.24072,0.6086,-0.75608,178.11,-0.8187,0.29109,0.49497,285.35,0.52133,0.73815,0.42819,134.78,#16,0.85782,0.51132,-0.051848,148.14,-0.18642,0.40358,0.89575,207.1,0.47894,-0.75873,0.44152,102.73,#17,-0.42368,-0.0075666,-0.90578,171.81,-0.89534,-0.14814,0.42003,228.34,-0.13736,0.98894,0.05599,81.142,#8,-0.46108,0.5647,0.68448,80.531,0.54831,-0.42517,0.72012,211.59,0.69768,0.70735,-0.11359,195.21,#9,1,0,0,-12.681,0,1,0,-1.7223,0,0,1,-7.8908,#10,0.99715,0.072954,-0.018974,-7.5052,0.056195,-0.55164,0.83219,-6.0261,0.050244,-0.83088,-0.55417,-8.6196,#11,-0.056865,-0.77148,-0.63371,-7.3464,-0.98854,-0.045419,0.144,-5.4156,-0.13987,0.63464,-0.76005,-12.726,#12,0.32123,0.94585,0.046696,-10.832,0.91723,-0.29849,-0.26382,-3.5132,-0.2356,0.12758,-0.96344,-13.271,#18,0.95192,0.26927,0.1461,-8.4839,0.23642,-0.94899,0.20861,-1.9572,0.19483,-0.16404,-0.96702,-10.748
> select /A:47-55
1442 atoms, 1437 bonds, 171 residues, 19 models selected
> show sel & #!9 surfaces
> hide sel & #!9 surfaces
> select /A:71-75
811 atoms, 798 bonds, 95 residues, 19 models selected
> show sel & #!9 surfaces
> hide sel & #!9 surfaces
[Repeated 2 time(s)]
> select clear
> select /B
21839 atoms, 22208 bonds, 2813 residues, 19 models selected
> hide sel & #!9 surfaces
> select clear
> show #10 models
> show #11 models
> hide #11 models
> show #!12 models
> show #11 models
> show #!18 models
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #!12 models
> hide #!18 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_0.cif
Chain information for fold_motb_1x2_ibpax2_model_0.cif #19
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_1.cif
Chain information for fold_motb_1x2_ibpax2_model_1.cif #21
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_2.cif
Chain information for fold_motb_1x2_ibpax2_model_2.cif #22
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_3.cif
Chain information for fold_motb_1x2_ibpax2_model_3.cif #23
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/DebbieH/MotB.1_IbpA/fold_motb_1x2_ibpax2/fold_motb_1x2_ibpax2_model_4.cif
Chain information for fold_motb_1x2_ibpax2_model_4.cif #24
---
Chain | Description
A B | .
C D | .
Computing secondary structure
[Repeated 4 time(s)]
> select /A
26734 atoms, 27273 bonds, 3359 residues, 24 models selected
> ui tool show Matchmaker
> matchmaker #21-24 & sel to #9 & sel
Computing secondary structure
[Repeated 4 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_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1x2_ibpax2_model_1.cif, chain A (#21), sequence alignment score =
587.2
RMSD between 86 pruned atom pairs is 0.349 angstroms; (across all 119 pairs:
9.985)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1x2_ibpax2_model_2.cif, chain A (#22), sequence alignment score =
584.2
RMSD between 85 pruned atom pairs is 0.578 angstroms; (across all 119 pairs:
11.734)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1x2_ibpax2_model_3.cif, chain A (#23), sequence alignment score =
555.7
RMSD between 85 pruned atom pairs is 0.352 angstroms; (across all 119 pairs:
15.604)
Matchmaker fold_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1x2_ibpax2_model_4.cif, chain A (#24), sequence alignment score =
597.4
RMSD between 76 pruned atom pairs is 0.381 angstroms; (across all 119 pairs:
16.342)
> show #!9 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #19 models
> show #19 models
> hide #!9 models
> color sel & #19 bychain
> show #!9 models
> matchmaker #19 & sel to #9 & 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_motb_1_ibpa_model_0.cif, chain A (#9) with
fold_motb_1x2_ibpax2_model_0.cif, chain A (#19), sequence alignment score =
578.8
RMSD between 84 pruned atom pairs is 0.544 angstroms; (across all 119 pairs:
16.385)
> hide #!9 models
> select /C
18212 atoms, 18468 bonds, 2333 residues, 19 models selected
> select #19/C
1116 atoms, 1137 bonds, 137 residues, 1 model selected
> rainbow sel
> select clear
> show #!9 models
> hide #19 models
> show #19 models
> hide #!9 models
> show #21 models
> hide #19 models
> select /A
26734 atoms, 27273 bonds, 3359 residues, 24 models selected
> color sel & #21 bychain
> show #22 models
> hide #21 models
> show #!18 models
> hide #!18 models
> show #19 models
> hide #19 models
> show #23 models
> hide #22 models
> show #24 models
> hide #23 models
> color sel & #24 bychain
> show #19 models
> hide #19 models
> show #23 models
> hide #24 models
> show #24 models
> show #22 models
> hide #23 models
> hide #24 models
> show #21 models
> show #23 models
> show #24 models
> hide #24 models
> hide #23 models
> hide #22 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> select /C
18212 atoms, 18468 bonds, 2333 residues, 19 models selected
> matchmaker #19,22-24 & sel to #21 & sel
Computing secondary structure
[Repeated 4 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_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
fold_motb_1x2_ibpax2_model_0.cif, chain C (#19), sequence alignment score =
692.7
RMSD between 101 pruned atom pairs is 0.566 angstroms; (across all 137 pairs:
16.843)
Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
fold_motb_1x2_ibpax2_model_2.cif, chain C (#22), sequence alignment score =
690.9
RMSD between 95 pruned atom pairs is 0.674 angstroms; (across all 137 pairs:
4.636)
Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
fold_motb_1x2_ibpax2_model_3.cif, chain C (#23), sequence alignment score =
684.3
RMSD between 93 pruned atom pairs is 0.441 angstroms; (across all 137 pairs:
4.461)
Matchmaker fold_motb_1x2_ibpax2_model_1.cif, chain C (#21) with
fold_motb_1x2_ibpax2_model_4.cif, chain C (#24), sequence alignment score =
684.9
RMSD between 95 pruned atom pairs is 0.438 angstroms; (across all 137 pairs:
4.124)
> hide #21 models
> show #21 models
> hide #19 models
> show #!18 models
> hide #!18 models
> show #19 models
> hide #21 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> hide #24 models
> hide #23 models
> hide #22 models
> show #22 models
> show #23 models
> select clear
> hide #22 models
> hide #23 models
> select /A/B
53443 atoms, 54481 bonds, 6767 residues, 24 models selected
> color sel & #19,21 bychain
> select clear
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #22 models
> show #23 models
> show #24 models
> hide #24 models
> hide #23 models
> show #23 models
> hide #21 models
> hide #22 models
> hide #23 models
> show #21 models
> show #19 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> select /A
26734 atoms, 27273 bonds, 3359 residues, 24 models selected
> rainbow sel & #19,21
> hide #21 models
> select /C
18212 atoms, 18468 bonds, 2333 residues, 19 models selected
> color sel & #19 bychain
> select clear
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #22 models
> hide #21 models
> show #23 models
> hide #22 models
> show #21 models
> hide #23 models
Drag select of 1 residues
> show #!18 models
> hide #!18 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> select /A
26734 atoms, 27273 bonds, 3359 residues, 24 models selected
> color sel & #21 bychain
> select /B
26709 atoms, 27208 bonds, 3408 residues, 24 models selected
> rainbow sel & #21
> select clear
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #21 models
> select /B
26709 atoms, 27208 bonds, 3408 residues, 24 models selected
> ui tool show "Color Actions"
> color sel medium slate blue
> color sel medium purple
> select clear
> show #21 models
> hide #19 models
> select /B
26709 atoms, 27208 bonds, 3408 residues, 24 models selected
> rainbow sel & #21
> select clear
> show #22 models
> show #23 models
> hide #22 models
> hide #21 models
> show #19 models
> show #22 models
> hide #22 models
> hide #23 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> show #21 models
> hide #19 models
> show #19 models
> hide #21 models
> select #19/B:48-54
45 atoms, 44 bonds, 7 residues, 1 model selected
> select #19/A:48-54
45 atoms, 44 bonds, 7 residues, 1 model selected
> color sel magenta
> select clear
> show #21 models
> hide #19 models
> select #21/B:48-54
45 atoms, 44 bonds, 7 residues, 1 model selected
> color sel magenta
> select clear
> show #19 models
> hide #21 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/DebbieH/MotB.1_IbpA/MotB.1_IbpA.cxs"
——— End of log from Thu Sep 25 11:20:40 2025 ———
opened ChimeraX session
> show #!8 models
> hide #!8 models
> show #!9 models
> show #10 models
> show #11 models
> show #!12 models
> show #!18 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> delete atoms #9-12,18-19,21-24
> delete bonds #9-12,18-19,21-24
> show #!13 models
> ui tool show "Color Actions"
> show #!14 models
> hide #!13 models
> hide #!14 surfaces
> show #15 models
> hide #!14 models
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #15 models
> hide #!13 models
> show #!6 models
> hide #!6 surfaces
> show #!13 models
> hide #!6 models
> ui tool show "Side View"
> select #13/L:31
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 20 atom styles
> select #13/M:158
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 21 atom styles
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #!6 models
> select #13/M:156
21 atoms, 23 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 21 atom styles
> show sel atoms
> select #13/M:158
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #13/L:32
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #13/L:33
42 atoms, 45 bonds, 2 residues, 2 models selected
> select add #13/L:34
61 atoms, 65 bonds, 3 residues, 2 models selected
> select add #13/L:35
82 atoms, 88 bonds, 4 residues, 2 models selected
> select add #13/L:36
104 atoms, 112 bonds, 5 residues, 2 models selected
> select add #13/L:37
123 atoms, 132 bonds, 6 residues, 2 models selected
> select add #13/M:156
144 atoms, 155 bonds, 7 residues, 2 models selected
> select add #13/M:155
163 atoms, 175 bonds, 8 residues, 3 models selected
> select add #13/M:153
185 atoms, 199 bonds, 9 residues, 3 models selected
> select add #13/M:152
205 atoms, 220 bonds, 10 residues, 3 models selected
> select add #13/M:151
224 atoms, 240 bonds, 11 residues, 3 models selected
> select add #13/M:150
246 atoms, 264 bonds, 12 residues, 3 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 246 atom styles
> show sel atoms
> select clear
Drag select of 2 residues
> select #13/L:33@C1'
1 atom, 1 residue, 1 model selected
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> select #13/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel light cyan
> select #13/M:146
19 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> select #13/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel honeydew
> color sel alice blue
> color sel powder blue
> color sel alice blue
> select #13/F:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #7 models
> hide #!13 models
> hide #7 models
> show #!6 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> select add #13/M:136
32 atoms, 33 bonds, 2 residues, 2 models selected
> select add #13/M:137
53 atoms, 56 bonds, 3 residues, 3 models selected
> select add #13/M:138
75 atoms, 80 bonds, 4 residues, 3 models selected
> select add #13/M:139
95 atoms, 101 bonds, 5 residues, 3 models selected
> select add #13/M:140
116 atoms, 124 bonds, 6 residues, 3 models selected
> select add #13/M:141
135 atoms, 144 bonds, 7 residues, 3 models selected
> select add #13/M:143
157 atoms, 168 bonds, 8 residues, 3 models selected
> select add #13/M:144
177 atoms, 189 bonds, 9 residues, 3 models selected
> select add #13/M:142
198 atoms, 212 bonds, 10 residues, 3 models selected
> select subtract #13/M:144
178 atoms, 191 bonds, 9 residues, 3 models selected
> label (#!13 & sel) attribute label_one_letter_code
> label height 3
> select clear
> select #13/F:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> ~label (#!13 & sel) residues
> select clear
> select #13/M:136
21 atoms, 23 bonds, 1 residue, 1 model selected
> ~label (#!13 & sel) residues
> select #13/L:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #!6 models
> hide #!13 models
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #!6 models
> select clear
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA1.AF3.png" width
> 922 height 681 supersample 4 transparentBackground true
> select #13/M:155
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #13/M:154
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 21 atom styles
> select clear
[Repeated 1 time(s)]
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.FOXA1bindingsite.png"
> width 922 height 681 supersample 4 transparentBackground true
> ui tool show "Color Actions"
Drag select of 6 residues
> select clear
> show #!6 models
> hide #!13 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> show #!8 models
> hide #!8 models
> show #!13 models
> hide #!6 models
> select #13/I:169-268
837 atoms, 863 bonds, 100 residues, 1 model selected
> show sel surfaces
> select #13/M:60
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #!6 models
