![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17334 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001043c0580 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 63)
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{
"uptime" : 320000,
"procLaunch" : "2025-04-08 08:38:07.7709 -0700",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"procStartAbsTime" : 7174720191672,
"coalitionID" : 3000,
"osVersion" : {
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"build" : "21G217",
"releaseType" : "User"
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"captureTime" : "2025-04-08 15:29:56.7489 -0700",
"incident" : "37B4B0AA-5DDB-456E-A96E-86A88DDBAFA2",
"bug_type" : "309",
"pid" : 69009,
"procExitAbsTime" : 7708744130993,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3963FDE2-4226-5C97-BDB6-0409F41D3D50","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1B4A0CC3-B743-B7C2-04B9-60B5BB2A8FBE",
"wakeTime" : 20453,
"sleepWakeUUID" : "B13EC46F-AAAE-48E1-8B5C-5CF09E9E67EA",
"sip" : "enabled",
"vmRegionInfo" : "0x125db9bc7a78 is not in any region. Bytes after previous region: 19712721058425 Bytes before following region: 85359358870920\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000125db9bc7a78","rawCodes":[1,20193757395576],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000125db9bc7a78"},
"vmregioninfo" : "0x125db9bc7a78 is not in any region. Bytes after previous region: 19712721058425 Bytes before following region: 85359358870920\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"name" : "libqcocoa.dylib"
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"size" : 4046848,
"uuid" : "c0fdf86c-f960-37a3-a380-db8700d43801",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"arch" : "arm64e",
"base" : 7243137024,
"size" : 290816,
"uuid" : "b3c7a004-1069-3171-b630-2c386a8b399c",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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{
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"arch" : "arm64e",
"base" : 7245299712,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5533696,
"uuid" : "fc3c193d-0cdb-3569-9f0e-bd2507ca1dbb",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1866"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7392706560,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "aaf900bd-bfb6-3af0-a8d3-e24bbe1d57f5",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4474585088,
"size" : 4849664,
"uuid" : "113c92ac-6022-34c0-8532-0a96c67af294",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4485857280,
"size" : 3112960,
"uuid" : "ee8cff87-6a5d-38d1-8403-031c9916b0fb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4364288000,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
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"base" : 4365516800,
"size" : 393216,
"uuid" : "24d09537-e51b-350e-b59e-181c9d94d291",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6109478912,
"size" : 165756928,
"uuid" : "72eb72da-af14-3e6d-a878-889044e69fe6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7244226560,
"size" : 421888,
"uuid" : "3d1e6031-901d-3df1-9e9a-f85ff1c2e803",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
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"arch" : "arm64",
"base" : 4492607488,
"size" : 21299200,
"uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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],
"sharedCache" : {
"base" : 7241678848,
"size" : 3144728576,
"uuid" : "7cf73f63-0640-33ec-8444-138d9834ecb5"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=8.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 7872K 8 \nCG image 688K 30 \nColorSync 640K 28 \nCoreAnimation 992K 43 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5136K 36 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.1G 477 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 496.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 672K 42 \nStack 157.5M 43 \nStack Guard 56.0M 1 \nVM_ALLOCATE 433.9M 429 \nVM_ALLOCATE (reserved) 192.0M 3 reserved VM address space (unallocated)\n__AUTH 2634K 322 \n__AUTH_CONST 21.1M 528 \n__CTF 756 1 \n__DATA 24.4M 685 \n__DATA_CONST 29.3M 688 \n__DATA_DIRTY 1941K 232 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 607.7M 159 \n__OBJC_CONST 3918K 300 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 766.7M 706 \n__UNICODE 592K 1 \ndyld private memory 1072K 2 \nmapped file 188.3M 53 \nshared memory 3792K 32 \n=========== ======= ======= \nTOTAL 10.5G 4890 \nTOTAL, minus reserved VM space 9.5G 4890 \n",
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"trialInfo" : {
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Mon Apr 7 18:37:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Mon Apr 7 13:04:37 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Fri Apr 4 19:43:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Fri Apr 4 07:40:37 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Thu Apr 3 14:02:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Wed Apr 2 18:08:08 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Wed Apr 2 07:26:28 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Tue Apr 1 10:02:02 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Log from Mon Mar 31 01:45:17 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_test.cxs
Log from Wed Mar 26 15:32:57 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jill/Documents/Yuki/REE_test.cxs
Log from Wed Mar 26 00:13:04 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jill/Downloads/fold_hor_194_ree_2023_720_mdh_test_plus_ca/fold_hor_194_ree_2023_720_mdh_test_plus_ca_model_0.cif
Chain information for fold_hor_194_ree_2023_720_mdh_test_plus_ca_model_0.cif
#1
---
Chain | Description
A | .