> hide #!13 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> select clear
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> hide #!13 surfaces
> show #!6 models
> hide #!6,13 surfaces
> hide #!13 models
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> show sel surfaces
> ui tool show "Color Actions"
> select #6/I:40
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel silver
> color sel gray
> select clear
> select #6/I:40
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #6/I:40
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel light steel blue
> color sel light slate gray
> select clear
> hide #!6 surfaces
> select #6/O#13/I:168-269
1712 atoms, 1766 bonds, 204 residues, 2 models selected
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!13 & sel to #6 & 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 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 522.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
> matchmaker #!13 & sel to #6 & 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 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 522.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
> ui tool show Matchmaker
> matchmaker #!13 & sel to #6 & 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 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 522.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
> matchmaker #!13 & sel to #6 & 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 8vg1, chain O (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain I (#13), sequence
alignment score = 522.2
RMSD between 85 pruned atom pairs is 0.866 angstroms; (across all 102 pairs:
1.960)
> hide #!13 models
> select clear
[Repeated 4 time(s)]
> show #!13 models
> hide #!6 models
> select #6/O#13/J:269-321
1270 atoms, 1303 bonds, 155 residues, 2 models selected
> show #!6 models
> hide #!13 models
> select #6/T#13/J:269-321
829 atoms, 840 bonds, 4 pseudobonds, 107 residues, 3 models selected
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!13 & sel to #6 & 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 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4nombp_zn_model_0.cif, chain J (#13), sequence
alignment score = 265
RMSD between 43 pruned atom pairs is 0.539 angstroms; (across all 53 pairs:
10.483)
> select clear
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #13/M:138
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #13/M:139
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #13/M:138
42 atoms, 45 bonds, 2 residues, 2 models selected
> select add #13/M:140
63 atoms, 68 bonds, 3 residues, 2 models selected
> select add #13/M:141
82 atoms, 88 bonds, 4 residues, 2 models selected
> select add #13/J:226
89 atoms, 95 bonds, 5 residues, 2 models selected
> select add #13/M:142
110 atoms, 118 bonds, 6 residues, 3 models selected
> select add #13/M:143
132 atoms, 142 bonds, 7 residues, 3 models selected
> ~label (#!13 & sel) residues
> select #13/M:56
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #13/M:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> ~label (#!13 & sel) residues
> select clear
> show #7 models
> hide #7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!13 models
> select #6/J:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #6/J:132
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #6/J:131
39 atoms, 41 bonds, 2 residues, 2 models selected
> select add #6/J:130
60 atoms, 64 bonds, 3 residues, 2 models selected
> select add #6/J:129
80 atoms, 85 bonds, 4 residues, 2 models selected
> show sel atoms
> select clear
> select ::name="ZN"
12 atoms, 12 residues, 12 models selected
> show sel & #!6 atoms
> select clear
> select add #6/T:274
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/T:295
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #6/T:292
18 atoms, 15 bonds, 3 residues, 2 models selected
> select add #6/T:271
24 atoms, 20 bonds, 4 residues, 2 models selected
> show sel atoms
> select clear
> show #!13 models
> hide #!6 models
> select ::name="ZN"
12 atoms, 12 residues, 12 models selected
> show sel & #!13 atoms
[Repeated 1 time(s)]
> select ::name="ZN"
12 atoms, 12 residues, 12 models selected
> select ::name="ZN"
12 atoms, 12 residues, 12 models selected
> show sel & #!13 atoms
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> style sel & #!13 sphere
Changed 1 atom style
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
——— End of log from Mon Sep 29 00:14:22 2025 ———
opened ChimeraX session
> show #2 models
> hide #!13 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!6 models
> select #6/T#2/J:662-714
829 atoms, 840 bonds, 4 pseudobonds, 107 residues, 3 models selected
> show #!6 models
> ui tool show Matchmaker
> matchmaker #2 & sel to #6 & 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 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
alignment score = 274
RMSD between 43 pruned atom pairs is 0.482 angstroms; (across all 53 pairs:
7.477)
> hide #!6 models
> select #2/J:662-714
414 atoms, 420 bonds, 53 residues, 1 model selected
> select #2/J:393-900
3133 atoms, 3217 bonds, 443 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel light blue
> color sel pale turquoise
> select #2/J:662-714
414 atoms, 420 bonds, 53 residues, 1 model selected
> color sel deep sky blue
> select clear
> select #2/L
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> color sel light gray
> select clear
> select add #2/L:58
21 atoms, 23 bonds, 1 residue, 1 model selected
> select subtract #2/L:58
Nothing selected
> select add #2/L:58
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/L:57
41 atoms, 45 bonds, 2 residues, 1 model selected
> select add #2/L:56
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #2/L:55
84 atoms, 91 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> select clear
> select #2/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> color sel lavender
> select clear
> select #2/J:609-646
292 atoms, 299 bonds, 38 residues, 1 model selected
> color sel light green
> select clear
> select #2/J:609-646
292 atoms, 299 bonds, 38 residues, 1 model selected
> color sel lawn green
> color sel chartreuse
> color sel lawn green
> color sel lime
> color sel chartreuse
> color sel lawn green
> select clear
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> ui tool show "Side View"
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> select #2/J:664
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/J:667
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #2/J:688
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> style sel sphere
Changed 18 atom styles
> style sel ball
Changed 18 atom styles
> color sel yellow
> select clear
> select #2/J:685
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel ball
Changed 6 atom styles
> show sel atoms
> color sel yellow
> select clear
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.MBP-
> GATA4.zoom.png" width 922 height 681 supersample 4 transparentBackground
> true
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.MBP-
> GATA4-ZnFs.png" width 922 height 681 supersample 4 transparentBackground
> true
> select #6/A/B/C/D/E/F/G/H#2/A/B/C/D/E/F/G/H
13860 atoms, 14040 bonds, 1765 residues, 2 models selected
> show #!6 models
> ui tool show Matchmaker
> matchmaker #2 & sel to #6 & 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 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
0.242)
> select #2/J:529
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #2 models
> show #2 models
> hide #!6 models
> select #2/A/B/C/D/E/F/G/H
7708 atoms, 7806 bonds, 990 residues, 1 model selected
> select ~sel & ##selected
17314 atoms, 18505 bonds, 1686 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!6 models
> select #6/A/B/C/D/E/F/G/H
6152 atoms, 6234 bonds, 775 residues, 1 model selected
> select ~sel & ##selected
8282 atoms, 9167 bonds, 421 pseudobonds, 498 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> hide #2 models
> show #2 models
> hide #!6 models
> select #2/B
800 atoms, 808 bonds, 103 residues, 1 model selected
> color sel medium aquamarine
> color sel light green
> color sel pale green
> select clear
> select #2/B/F
1600 atoms, 1616 bonds, 206 residues, 1 model selected
> color sel pale green
> select clear
> show #!6 models
> select #6/A/B/C/D/E/F/G/H#2/A/B/C/D/E/F/G/H
13860 atoms, 14040 bonds, 1765 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #6 & 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 8vg1, chain E (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain A (#2), sequence
alignment score = 628.4
RMSD between 97 pruned atom pairs is 0.242 angstroms; (across all 97 pairs:
0.242)
> select clear
> hide #2 models
> select #6/B
662 atoms, 669 bonds, 83 residues, 1 model selected
> color sel forest green
> color sel green
> select clear
> show #2 models
> select clear
> hide #2 models
> show #2 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.histones.vs.AF3.png"
> width 922 height 681 supersample 4 transparentBackground true
> show #2#!6 cartoons
> hide #2 models
> show #2 models
> hide #!6 models
> select #13/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> show #2 cartoons
> select #13/J
3128 atoms, 3212 bonds, 442 residues, 1 model selected
> select #13/J
3128 atoms, 3212 bonds, 442 residues, 1 model selected
> select #2/I/J
9685 atoms, 9949 bonds, 1313 residues, 1 model selected
> show sel cartoons
> select clear
> select #2/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> select #2/I:
Expected an objects specifier or a keyword
> color sel lavender
> select clear
> select #2/IL
Nothing selected
> color light gray
> undo
> select #2/L
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> color sel light gray
> select clear
> select #2/I:
Expected an objects specifier or a keyword
> select #2/I
3502 atoms, 3604 bonds, 478 residues, 1 model selected
> select #2/I:168-269
856 atoms, 883 bonds, 102 residues, 1 model selected
> select clear
> select #2/I:168-269
856 atoms, 883 bonds, 102 residues, 1 model selected
> color sel medium purple
> select clear
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/L
Alignment identifier is 2/L
> sequence chain #2/M
Alignment identifier is 2/M
> ui tool show "Show Sequence Viewer"
> sequence chain #2/L
Destroying pre-existing alignment with identifier 2/L
Alignment identifier is 2/L
> select #2/L
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> color sel gray
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel light gray
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel light steel blue
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel gainsboro
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel white smoke
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel light gray
> color sel dark gray
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel white smoke
> color sel beige
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel gainsboro
> select clear
> select #2/M
3817 atoms, 4286 bonds, 186 residues, 1 model selected
> color sel alice blue
> color sel honeydew
> select clear
> select #2/L:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> color sel bynucleotide
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
> select #2/L
3811 atoms, 4270 bonds, 186 residues, 1 model selected
> select #2/L:55-58
84 atoms, 94 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 84 atom styles
> select #2/L:29-41
269 atoms, 301 bonds, 13 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/L
Alignment identifier is 2/L
> select #2/L:31
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/L:31-37
143 atoms, 159 bonds, 7 residues, 1 model selected
> color sel bynucleotide
> show sel atoms
> style sel ball
Changed 143 atom styles
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #!6 models
> select #2/J:1-330
2573 atoms, 2642 bonds, 330 residues, 1 model selected
> color sel light cyan
> select clear
> show #!6 models
> hide #!6 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.AF3.FOXA1.MBP-
> GATA4.png" width 922 height 681 supersample 4 transparentBackground true
> show #!6 models
> hide #2 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1.FOXA1.GATA4-2.png"
> width 922 height 681 supersample 4 transparentBackground true
> show #2 models
> hide #!6 models
Drag select of 83 atoms, 19 residues, 93 bonds
> nucleotides sel atoms
> style nucleic & sel stick
Changed 405 atom styles
> select #2/L:35@N1
1 atom, 1 residue, 1 model selected
Drag select of 56 atoms, 79 residues, 64 bonds
> nucleotides sel atoms
> style nucleic & sel stick
Changed 161 atom styles
> select #2/J:664-712
380 atoms, 386 bonds, 49 residues, 1 model selected
> show #!6 models
> select #6/T#2/J:664-712
795 atoms, 806 bonds, 4 pseudobonds, 103 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #6 & 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 8vg1, chain T (#6) with