> save /Users/jill/Documents/Yuki/REE_test.cxs
Drag select of 10 atoms, 40 residues, 7 bonds
> show sel atoms
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open
> /Users/jill/Downloads/fold_hor_194_ree_2023_6235_gluc_dh_w_ca/fold_hor_194_ree_2023_6235_gluc_dh_w_ca_model_0.cif
Chain information for fold_hor_194_ree_2023_6235_gluc_dh_w_ca_model_0.cif #2
---
Chain | Description
A | .
> hide #1 models
> view clip false
> color #2 #ec9d2cff
> color #1 #d7c609ff
> ui tool show "Side View"
> set bgColor white
> select Ca
2 atoms, 2 residues, 2 models selected
> color (#2 & sel) forest green
> save /Users/jill/Documents/Yuki/REE_test.cxs
[Repeated 1 time(s)]
> select add #1
2687 atoms, 2747 bonds, 365 residues, 2 models selected
> select subtract #1
1 atom, 1 residue, 1 model selected
> view clip false
> hide #2 models
> select add #2
4832 atoms, 4964 bonds, 642 residues, 1 model selected
> select subtract #2
Nothing selected
> show #1 models
> select add #1
2686 atoms, 2747 bonds, 364 residues, 1 model selected
Alignment identifier is 1/A
> select subtract #1
Nothing selected
> hide #1 models
> show #2 models
> select add #2
4832 atoms, 4964 bonds, 642 residues, 1 model selected
Alignment identifier is 2/A
> select ::name="ASP"
504 atoms, 444 bonds, 63 residues, 2 models selected
> select #2/A:326
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:320-326
65 atoms, 67 bonds, 7 residues, 1 model selected
> color sel byhetero
> select #2/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #2/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> color #2 byhetero
> select #2/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:323-325
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #2/A:321-322
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #2/A:321-327
64 atoms, 67 bonds, 7 residues, 1 model selected
> open
> /Users/jill/Downloads/fold_hor_194_ree_2023_896_w_ca/fold_hor_194_ree_2023_896_w_ca_model_0.cif
Chain information for fold_hor_194_ree_2023_896_w_ca_model_0.cif #3
---
Chain | Description
A | .
> select add #2
4832 atoms, 4964 bonds, 642 residues, 1 model selected
> hide #2 models
> select subtract #2
Nothing selected
> select add #3
4949 atoms, 5068 bonds, 650 residues, 1 model selected
Alignment identifier is 3/A
> select clear
Drag select of 6 residues
> select clear
> select ::name="ASP"
840 atoms, 739 bonds, 105 residues, 3 models selected
> select #3/A:301
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:297-301
38 atoms, 38 bonds, 5 residues, 1 model selected
> select #3/A:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:277-283
44 atoms, 44 bonds, 7 residues, 1 model selected
> select #3/A:400
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:399-400
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/A:402
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:400-402
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #3/A:399
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:382-399
136 atoms, 137 bonds, 18 residues, 1 model selected
> select #3/A:379
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:364-379
120 atoms, 123 bonds, 16 residues, 1 model selected
> select #3/A:376
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:376
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_hor_194_ree_2023_896_w_ca_model_0.cif_A SES surface
#3.1: minimum, -15.54, mean -2.03, maximum 10.48
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_hor_194_ree_2023_896_w_ca_model_0.cif_A SES surface
#3.1: minimum, -15.54, mean -2.03, maximum 10.48
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color sel byhetero
> select #3/A:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:411-412
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:443
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:443
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:430
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:430
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:421
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:420-421
20 atoms, 20 bonds, 2 residues, 1 model selected
> color (#!3 & sel) lime
> color sel byhetero
> select #3/A:420
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:420
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:380
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:380
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!3 & sel) hot pink
> color sel byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open
> /Users/jill/Downloads/fold_hor_194_ree_2023_1429_w_ca/fold_hor_194_ree_2023_1429_w_ca_model_0.cif
Chain information for fold_hor_194_ree_2023_1429_w_ca_model_0.cif #4
---
Chain | Description
A | .
> hide #!3 models
> select add #3
4949 atoms, 5068 bonds, 650 residues, 2 models selected
> select subtract #3
1 model selected
> color #4 #c36becff
> color #4 #894cecff
> color #4 #308cecff
> select ions
4 atoms, 4 residues, 4 models selected
> color (#4 & sel) forest green
> color sel & #4 byhetero
> select clear
> color #4 byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
[Repeated 1 time(s)]
> open
> /Users/jill/Downloads/fold_hor_194_ree_2023_2361_w_ca/fold_hor_194_ree_2023_2361_w_ca_model_0.cif
Chain information for fold_hor_194_ree_2023_2361_w_ca_model_0.cif #5
---
Chain | Description
A | .
> hide #4 models
> color #5 byhetero
> ui tool show "Side View"
> hide #5 models
> show #4 models
> select add #4
4480 atoms, 4604 bonds, 596 residues, 1 model selected
Alignment identifier is 4/A
> ui tool show "Side View"
> open 4CVB
Summary of feedback from opening 4CVB fetched from pdb
---
note | Fetching compressed mmCIF 4cvb from http://files.rcsb.org/download/4cvb.cif
4cvb title:
Crystal structure of quinone-dependent alcohol dehydrogenase from
Pseudogluconobacter saccharoketogenenes [more info...]
Chain information for 4cvb #6
---
Chain | Description | UniProt
A | ALCOHOL DEHYDROGENASE | Q93RE9_9BACT 37-608
Non-standard residues in 4cvb #6
---
CA — calcium ion
CL — chloride ion
PPI — propanoic acid
PQQ — pyrroloquinoline quinone
ZN — zinc ion
4cvb mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select clear
> ui tool show Matchmaker
> matchmaker #5 to #6
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 4cvb, chain A (#6) with
fold_hor_194_ree_2023_2361_w_ca_model_0.cif, chain A (#5), sequence alignment
score = 820.5
RMSD between 325 pruned atom pairs is 1.067 angstroms; (across all 500 pairs:
6.829)
> hide #4 models
> show #5 models
> color #6 #4b73dbff
> color #5 #efc733ff
> hide #5#!6 atoms
> select ions
11 atoms, 1 pseudobond, 11 residues, 7 models selected
> show (#5#!6 & sel) target ab
> select Co
Nothing selected
> color #5-6 forest green
> color #5 #978c1eff
> color #5 #978932ff
> color #5 #bcab3eff
> color #6 #254e97ff
> color #6 #3268c8ff
> select clear
> select Co
Nothing selected
> color #5-6 forest green
> undo
> hide #5 models
> select Ca
6 atoms, 6 residues, 6 models selected
> color (#!6 & sel) forest green
> select add #5
5316 atoms, 5456 bonds, 712 residues, 6 models selected
> select add #4
9795 atoms, 10060 bonds, 1307 residues, 6 models selected
> select subtract #4
5315 atoms, 5456 bonds, 711 residues, 5 models selected
> select add #3
10263 atoms, 10524 bonds, 1360 residues, 5 models selected
> select add #2
15094 atoms, 15488 bonds, 2001 residues, 6 models selected
> select subtract #2
10262 atoms, 10524 bonds, 1359 residues, 5 models selected
> select add #1
12947 atoms, 13271 bonds, 1722 residues, 5 models selected
> select subtract #1
10261 atoms, 10524 bonds, 1358 residues, 4 models selected
> select subtract #3
5312 atoms, 5456 bonds, 708 residues, 3 models selected
> show #5 models
> hide #5 models
> show #5 models
> hide #!6 models
> select add #6
10223 atoms, 9845 bonds, 23 pseudobonds, 1903 residues, 3 models selected
> select subtract #6
5311 atoms, 5456 bonds, 707 residues, 1 model selected
> select clear
> select Ca
6 atoms, 6 residues, 6 models selected
> color (#5 & sel) forest green
> select clear
> show #!6 models
Drag select of 18 residues
> hide #!6 models
> select add #6
4959 atoms, 4389 bonds, 23 pseudobonds, 1203 residues, 3 models selected
> select subtract #6
47 atoms, 7 residues, 1 model selected
> select clear
> select add #5
5311 atoms, 5456 bonds, 707 residues, 1 model selected
Alignment identifier is 5/A
> select #5/A:661-706
382 atoms, 396 bonds, 46 residues, 1 model selected
> select #5/A:566-706
1078 atoms, 1113 bonds, 141 residues, 1 model selected
> select #5/A:706
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #5/A:586-706
927 atoms, 957 bonds, 121 residues, 1 model selected
> select #5/A:706
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #5/A:596-706
855 atoms, 881 bonds, 111 residues, 1 model selected
> save /Users/jill/Documents/Yuki/Hor_194_2361_C-term.pdb selectedOnly true
> open "/Users/jill/Downloads/Hor_194_REE_2023_2361 w. sorbitol
> dehyd/pred.rank_0.cif"
Summary of feedback from opening /Users/jill/Downloads/Hor_194_REE_2023_2361
w. sorbitol dehyd/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG2': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #7
---
Chain | Description
A | Entity A
Non-standard residues in pred.rank_0.cif #7
---
LIG2 — (LIG2)
Color pred.rank_0.cif by residue attribute pLDDT_score
> hide #5 models
> select add #5
5311 atoms, 5456 bonds, 707 residues, 1 model selected
> view #5 clip false
No displayed objects specified.