fold_nucleosome_foxa1_gata4_zn_8vg1_model_0.cif, chain J (#2), sequence
alignment score = 256.6
RMSD between 41 pruned atom pairs is 0.479 angstroms; (across all 49 pairs:
5.360)
> hide #!6 models
> show #!8 models
> hide #2 models
> show #!6 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/O
Alignment identifier is 6/O
> sequence chain #6/T
Alignment identifier is 6/T
> select #6/O:168
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/O
856 atoms, 883 bonds, 102 residues, 1 model selected
> select clear
> select #6/T:269
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/T:269-321
414 atoms, 420 bonds, 53 residues, 1 model selected
> select clear
> select #6/T:269-321
414 atoms, 420 bonds, 53 residues, 1 model selected
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/CASP16/yet2solve/Fig/8VG1_nucleosome.cxs"
> save /Users/taic/mine/Job/project/CASP16/AF3/8VG1.cxs
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
opened ChimeraX session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_0.cif
Chain information for fold_rcsdx2_model_0.cif #4
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_1.cif
Chain information for fold_rcsdx2_model_1.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_2.cif
Chain information for fold_rcsdx2_model_2.cif #9
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_3.cif
Chain information for fold_rcsdx2_model_3.cif #11
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_4.cif
Chain information for fold_rcsdx2_model_4.cif #12
---
Chain | Description
A B | .
Computing secondary structure
> hide #!2 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #5 models
> hide #9 models
> hide #11 models
> hide #12 models
> color #4 bychain
> show #5 models
> hide #4 models
> hide #5 models
> show #4 models
> show #!2 models
> hide #4 models
> show #12 models
> hide #!2 models
> show #11 models
> select add #11
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> select add #12
28232 atoms, 28704 bonds, 3560 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> show #5 models
> select add #5
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #9 models
> select add #9
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #4 models
> hide #4 models
> show #!2 models
> hide #!2 models
> show #1 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_1.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_2.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_3.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_4.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/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.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/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_0.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_0.cif #5
---
Chain | Description
A | .
B C | .
D E | .
> hide #1,5 surfaces
> show #1,5 cartoons
Computing secondary structure
> hide #1,5 surfaces
> select add #5
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> style sel stick
Changed 34679 atom styles
> hide sel atoms
> select clear
> hide #1 models
> color #5 bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_1.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_1.cif #9
---
Chain | Description
A | .
B C | .
D E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_4.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_4.cif #11
---
Chain | Description
A | .
B C | .
D E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_2.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_2.cif #12
---
Chain | Description
A | .
B C | .
D E | .
> show #5,9,11-12 cartoons
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_3.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_3.cif #13
---
Chain | Description
A | .
B C | .
D E | .
> hide #5,9,11-13 atoms
> hide #5 models
> hide #9 models
> show #9 models
> hide #11 models
> hide #12 models
> hide #13 models
> color #9 bychain
> show #11 models
> hide #9 models
> color #11 bychain
> show #12 models
> hide #11 models
> color #12 bychain
> select add #12
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #13 models
> select add #13
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> show #11 models
> hide #13 models
> select subtract #13
Nothing selected
> show #13 models
> hide #11 models
> select add #13
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #11 models
> show #9 models
> show #10 models
> hide #9 models
> hide #11 models
> show #11 models
> hide #10 models
> show #!2 models
> hide #11 models
> show #10 models
> hide #!2 models
> show #9 models
> hide #10 models
> show #1 models
> show #!2 models
> hide #1 models
> hide #9 models
> show #9 models
> hide #!2 models
> show #4 models
> hide #9 models
> select add #4
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #7 models
> show #8 models
> hide #8 models
> hide #7 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.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/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.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
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_0.cif
Chain information for fold_rcsdx2_rcscx2_model_0.cif #4
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> color #4 bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_1.cif
Chain information for fold_rcsdx2_rcscx2_model_1.cif #12
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_3.cif
Chain information for fold_rcsdx2_rcscx2_model_3.cif #13
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_4.cif
Chain information for fold_rcsdx2_rcscx2_model_4.cif #14
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_2.cif
Chain information for fold_rcsdx2_rcscx2_model_2.cif #15
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #4 models
> hide #13 models
> hide #14 models
> hide #15 models
> color #12 bychain
> hide #12 models
> show #13 models
> color #13 bychain
> show #14 models
> hide #13 models
> color #14 bychain
> show #15 models
> hide #14 models
> color #15 bychain
> show #14 models
> hide #15 models
> show #4 models
> hide #14 models
> show #12 models
> hide #12 models
> show #12 models
> hide #4 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> hide #15 models
> show #15 models
> show #4 models
> hide #15 models
> show #12 models
> hide #4 models
> show #9 models
> hide #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/D
Alignment identifier is 9/D
> select
> #9/D:91-96,99-103,110-114,144-148,155-159,197-199,203-205,210-219,227-234,248-252,270-274,278-285,290-297,367-372,377-381,407-412,415-423,430-437,525-528,550-555,562-565,589-596,603-610,657-663,667-675,695-699,719-721,734-737,747-751,757-761,764-768
1522 atoms, 1520 bonds, 183 residues, 1 model selected
> hide #9 models
> show #7 models
> show #1 models
> hide #7 models
> color #1 bychain
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> rainbow sel & #1
> select clear
> show #4 models
> hide #4 models
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> ui tool show Matchmaker
> matchmaker #4-15#!2 & sel 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_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> matchmaker #4-15#!2 & sel 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_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> matchmaker #4-15#!2 & sel 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_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> 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
> show #13 models
> show #14 models
> show #15 models
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> rainbow sel
> 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
> hide #13 models
> hide #14 models
> hide #15 models
> select clear
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #1 models
> show #4 models
> hide #!2 models
> show #5 models
> hide #4 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> show #5 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #5 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #15 models
> show #5 models
> hide #!2 models
> show #12 models
> hide #5 models
> show #13 models
> hide #12 models
> hide #13 models
> show #14 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #15 models
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> color #!2 bychain
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> select ~sel & ##selected
15100 atoms, 15353 bonds, 1028 pseudobonds, 1914 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> show sel cartoons
> select ~sel & ##selected
19719 atoms, 20089 bonds, 1028 pseudobonds, 2491 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> rainbow sel
> hide sel cartoons
> select #2/C/D
14116 atoms, 14352 bonds, 638 pseudobonds, 1780 residues, 2 models selected
> show sel cartoons
> rainbow sel
> select clear
> hide #!2 cartoons
> show #!2 cartoons
> color #!2 bychain
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> color sel bychain
> select clear
> color #!2 bychain
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> rainbow sel
> select clear
> show #9 models
> hide #!2 models
> show #!2 models
> hide #9 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_3.cif
Chain information for fold_rcsdx2_rcsbx2_model_3.cif #16
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_4.cif
Chain information for fold_rcsdx2_rcsbx2_model_4.cif #17
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_0.cif
Chain information for fold_rcsdx2_rcsbx2_model_0.cif #18
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #!2 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_1.cif
Chain information for fold_rcsdx2_rcsbx2_model_1.cif #19
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_2.cif
Chain information for fold_rcsdx2_rcsbx2_model_2.cif #20
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #16 models
> hide #17 models
> hide #19 models
> hide #20 models
> color #18 bychain
> show #19 models
> hide #18 models
> color #19 bychain
> show #20 models
> hide #19 models
> color #20 bychain
> show #17 models
> hide #20 models
> color #17 bychain
> show #1 models
> hide #17 models
> show #4 models
> hide #1 models
> show #1 models
> hide #1 models
> color #4 bychain
> select #4/B
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> select #4/C
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> rainbow sel
> select clear
> select #4/A/B/C
21596 atoms, 21969 bonds, 2729 residues, 1 model selected
> hide sel cartoons
> undo
> select #4/A/B/D
21596 atoms, 21969 bonds, 2729 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> color #4 bychain
> select #4/A
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select clear
> select #4/B/C/D
22018 atoms, 22410 bonds, 2788 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #4/D
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> rainbow sel
> select clear
> select #4/D
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> select clear
> hide #4 models
> show #1 models
> color #1 bychain
> select #1/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #8 models
> hide #1 models
Drag select of 12 residues
Drag select of 1 residues
> show #3 models
Drag select of 3 atoms, 5 residues
> select #8/A:472
8 atoms, 7 bonds, 1 residue, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 69358 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #3 models
> show #4 models
> hide #8 models
> select #4/A/B
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> rainbow sel
> select clear
> color #4 bychain
> select #4/A/B
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> rainbow sel
> select clear
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> color #4,12-15 bychain
> select #4/A/B#12/A/B#13/A/B#14/A/B#15/A/B
70580 atoms, 71760 bonds, 8900 residues, 5 models selected
> rainbow sel
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> select clear
> hide #4 models
> show #12 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #15 models
> color #5 bychain
> select #5/B/C
14960 atoms, 15234 bonds, 1898 residues, 1 model selected
> rainbow sel
> select clear
> hide #5 models
> show #4 models
> show #!2 models
> hide #4 models
Drag select of 18 residues
> show #4 models
> hide #!2 models
> show #12 models
> hide #4 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> hide #15 models
> show #12 models
> show #4 models
> hide #12 models
> show #13 models
> hide #4 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #12 models
> hide #15 models
> show #!2 models
> hide #12 models
Drag select of 6 residues
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #2 magenta
> undo
> select #2/C:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #3 models
> select #2/C:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #2/C:410
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) yellow
> ui tool show "Color Actions"
> color sel green yellow
> select clear
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> select clear
> select #2/C:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/C:414
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cornflower blue
> select add #2/C:413
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #2/C:414
21 atoms, 18 bonds, 3 residues, 3 models selected
> color (#!2 & sel) yellow
> select clear
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select clear
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> color sel bychain
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light steel blue
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel burly wood
> color sel rosy brown
> color sel tan
> color sel dark salmon
> color sel peru
> color sel dark goldenrod
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> color sel light slate gray
> select clear
> select #2/D
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light steel blue
> select clear
Drag select of 4 residues
> select clear
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/A:96
12 atoms, 10 bonds, 2 residues, 2 models selected
> select subtract #2/A:96
5 atoms, 4 bonds, 1 residue, 2 models selected
> select add #2/A:96
12 atoms, 10 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cyan
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> undo
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel gray
> color sel silver
> color sel dark gray
> select clear
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> color sel deep sky blue
> select add #2/C:411
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #2/C:413
31 atoms, 27 bonds, 4 residues, 3 models selected
> select add #2/C:414
39 atoms, 34 bonds, 5 residues, 3 models selected
> color sel plum
> color sel pale violet red
> color sel magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> color sel deep sky blue
> select clear
> select add #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/C:413
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #2/C:414
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #2/A:97
34 atoms, 30 bonds, 4 residues, 2 models selected
> select add #2/A:94
39 atoms, 34 bonds, 5 residues, 3 models selected
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
> hide #3 models
> show #3 models
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
---
note | Fetching CCD CO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CO/CO.cif
Chain information for fold_hqba_yhbq_co_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
Chain information for fold_hqba_yhbq_co_model_1.cif #2
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
Chain information for fold_hqba_yhbq_co_model_2.cif #3
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
Chain information for fold_hqba_yhbq_co_model_3.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
Chain information for fold_hqba_yhbq_co_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
Chain information for fold_hqba_yhbp_co_model_0.cif #6
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
Chain information for fold_hqba_yhbp_co_model_2.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
Chain information for fold_hqba_yhbp_co_model_3.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
Chain information for fold_hqba_yhbp_co_model_4.cif #10
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
Chain information for fold_hqba_ubiu_model_0.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
Chain information for fold_hqba_ubiu_model_1.cif #12
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
Chain information for fold_hqba_ubiu_model_2.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
Chain information for fold_hqba_ubiu_model_3.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
Chain information for fold_hqba_ubiu_model_4.cif #15
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
---
note | Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif
Chain information for fold_hqba_nfua_fe4_co_model_0.cif #16
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_1.cif
Chain information for fold_hqba_nfua_fe4_co_model_1.cif #17
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_2.cif
Chain information for fold_hqba_nfua_fe4_co_model_2.cif #18
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_3.cif
Chain information for fold_hqba_nfua_fe4_co_model_3.cif #19
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_4.cif
Chain information for fold_hqba_nfua_fe4_co_model_4.cif #20
---
Chain | Description
A | .
B | .
Computing secondary structure
> color bychain
> select /AA
Nothing selected
> select /A
26220 atoms, 26820 bonds, 3340 residues, 20 models selected
> ui tool show Matchmaker
> matchmaker #2-20 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_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
0.416)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
0.283)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
0.340)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
0.303)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4
RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
0.452)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4
RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
0.507)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
0.304)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
0.350)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
0.343)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
0.286)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
0.302)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
0.276)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
0.268)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
0.331)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
0.226)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
871.4
RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
0.589)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
0.390)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
849.8
RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
0.211)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> open 4RS2 fromDatabase pdb format mmcif
Summary of feedback from opening 4RS2 fetched from pdb
---
notes | Fetching compressed mmCIF 4rs2 from http://files.rcsb.org/download/4rs2.cif
Fetching CCD COA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #21
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #21
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /A
27898 atoms, 28311 bonds, 3744 residues, 21 models selected
> ui tool show Matchmaker
> matchmaker #21 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_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> select clear
> select #21/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 8 GLN B 8 GLU B 18 1 11
Start residue of secondary structure not found: HELIX 9 9 LYS B 56 ALA B 58 1
3
Start residue of secondary structure not found: HELIX 10 10 GLN C 8 GLU C 18 1
11
Start residue of secondary structure not found: HELIX 11 11 LYS C 56 ALA C 58
1 3
Start residue of secondary structure not found: HELIX 12 12 SER C 72 ASN C 74
1 3
39 messages similar to the above omitted
Chain information for Hfq6_YhbS.af2.4rs2.pdb
---
Chain | Description
22.1/A | No description available
22.2/A | No description available
22.1/B 22.1/C 22.1/D 22.1/E 22.1/F 22.1/G | No description available
22.2/B | No description available
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #1-5,21#!22.1-2 atoms
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.1 models
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!22.2 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_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> hide #21 models
> show #21 models
> ui tool show Matchmaker
> matchmaker #!22.1-2 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_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain A (#22.1), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> hide #21 models
> show #21 models
> hide #21 models
> show #21 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #21 models
> select add #22
16588 atoms, 16330 bonds, 40 pseudobonds, 1769 residues, 6 models selected
> delete atoms (#!22.1-2 & sel)
> delete bonds (#!22.1-2 & sel)
> show #21 models
> select add #21
4709 atoms, 4356 bonds, 990 residues, 3 models selected
> select subtract #21
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> hide #22 models
> hide #21 models
> select subtract #22
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show #22 models
> select add #22
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> select add #1
2107 atoms, 2148 bonds, 268 residues, 2 models selected
> select subtract #1
1 model selected
> show #1 models
> hide #1 models
> delete atoms #22
> delete bonds #22
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/AF2-multi/Hfq6mer_YhbS/YhbS-
> Hfq6mer.ranked_0.pdb
Chain information for YhbS-Hfq6mer.ranked_0.pdb #23
---
Chain | Description
A | No description available
B C D E F G | No description available
> hide #23 atoms
> show #23 cartoons
Computing secondary structure
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2-21,23 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_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
0.416)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
0.283)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
0.340)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
0.303)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4
RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
0.452)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4
RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
0.507)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
0.304)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
0.350)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
0.343)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
0.286)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
0.302)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
0.276)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
0.268)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
0.331)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
0.226)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
871.4
RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
0.589)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
0.390)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
849.8
RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
0.211)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> hide #22 models
> show #1 models
> hide #1 models
> select #23/B
1552 atoms, 1566 bonds, 102 residues, 1 model selected
> Sel #23/B/C/D/E/F/G
Unknown command: Sel #23/B/C/D/E/F/G
> Sel #23/B#23/C#23/D#23/E#23/F#23/G
Unknown command: Sel #23/B#23/C#23/D#23/E#23/F#23/G
> select #23/B#23/C#23/D#23/E#23/F#23/G
9312 atoms, 9396 bonds, 612 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel royal blue
> color sel dodger blue
> color sel royal blue
> select clear
> show #21 models
> select #21
3398 atoms, 3015 bonds, 823 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide #23 models
> delete atoms sel
> delete bonds sel
> open 4RS2 fromDatabase pdb format mmcif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #21
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #21
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #23 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_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> matchmaker #23 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_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> show #1 models
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> matchmaker #21 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_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> select #21/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #21 models
> select #1
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> show sel atoms
> select #1/C:1@CO
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
2106 atoms, 2148 bonds, 267 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/C:1@CO
1 atom, 1 residue, 1 model selected
> select ::name="CO"
15 atoms, 15 residues, 15 models selected
> ui tool show "Color Actions"
> color sel dim gray
> select clear
> show #21 models
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_0.cif
Chain information for fold_hqba_hfq1_65x6_co_model_0.cif #24
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_1.cif
Chain information for fold_hqba_hfq1_65x6_co_model_1.cif #25
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_2.cif
Chain information for fold_hqba_hfq1_65x6_co_model_2.cif #26
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_3.cif
Chain information for fold_hqba_hfq1_65x6_co_model_3.cif #27
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_4.cif
Chain information for fold_hqba_hfq1_65x6_co_model_4.cif #28
---
Chain | Description
A | .
B C D E F G | .
> hide #21 models
> select #24#25#26#27#28
22010 atoms, 22395 bonds, 2790 residues, 5 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
Chain information for fold_hqba_hfqx6_co_model_0.cif #29
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
Chain information for fold_hqba_hfqx6_co_model_1.cif #30
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
Chain information for fold_hqba_hfqx6_co_model_2.cif #31
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
Chain information for fold_hqba_hfqx6_co_model_3.cif #32
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
Chain information for fold_hqba_hfqx6_co_model_4.cif #33
---
Chain | Description
A | .
B C D E F G | .
> select add #29
28038 atoms, 28536 bonds, 3570 residues, 6 models selected
> select add #30
34066 atoms, 34677 bonds, 4350 residues, 7 models selected
> select add #31
40094 atoms, 40818 bonds, 5130 residues, 8 models selected
> select add #32
46122 atoms, 46959 bonds, 5910 residues, 9 models selected
> select add #33
52150 atoms, 53100 bonds, 6690 residues, 10 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select #1
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #24-33 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_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_0.cif, chain A (#24), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.225 angstroms; (across all 167 pairs:
0.225)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_1.cif, chain A (#25), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.181 angstroms; (across all 167 pairs:
0.181)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_2.cif, chain A (#26), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.299 angstroms; (across all 167 pairs:
0.299)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_3.cif, chain A (#27), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.368 angstroms; (across all 167 pairs:
0.368)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_4.cif, chain A (#28), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.255 angstroms; (across all 167 pairs:
0.255)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#29), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
0.202)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_1.cif, chain A (#30), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.220 angstroms; (across all 167 pairs:
0.220)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_2.cif, chain A (#31), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_3.cif, chain A (#32), sequence alignment score =
868.4
RMSD between 167 pruned atom pairs is 0.264 angstroms; (across all 167 pairs:
0.264)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_4.cif, chain A (#33), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.315 angstroms; (across all 167 pairs:
0.315)
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> hide #25 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #30 models
> hide #31 models
> show #31 models
> show #30 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> hide #25 models
> hide #24 models
> hide #33 models
> hide #29 models
> show #25 models
> show #33 models
> select add #24
5713 atoms, 5820 bonds, 725 residues, 2 models selected
> select subtract #24
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select add #25
5713 atoms, 5820 bonds, 725 residues, 2 models selected
> select add #26
10115 atoms, 10299 bonds, 1283 residues, 3 models selected
> select add #27
14517 atoms, 14778 bonds, 1841 residues, 4 models selected
> select add #28
18919 atoms, 19257 bonds, 2399 residues, 5 models selected
> select add #30
24947 atoms, 25398 bonds, 3179 residues, 6 models selected
> select add #31
30975 atoms, 31539 bonds, 3959 residues, 7 models selected
> select add #32
37003 atoms, 37680 bonds, 4739 residues, 8 models selected
> select add #33
43031 atoms, 43821 bonds, 5519 residues, 9 models selected
> select add #1
43827 atoms, 44628 bonds, 5620 residues, 9 models selected
> hide #1 models
> select subtract #1
41720 atoms, 42480 bonds, 5352 residues, 8 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #21 models
> hide #21 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select ::name="CO"
17 atoms, 17 residues, 17 models selected
> show sel & #1-5 atoms
> select #4/A:32
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> ui tool show "Color Actions"
> color sel magenta
> select clear
> select add #2
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> select add #3
4214 atoms, 4296 bonds, 536 residues, 2 models selected
> select add #4
6321 atoms, 6444 bonds, 804 residues, 3 models selected
> select add #5
8428 atoms, 8592 bonds, 1072 residues, 4 models selected
> select clear
> show #21 models
> select #21/B:-10
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #21/B:0
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add #21/B:-1
29 atoms, 27 bonds, 3 residues, 1 model selected
> select add #21/B:-2
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #21/B:-3
41 atoms, 38 bonds, 5 residues, 1 model selected
> select add #21/B:-4
49 atoms, 45 bonds, 6 residues, 1 model selected
> select add #21/B:-5
56 atoms, 51 bonds, 7 residues, 1 model selected
> select add #21/B:-6
66 atoms, 61 bonds, 8 residues, 1 model selected
> select add #21/B:-7
76 atoms, 71 bonds, 9 residues, 1 model selected
> select add #21/B:-8
86 atoms, 81 bonds, 10 residues, 1 model selected
> select add #21/B:-9
96 atoms, 91 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select clear
> select ::name="HIS"
3382 atoms, 3436 bonds, 313 residues, 24 models selected
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #21 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #4 models
> hide #2 models
> hide #3 models
> hide #5 models
> select #1/A:32
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel magenta
> hide sel atoms
> show sel atoms
> select clear
> show #21 models
> show #29 models
> hide #21 models
> hide #1 models
> show #23 models
> hide #29 models
> select #23/G:30
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #23/G:31
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> show #29 models
> hide #23 models
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #23 models
> hide #23 models
> show #1 models
> hide #1 models
> color sel cornflower blue
> select clear
> show #23 models
> hide #29 models
> show #29 models
> hide #23 models
> hide #29 models
> show #29 models
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
> ui tool show "Color Actions"
> color sel pale violet red
> color sel light pink
> color sel hot pink
> color sel plum
> select clear
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel plum
> color sel violet
> select clear
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #29/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #29/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
Drag select of 3 residues
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #29/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium blue
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> show #23 models
> select #23/C:31
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> hide #23 models
> select #29/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> color sel tan
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel royal blue
> select #29/G:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #21 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni.cxs
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_0.cif
Chain information for fold_azor_monomer_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_1.cif
Chain information for fold_azor_monomer_model_1.cif #2
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_2.cif
Chain information for fold_azor_monomer_model_2.cif #3
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_3.cif
Chain information for fold_azor_monomer_model_3.cif #4
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_4.cif
Chain information for fold_azor_monomer_model_4.cif #5
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
---
note | Fetching CCD FAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FAD/FAD.cif
Chain information for fold_azor_monomer_fad_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> rainbow
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
Chain information for fold_azor_monomer_fad_model_1.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
Chain information for fold_azor_monomer_fad_model_2.cif #8
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif
Chain information for fold_azor_monomer_fad_model_3.cif #9
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif
Chain information for fold_azor_monomer_fad_model_4.cif #10
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif
---
note | Fetching CCD NAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif
Chain information for fold_azor_monomer_nad_model_0.cif #11
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_1.cif
Chain information for fold_azor_monomer_nad_model_1.cif #12
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_2.cif
Chain information for fold_azor_monomer_nad_model_2.cif #13
---
Chain | Description
A | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_3.cif
Chain information for fold_azor_monomer_nad_model_3.cif #14
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_4.cif
Chain information for fold_azor_monomer_nad_model_4.cif #15
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #2-12 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_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_1.cif, chain A (#2), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
0.117)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_2.cif, chain A (#3), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
0.103)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_3.cif, chain A (#4), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
0.129)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_4.cif, chain A (#5), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
0.121)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_1.cif, chain A (#7), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_2.cif, chain A (#8), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
0.447)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_3.cif, chain A (#9), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
0.420)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_4.cif, chain A (#10), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
0.291)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_1.cif, chain A (#12), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.353 angstroms; (across all 208 pairs:
0.353)
> matchmaker #13-15 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_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_2.cif, chain A (#13), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.368 angstroms; (across all 208 pairs:
0.368)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_3.cif, chain A (#14), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.329 angstroms; (across all 208 pairs:
0.329)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_4.cif, chain A (#15), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.287 angstroms; (across all 208 pairs:
0.287)
> select add #2
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> select add #3
3292 atoms, 3370 bonds, 416 residues, 2 models selected
> select add #4
4938 atoms, 5055 bonds, 624 residues, 3 models selected
> select add #5
6584 atoms, 6740 bonds, 832 residues, 4 models selected
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> delete atoms sel
> delete bonds sel
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> hide #1 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> select add #7
1699 atoms, 1743 bonds, 209 residues, 1 model selected
> select add #8
3398 atoms, 3486 bonds, 418 residues, 2 models selected
> select add #9
5097 atoms, 5229 bonds, 627 residues, 3 models selected
> select add #10
6796 atoms, 6972 bonds, 836 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #11 models
> hide #6 models
> show #12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> show #13 models
> show #14 models
> show #15 models
> select add #12
1690 atoms, 1733 bonds, 209 residues, 1 model selected
> select add #13
3380 atoms, 3466 bonds, 418 residues, 2 models selected
> select add #14
5070 atoms, 5199 bonds, 627 residues, 3 models selected
> select add #15
6760 atoms, 6932 bonds, 836 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #6 models
> hide #6 models
> hide #11 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_0.cif
Chain information for fold_azor_dimer_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_1.cif
Chain information for fold_azor_dimer_model_1.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_2.cif
Chain information for fold_azor_dimer_model_2.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_3.cif
Chain information for fold_azor_dimer_model_3.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_4.cif
Chain information for fold_azor_dimer_model_4.cif #7
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-7,11 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_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_1.cif, chain A (#3), sequence alignment score = 1080.8
RMSD between 208 pruned atom pairs is 0.383 angstroms; (across all 208 pairs:
0.383)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_2.cif, chain A (#4), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.452 angstroms; (across all 208 pairs:
0.452)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_3.cif, chain A (#5), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.377 angstroms; (across all 208 pairs:
0.377)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_4.cif, chain A (#7), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.371 angstroms; (across all 208 pairs:
0.371)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
> show #6 models
> hide #2 models
> show #2 models
> hide #7 models
> hide #6 models
> show #7 models
> select add #3
3292 atoms, 3370 bonds, 416 residues, 1 model selected
> select add #4
6584 atoms, 6740 bonds, 832 residues, 2 models selected
> select add #5
9876 atoms, 10110 bonds, 1248 residues, 3 models selected
> select add #7
13168 atoms, 13480 bonds, 1664 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> hide #1 models
> show #6 models
> hide #2 models
> select /A
6584 atoms, 6740 bonds, 832 residues, 4 models selected
> show sel & #6 surfaces
> show #2 models
> select /B
1743 atoms, 1791 bonds, 210 residues, 3 models selected
> hide #2 models
> show #2 models
> select #2/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> hide #!6 models
> show #1 models
> show #!6 models
> hide #1 models
> hide #!6 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_0.cif
Chain information for fold_azor_dimer_fad_model_0.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_1.cif
Chain information for fold_azor_dimer_fad_model_1.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_2.cif
Chain information for fold_azor_dimer_fad_model_2.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> hide sel surfaces
> ui tool show Matchmaker
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_3.cif
Chain information for fold_azor_dimer_fad_model_3.cif #7
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_4.cif
Chain information for fold_azor_dimer_fad_model_4.cif #8
---
Chain | Description
A B | .
Computing secondary structure
> matchmaker #3-5,7-8#!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_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_1.cif, chain A (#4), sequence alignment score = 1049
RMSD between 208 pruned atom pairs is 0.456 angstroms; (across all 208 pairs:
0.456)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_2.cif, chain A (#5), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.435 angstroms; (across all 208 pairs:
0.435)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_3.cif, chain A (#7), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.408 angstroms; (across all 208 pairs:
0.408)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_4.cif, chain A (#8), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.428 angstroms; (across all 208 pairs:
0.428)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_0.cif
Chain information for fold_hqba_hfqx6_vcholera_model_0.cif #1
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_1.cif
Chain information for fold_hqba_hfqx6_vcholera_model_1.cif #2
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_2.cif
Chain information for fold_hqba_hfqx6_vcholera_model_2.cif #3
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_3.cif
Chain information for fold_hqba_hfqx6_vcholera_model_3.cif #4
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/fold_hqba_hfqx6_vcholera/fold_hqba_hfqx6_vcholera_model_4.cif
Chain information for fold_hqba_hfqx6_vcholera_model_4.cif #5
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
Chain information for fold_hqba_hfqx6_co_model_0.cif #6
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
Chain information for fold_hqba_hfqx6_co_model_1.cif #7
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
Chain information for fold_hqba_hfqx6_co_model_2.cif #8
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
Chain information for fold_hqba_hfqx6_co_model_3.cif #9
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
Chain information for fold_hqba_hfqx6_co_model_4.cif #10
---
Chain | Description
A | .
B C D E F G | .
> hide atoms
> show cartoons
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-10 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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_1.cif, chain A (#2), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.168 angstroms; (across all 167 pairs:
0.168)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_2.cif, chain A (#3), sequence alignment score =
863.8
RMSD between 167 pruned atom pairs is 0.134 angstroms; (across all 167 pairs:
0.134)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_3.cif, chain A (#4), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.135 angstroms; (across all 167 pairs:
0.135)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_4.cif, chain A (#5), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.121 angstroms; (across all 167 pairs:
0.121)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3
RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
0.862)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_1.cif, chain A (#7), sequence alignment score = 569.3
RMSD between 162 pruned atom pairs is 0.700 angstroms; (across all 167 pairs:
0.870)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_2.cif, chain A (#8), sequence alignment score = 569.3
RMSD between 162 pruned atom pairs is 0.670 angstroms; (across all 167 pairs:
0.842)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_3.cif, chain A (#9), sequence alignment score = 572.9
RMSD between 161 pruned atom pairs is 0.684 angstroms; (across all 167 pairs:
0.877)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_4.cif, chain A (#10), sequence alignment score =
569.3
RMSD between 162 pruned atom pairs is 0.660 angstroms; (across all 167 pairs:
0.836)
> matchmaker #2-10 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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_1.cif, chain A (#2), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.168 angstroms; (across all 167 pairs:
0.168)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_2.cif, chain A (#3), sequence alignment score =
863.8
RMSD between 167 pruned atom pairs is 0.134 angstroms; (across all 167 pairs:
0.134)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_3.cif, chain A (#4), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.135 angstroms; (across all 167 pairs:
0.135)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_vcholera_model_4.cif, chain A (#5), sequence alignment score =
867.4
RMSD between 167 pruned atom pairs is 0.121 angstroms; (across all 167 pairs:
0.121)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3
RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
0.862)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_1.cif, chain A (#7), sequence alignment score = 569.3
RMSD between 162 pruned atom pairs is 0.700 angstroms; (across all 167 pairs:
0.870)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_2.cif, chain A (#8), sequence alignment score = 569.3
RMSD between 162 pruned atom pairs is 0.670 angstroms; (across all 167 pairs:
0.842)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_3.cif, chain A (#9), sequence alignment score = 572.9
RMSD between 161 pruned atom pairs is 0.684 angstroms; (across all 167 pairs:
0.877)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_4.cif, chain A (#10), sequence alignment score =
569.3
RMSD between 162 pruned atom pairs is 0.660 angstroms; (across all 167 pairs:
0.836)
> select add #7
6028 atoms, 6141 bonds, 780 residues, 1 model selected
> select add #8
12056 atoms, 12282 bonds, 1560 residues, 2 models selected
> select add #9
18084 atoms, 18423 bonds, 2340 residues, 3 models selected
> select add #10
24112 atoms, 24564 bonds, 3120 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> hide #6 models
> show #6 models
> hide #6 models
> select add #2
5420 atoms, 5522 bonds, 689 residues, 1 model selected
> select add #3
10840 atoms, 11044 bonds, 1378 residues, 2 models selected
> select add #4
16260 atoms, 16566 bonds, 2067 residues, 3 models selected
> select add #5
21680 atoms, 22088 bonds, 2756 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #6 models
> ui tool show Matchmaker
> select #B
Expected an objects specifier or a keyword
> select /B
1474 atoms, 1501 bonds, 189 residues, 2 models selected
No reference and/or match structure/chain chosen
> hide #1 models
> show #1 models
> matchmaker #6 & sel 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_hqba_hfqx6_vcholera_model_0.cif, chain B (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain B (#6), sequence alignment score = 372.4
RMSD between 69 pruned atom pairs is 0.218 angstroms; (across all 87 pairs:
5.281)
> matchmaker #6 & sel 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_hqba_hfqx6_vcholera_model_0.cif, chain B (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain B (#6), sequence alignment score = 372.4
RMSD between 69 pruned atom pairs is 0.218 angstroms; (across all 87 pairs:
5.281)
> select clear
No reference and/or match structure/chain chosen
> matchmaker #6 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3
RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
0.862)
> matchmaker #6 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3
RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
0.862)
> select /B
1474 atoms, 1501 bonds, 189 residues, 2 models selected
> hide #6 models
> select #1/D:22
7 atoms, 6 bonds, 1 residue, 1 model selected
> select .31
Expected an objects specifier or a keyword
> select clear
> select #1/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> show #6 models
> hide #1 models
> select #6/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> show #1 models
> hide #1 models
> select #6/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select #6/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel medium blue
> select #6/A:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> color sel gray
> ui tool show "Color Actions"
> color sel dark khaki
> select clear
> select #6/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium blue
> select clear
> show #1 models
> hide #6 models
> select #1/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel medium blue
> select clear
> show #6 models
> hide #6 models
> select #1/A:98
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> show sel atoms
> color sel orange
> show #6 models
> hide #6 models
> select #1/A:99
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> ui tool show Contacts
> show #6 models
> hide #1 models
> hide #6 models
> show #1 models
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> show #6 models
> select /A
2603 atoms, 2657 bonds, 334 residues, 2 models selected
> contacts sel saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
> restrict both resSeparation 5 interModel false intraMol false
> ignoreHiddenModels true color #c7ff92 radius 0.06 reveal true
No contacts
> hide #6 models
> select clear
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #1/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:98
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/C:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 20
> label height 6
> label height 3
> label height 2
> select clear
> show #6 models
> hide #!1 models
> show #!1 models
> hide #6 models
> show #6 models
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #6 models
> select #1
5420 atoms, 5522 bonds, 689 residues, 2 models selected
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4128 atoms, 4206 bonds, 522 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray
> select clear
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> color sel orange
> select #1/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:98
15 atoms, 13 bonds, 2 residues, 1 model selected
> color sel magenta
> select #1/C:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/C:31
17 atoms, 15 bonds, 2 residues, 1 model selected
> select clear
> select add #1/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium blue
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 11397 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select add #1/A:98
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:102
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/C:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> select add #1/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:98
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/C:31
24 atoms, 21 bonds, 3 residues, 1 model selected
> ~label sel residues
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.png
> width 600 height 417 supersample 4 transparentBackground true
> open 4RS2 fromDatabase pdb format mmcif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #3
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #3
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> matchmaker #3 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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
B (#3), sequence alignment score = 540.5
RMSD between 157 pruned atom pairs is 0.811 angstroms; (across all 167 pairs:
1.074)
> select #3/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #3/B
1720 atoms, 1524 bonds, 419 residues, 1 model selected
> hide sel cartoons
> select clear
> hide #1,3 atoms
> show #1,3 atoms
> hide #1,3 atoms
> hide #1 models
> select add #3
3398 atoms, 3015 bonds, 823 residues, 1 model selected
> select subtract #2
3398 atoms, 3015 bonds, 823 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #1 models
> open 4RS2 fromDatabase pdb format mmcif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #3
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #3
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> matchmaker #3,6 to #1/A & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
B (#3), sequence alignment score = 540.5
RMSD between 157 pruned atom pairs is 0.811 angstroms; (across all 167 pairs:
1.074)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 572.3
RMSD between 162 pruned atom pairs is 0.687 angstroms; (across all 167 pairs:
0.862)
> select #3/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #3 models
> show #3 models
> select #1/A:115
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> select #1/A:119
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #1/A:84
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #1/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> select #1/A:22
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #1/A:79
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide #1 models
> show #1 models
> select #3/B:78
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> hide #3 models
> show #3 models
> select #1/A:78
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
Drag select of 113 atoms, 118 residues, 97 bonds
> select clear
Drag select of 154 atoms, 195 residues, 130 bonds
> matchmaker #3,6 to #1/A & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with 4rs2, chain
B (#3), sequence alignment score = 306.5
RMSD between 90 pruned atom pairs is 0.825 angstroms; (across all 96 pairs:
1.120)
Matchmaker fold_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 331.7
RMSD between 92 pruned atom pairs is 0.629 angstroms; (across all 96 pairs:
0.916)
> matchmaker #6 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_hqba_hfqx6_vcholera_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#6), sequence alignment score = 331.7
RMSD between 92 pruned atom pairs is 0.629 angstroms; (across all 96 pairs:
0.916)
> matchmaker #6 to #3/A & sel pairing bs
No 'to' chains specified
> select clear
Drag select of 147 atoms, 178 residues, 126 bonds
> matchmaker #6 to #3/B & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 4rs2, chain B (#3) with fold_hqba_hfqx6_co_model_0.cif, chain A
(#6), sequence alignment score = 429.6
RMSD between 85 pruned atom pairs is 0.643 angstroms; (across all 86 pairs:
0.720)
> matchmaker #1 to #3/B & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 4rs2, chain B (#3) with fold_hqba_hfqx6_vcholera_model_0.cif, chain
A (#1), sequence alignment score = 277
RMSD between 80 pruned atom pairs is 0.852 angstroms; (across all 86 pairs:
1.167)
> matchmaker #1 & sel to #3/B & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 4rs2, chain B (#3) with fold_hqba_hfqx6_vcholera_model_0.cif, chain
A (#1), sequence alignment score = 271
RMSD between 79 pruned atom pairs is 0.855 angstroms; (across all 85 pairs:
1.172)
> select clear
> hide #3 models
> show #3 models
> select ::name="COA"
96 atoms, 100 bonds, 2 residues, 1 model selected
> color sel lime
> hide #3 models
> show #3 models
> select #1/A:86
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #3 models
> select #1/A:116
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> show #3 models
> hide #1 models
> select #3/B:117
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> show #1 models
> hide #3 models
> select #1/A:117
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> show #3 models
> hide #3 models
> select #1/A:116
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #3 models
> hide #3 models
> select add #1/A:102
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add #1/A:98
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #1/C:31
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #1/A:116
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.cxs
> select N
2579 atoms, 1833 residues, 3 models selected
> color (#1 & sel) blue
> undo
> select N1
Nothing selected
> show #3 models
> select add #1/A:86@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select add #1/A:86@NE2
1 atom, 1 residue, 1 model selected
> select add #1/A:84@NH1
2 atoms, 2 residues, 1 model selected
> select add #1/A:119@NH2
3 atoms, 3 residues, 1 model selected
> select add #1/A:119@NH1
4 atoms, 3 residues, 1 model selected
> select add #1/A:84@NE
5 atoms, 3 residues, 1 model selected
> select add #1/A:84@NH2
6 atoms, 3 residues, 1 model selected
> color sel blue
> select clear
> select #1/A:119
11 atoms, 10 bonds, 1 residue, 1 model selected
> undo
> select clear
> select #1/A:119
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> select subtract #1/A:119
1281 atoms, 1304 bonds, 166 residues, 1 model selected
> select clear
> select #1/A:119
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/A:84
22 atoms, 20 bonds, 2 residues, 1 model selected
> select add #1/A:86
31 atoms, 28 bonds, 3 residues, 1 model selected
> color sel orange
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> select #3/B:117
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel purple
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.png
> width 600 height 417 supersample 4 transparentBackground true
> show #1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #1 models
> select #3/B:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3/B:98
17 atoms, 15 bonds, 2 residues, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel magenta
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.png
> width 600 height 417 supersample 4 transparentBackground true
> show #1 models
> hide #3 models
> show #3 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/4RS2.vs.HqbA_Hfq_Vcholera.png
> width 600 height 417 supersample 4 transparentBackground true
> hide #3 models
> select #1/A:117
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel purple
> select clear
> show #3 models
> select ::name="COA"
96 atoms, 100 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
3302 atoms, 2915 bonds, 821 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_CoA_Hfq_Vcholera.png
> width 600 height 417 supersample 4 transparentBackground true
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_CoA_Hfq_Vcholera-2.png
> width 600 height 417 supersample 4 transparentBackground true
> show #6 models
> hide #1 models
> show #1 models
> hide #1 models
> select #6/C:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #6 models
> show #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.cxs
> hide #3 models
> show #3 models
> show #6 models
> hide #1 models
> select #6/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6/A:102
17 atoms, 15 bonds, 2 residues, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> select add #6/C:31
26 atoms, 23 bonds, 3 residues, 1 model selected
> style sel stick
Changed 26 atom styles
> show sel atoms
> show #1 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #1 models
> show #1 models
> hide #6 models
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #c7ff92 radius 0.06 reveal true
1820 contacts
> select #1/A
1292 atoms, 1316 bonds, 167 residues, 1 model selected
> contacts sel saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #c7ff92 radius 0.06 reveal true
84 contacts
> undo
Drag select of 1811 atoms, 404 residues, 1499 bonds, 3 pseudobonds
> select clear
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #c7ff92 radius 0.06 reveal true
1820 contacts
> hide #!3 models
Drag select of 860 atoms, 363 residues, 736 bonds
> select clear
Drag select of 830 atoms, 348 residues, 714 bonds
> hide sel atoms
> select clear
> show #2 models
> hide #2 models
> show #!3 models
> select #3/A
1678 atoms, 1491 bonds, 631 pseudobonds, 404 residues, 3 models selected
> hide sel atoms
> select ::name="HOH"
458 atoms, 205 pseudobonds, 458 residues, 2 models selected
> hide sel atoms
> select ::name="COA"
96 atoms, 100 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
3302 atoms, 2915 bonds, 1361 pseudobonds, 821 residues, 3 models selected
> hide sel atoms
> select clear
> show #6 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
opened ChimeraX session
> hide #!2 models
> hide #4 models
> hide #5 models
> hide #7 models
> hide #8 models
> show #4 models
> hide #3 models
> show #5 models
> show #7 models
> show #8 models
> select add #4
4991 atoms, 5113 bonds, 625 residues, 2 models selected
> select add #5
8336 atoms, 8541 bonds, 1042 residues, 3 models selected
> select add #7
11681 atoms, 11969 bonds, 1459 residues, 4 models selected
> select add #8
15026 atoms, 15397 bonds, 1876 residues, 5 models selected
> delete atoms (#4-5,7-8 & sel)
> delete bonds (#4-5,7-8 & sel)
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
Chain information for fold_azor_monomer_fad_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_nad/fold_azor_dimer_nad_model_0.cif
Chain information for fold_azor_dimer_nad_model_0.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/icd/fold_icd_model_0.cif
Chain information for fold_icd_model_0.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/mqo/fold_mqo_model_0.cif
Chain information for fold_mqo_model_0.cif #8
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhc/fold_ndhc_model_0.cif
Chain information for fold_ndhc_model_0.cif #9
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhf/fold_ndhf_model_0.cif
Chain information for fold_ndhf_model_0.cif #10
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/suca/fold_suca_model_0.cif
Chain information for fold_suca_model_0.cif #12
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #3-5,7-12#!2,6 to #1/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain B (#5), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.362 angstroms; (across all 208 pairs:
0.362)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
> hide #12 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> hide #5 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #4 models
> show #3 models
> hide #!2 models
> hide #1 models
> show #!6 models
> hide #3#!6 surfaces
> show #7 models
> hide #!6 models
> hide #3 models
> show #8 models
> hide #7 models
> show #9 models
> hide #8 models
> rainbow #9
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> show #1 models
> hide #1 models
> show #1 models
> hide #11 models
> show #11 models
> show #12 models
> hide #11 models
> hide #1 models
> matchmaker #8-10,12 to #7/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
chain A (#12), sequence alignment score = 124
RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
29.841)
> show #7 models
> hide #12 models
> show #8 models
> show #9 models
> hide #8 models
> hide #7 models
> show #8 models
> hide #9 models
> show #12 models
> hide #8 models
> rainbow #12
> show #7 models
> hide #12 models
> show #8 models
> hide #7 models
> show #5 models
> hide #8 models
> color #5 bychain
> show #!6 models
> hide #5 models
> show #11 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #5 models
> select /A
32114 atoms, 32801 bonds, 4077 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
0.359)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)
> show #1 models
> hide #1 models
> show #5 models
> hide #11 models
> show #11 models
> hide #5 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ~sel & ##selected
4938 atoms, 5055 bonds, 624 residues, 2 models selected
> rainbow sel & #11
> select clear
> show #1 models
> hide #11 models
> open 9H2I fromDatabase pdb format mmcif
Summary of feedback from opening 9H2I fetched from pdb
---
note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif
9h2i title:
Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
dehydrogenase complex [more info...]
Chain information for 9h2i #13
---
Chain | Description | UniProt
A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379
B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474
Non-standard residues in 9h2i #13
---
FAD — flavin-adenine dinucleotide
> ui tool show Matchmaker
> matchmaker #13 to #1/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
18.939)
> undo
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> hide #11 models
> hide #1 models
> show #4 models
> hide #13 models
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> show #13 models
> hide #4 models
> color sel & #13 bychain
> undo
> select clear
> color #13 bychain
> undo
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #6 & sel
No matrix compatible with both reference structure and all match structures
> select clear
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 to #6 & sel
No matrix compatible with both reference structure and all match structures
> matchmaker #13 to #6
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_fad_model_0.cif, chain A (#6) with 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
18.887)
> show #!6 models
> hide #13 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open 8RX4 fromDatabase pdb format mmcif
Summary of feedback from opening 8RX4 fetched from pdb
---
notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
8rx4 title:
Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
and redox co-factor NADP(H) [more info...]
Chain information for 8rx4 #14
---
Chain | Description | UniProt
A B | Mycothione reductase | X8E6Y0_MYCXE 1-459
Non-standard residues in 8rx4 #14
---
FAD — flavin-adenine dinucleotide
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
> hide #!6 models
> matchmaker #14 to #13
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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #13-14 bychain
> select clear
> hide #14 models
> show #14 models
> hide #13 models
> show #13 models
> hide #14 models
> show #14 models
> hide #13 models
> select #14/B
3646 atoms, 3705 bonds, 481 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #13 models
> hide #14 models
> select #13/C
3803 atoms, 3650 bonds, 693 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> select #13/B
3924 atoms, 3668 bonds, 798 residues, 1 model selected
> rainbow sel
> select clear
> show #4 models
> hide #13 models
> show #14 models
> show #13 models
> hide #14 models
> hide #4 models
> show #!6 models
> hide #13 models
> show #13 models
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "move picked models"
> view matrix models
> #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123
> select clear
> show #3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> hide #13 models
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #3 bychain
> select clear
> show #13 models
> select #13/B:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908
> view matrix models
> #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524
Drag select of 1 residues
> view matrix models
> #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933
> view matrix models
> #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363
> view matrix models
> #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081
> view matrix models
> #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262
> view matrix models
> #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418
> view matrix models
> #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733
> view matrix models
> #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879
> select clear
> select #13/B:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27
> view matrix models
> #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67
> view matrix models
> #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714
> view matrix models
> #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802
> view matrix models
> #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54
> select clear
Drag select of 5 residues, 1 bonds
> show #5 models
> hide #3 models
> show #3 models
> hide #5 models
> show #14 models
> matchmaker #14 to #13
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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> hide #13 models
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> show sel & #3,13-14 surfaces
> hide #!14 models
> hide sel & #!3,13 surfaces
> show #!14 models
> hide #!13 models
> hide sel & #!3,14 surfaces
> select clear
> hide #!3 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> show #!13 models
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> rainbow sel & #!14
> select clear
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.051654 seconds
| QMMM: Dspev diag routine = 0.044332 seconds
| QMMM: Dspevd diag routine = 0.032116 seconds
| QMMM: Dspevx diag routine = 0.153242 seconds
| QMMM: Dsyev diag routine = 0.047097 seconds
| QMMM: Dsyevd diag routine = 0.033935 seconds
| QMMM: Dsyevr diag routine = 0.038554 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.022789 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.050281 seconds
| QMMM: Dspev diag routine = 0.043968 seconds
| QMMM: Dspevd diag routine = 0.032120 seconds
| QMMM: Dspevx diag routine = 0.153124 seconds
| QMMM: Dsyev diag routine = 0.047103 seconds
| QMMM: Dsyevd diag routine = 0.033926 seconds
| QMMM: Dsyevr diag routine = 0.039887 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.024004 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> color bfactor sel
96 atoms, 2 residues, atom bfactor range 41.3 to 73.2
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!6 models
> select #14/A:97
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454
> view matrix models
> #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003
> view matrix models
> #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104
> view matrix models
> #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309
> hide #!6 models
> show #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #4 models
> show #5 models
> hide #!6 models
> show #!6 models
> hide #5 models
> select #14/A:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425
> view matrix models
> #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602
> view matrix models
> #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335
> select clear
> select #14/A:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913
> select clear
> hide #!6 models
> show #!6 models
> select clear
Drag select of 26 atoms, 132 residues, 25 bonds
Drag select of 40 atoms, 192 residues, 36 bonds
> hide sel cartoons
> view matrix models
> #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964
> select clear
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> select #14/A
3671 atoms, 3705 bonds, 506 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!3 models
> open 3w78 fromDatabase pdb format mmcif
Summary of feedback from opening 3w78 fetched from pdb
---
notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif
Fetching CCD CBD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif
Fetching CCD FMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif
3w78 title:
Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
Cibacron Blue [more info...]
Chain information for 3w78 #15
---
Chain | Description | UniProt
A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211
Non-standard residues in 3w78 #15
---
CBD — cibacron blue
FMN — flavin mononucleotide (riboflavin monophosphate)
3w78 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> matchmaker #15 to #6
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_fad_model_0.cif, chain A (#6) with 3w78, chain A
(#15), sequence alignment score = 709.3
RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
1.539)
> hide #!6 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #15/D
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!3 models
> hide #!14 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> rainbow sel
> select clear
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> rainbow sel
> select clear
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> select #3/B:169
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select clear
> show #15 models
> hide #15 models
> show #15 models
> select #3/B:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> select clear
> select #3/A:184
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #15 models
> select clear
> show #15 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #15/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> color sel light gray
> color sel gray
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/A:147
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide sel atoms
> select clear
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> select #3/B:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> select #3/B:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> open 4m0C fromDatabase pdb format mmcif
Summary of feedback from opening 4m0C fetched from pdb
---
note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif
4m0c title:
The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
anthracis str. Ames Ancestor in complex with FMN. [more info...]
Chain information for 4m0c #16
---
Chain | Description | UniProt
A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220
Non-standard residues in 4m0c #16
---
FMN — flavin mononucleotide (riboflavin monophosphate)
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
> hide #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #!16 models
> show #15 models
> hide #15 models
> matchmaker #!16 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 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
> show #!16 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> select #3/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #3/A:28
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> show #!16 models
> select #3/A:24@NZ
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) blue
> select clear
> hide #!3 models
> show #!3 models
> select #3/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #!16 bypolymer
> color #!16 bychain
> undo
> show #!14 models
> hide #!14 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612
> show #!3 models
> hide #!3 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041
> show #!3 models
> hide #!3 models
> show #15 models
> hide #!16 models
> hide #15 models
> show #15 models
> show #!16 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!16 models
> show #!3 models
> hide #15 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471
> select #/B
Expected an objects specifier or a keyword
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select #3/A:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #5 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #5 models
> hide #!3 models
> hide #!6 models
> show #8 models
> rainbow #8
> show #9 models
> hide #9 models
> show #9 models
> hide #8 models
> show #10 models
> hide #9 models
> rainbow #10
> show #9 models
> show #11 models
> hide #11 models
> ui tool show Matchmaker
> matchmaker #8-10 to #7
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_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
> view matrix models
> #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815
> hide #9 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> hide #12 models
> show #7 models
> rainbow #7
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> select #7/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931
> ui mousemode right "rotate selected models"
> select #7/A:168
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882
> view matrix models
> #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624
> view matrix models
> #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657
> view matrix models
> #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396
> view matrix models
> #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757
> view matrix models
> #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601
> view matrix models
> #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434
> view matrix models
> #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31
> select clear
> hide #7 models
> show #8 models
> select #8/A:495
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568
> ui mousemode right "rotate selected models"
> select #8/A:464
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42
> view matrix models
> #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86
> view matrix models
> #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983
> view matrix models
> #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383
> view matrix models
> #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657
> view matrix models
> #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89
> view matrix models
> #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004
> view matrix models
> #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708
> view matrix models
> #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> hide #8 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!16 models
> open 1v4B fromDatabase pdb format mmcif
Summary of feedback from opening 1v4B fetched from pdb
---
notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif
1v4b title:
The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
form [more info...]
Chain information for 1v4b #17
---
Chain | Description | UniProt
A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200
Non-standard residues in 1v4b #17
---
EDO — 1,2-ethanediol (ethylene glycol)
FMN — flavin mononucleotide (riboflavin monophosphate)
IPA — isopropyl alcohol (2-propanol)
1v4b mmCIF Assemblies
---
1| author_defined_assembly
> open 2B3D fromDatabase pdb format mmcif
Summary of feedback from opening 2B3D fetched from pdb
---
note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif
2b3d title:
Crystal structure of Modulator of Drug activity B in complex with flavin
adenine dinucleotide [more info...]
Chain information for 2b3d #18
---
Chain | Description | UniProt
A B | Modulator of drug activity B | MDAB_ECOLI 13-204
Non-standard residues in 2b3d #18
---
FAD — flavin-adenine dinucleotide
> hide #!16 models
> hide #!17 models
> matchmaker #!18 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 2b3d, chain B
(#18), sequence alignment score = 156.9
RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
6.190)
> show #!3 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> select /A
43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected
> hide #!3 models
> show #!3 models
> show #7 models
> hide #7 models
> hide #!6 models
> matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel 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
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)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
0.436)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085
RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
0.263)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1074.2
RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
0.269)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4
RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
23.782)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8
RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
22.736)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4
RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
32.226)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3
RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
21.293)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
17.171)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
(#13), sequence alignment score = 24
RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
11.957)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
(#14), sequence alignment score = 51.5
RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
29.959)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
(#15), sequence alignment score = 716.5
RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
1.461)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
(#17), sequence alignment score = 427.4
RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
2.701)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
(#18), sequence alignment score = 150.4
RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
6.224)
> show #!6 models
> hide #!6 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> hide #!3 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!16 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> view matrix models
> #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#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,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!6 models
> hide #1 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #4 models
> show #1 models
> hide #!3 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #1 models
> hide #!3 models
> show #1 models
> hide #1 models
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> show #!6 models
> hide #!6 models
> color sel & #!18 bychain
> undo
> select clear
> color #!18 bychain
> undo
> show #!3 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!18 models
> hide #!3 models
> show #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #!3 models
> show #!18 models
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #1 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel goldenrod
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> color sel dark goldenrod
> color sel salmon
> color sel dark goldenrod
> color sel peru
> color sel dark orange
> color sel saddle brown
> color sel dark goldenrod
> color sel slate gray
> color sel steel blue
> color sel cadet blue
> color sel dark olive green
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> show #1 models
> hide #!3 models
> show #!13 models
> hide #!13 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #4 models
> hide #1 models
> show #1 models
> hide #4 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
> 600 height 489 supersample 4 transparentBackground true
> show #4 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> select clear
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> hide #!3 models
> show #1 models
> show #!6 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #!6 models
> hide #1 models
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
> width 600 height 489 supersample 4 transparentBackground true
> show #11 models
> hide #!3 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 #12 models
> hide #12 models
> show #!6 models
> hide #11 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!6 models
> hide #!3 surfaces
> select add #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 clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
> width 600 height 489 supersample 4 transparentBackground true
> 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
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