> view
> show #!6 models
> select subtract #5
Nothing selected
> ui tool show Matchmaker
> matchmaker #7 to #6
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 4cvb, chain A (#6) with pred.rank_0.cif, chain A (#7), sequence
alignment score = 801.3
RMSD between 327 pruned atom pairs is 1.067 angstroms; (across all 496 pairs:
5.729)
> close #7
> open "/Users/jill/Downloads/Hor_194_REE_2023_2361 w. sorbitol
> dehyd/Hor_194_2023_REE_2361_La_rank_0.cif"
Summary of feedback from opening /Users/jill/Downloads/Hor_194_REE_2023_2361
w. sorbitol dehyd/Hor_194_2023_REE_2361_La_rank_0.cif
---
warning | Unable to fetch template for 'LIG2': will connect using distance criteria
Hor_194_2023_REE_2361_La_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_2023_REE_2361_La_rank_0.cif #7
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_2023_REE_2361_La_rank_0.cif #7
---
LIG2 — (LIG2)
Color Hor_194_2023_REE_2361_La_rank_0.cif by residue attribute pLDDT_score
> color #7 #edc813ff
> color #7 #caaa10ff
> ui tool show Matchmaker
> matchmaker #7 to #6
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 4cvb, chain A (#6) with Hor_194_2023_REE_2361_La_rank_0.cif, chain
A (#7), sequence alignment score = 801.3
RMSD between 327 pruned atom pairs is 1.067 angstroms; (across all 496 pairs:
5.729)
> hide #7 models
> hide #!6 models
> show #7 models
> select Ca
6 atoms, 6 residues, 6 models selected
> color #7 lime
> undo
> select add #1
2691 atoms, 2747 bonds, 369 residues, 6 models selected
> select subtract #1
5 atoms, 5 residues, 5 models selected
> select add #2
4836 atoms, 4964 bonds, 646 residues, 5 models selected
> select subtract #2
4 atoms, 4 residues, 4 models selected
> select add #3
4952 atoms, 5068 bonds, 653 residues, 4 models selected
> select subtract #3
3 atoms, 3 residues, 4 models selected
> select add #4
4482 atoms, 4604 bonds, 598 residues, 3 models selected
> select subtract #4
2 atoms, 2 residues, 2 models selected
> select add #5
5312 atoms, 5456 bonds, 708 residues, 2 models selected
> select subtract #5
1 atom, 1 residue, 1 model selected
> select add #6
4912 atoms, 4389 bonds, 23 pseudobonds, 1196 residues, 2 models selected
> select subtract #6
Nothing selected
> select add #7
5310 atoms, 5455 bonds, 707 residues, 1 model selected
> select La
1 atom, 1 residue, 1 model selected
> color sel lime
> show #!6 models
> select add #7
5310 atoms, 5455 bonds, 707 residues, 1 model selected
> select subtract #7
Nothing selected
> open 5FC9
Summary of feedback from opening 5FC9 fetched from pdb
---
note | Fetching compressed mmCIF 5fc9 from http://files.rcsb.org/download/5fc9.cif
5fc9 title:
Novel Purple Cupredoxin from Nitrosopumilus maritimus [more info...]
Chain information for 5fc9 #8
---
Chain | Description | UniProt
A B C D | Blue (Type 1) copper domain protein | A9A2G4_NITMS 1002-1096 2002-2096 3002-3096 4002-4096
Non-standard residues in 5fc9 #8
---
CU — copper (II) ion
> hide #7 models
> hide #!6 models
> color #8 #3e86faff
> color #8 #326cc9ff
> view clip false
> open /Users/jill/Documents/Yuki/Hor_194_2361_C-term.pdb
Summary of feedback from opening /Users/jill/Documents/Yuki/Hor_194_2361_C-
term.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 LYS A 43 GLN A 49 0
Start residue of secondary structure not found: SHEET 2 2 1 ALA A 59 ALA A 61
0
Start residue of secondary structure not found: SHEET 3 3 1 VAL A 64 GLY A 68
0
Start residue of secondary structure not found: SHEET 4 4 1 GLU A 73 ASP A 78
0
Start residue of secondary structure not found: SHEET 5 5 1 SER A 84 LYS A 89
0
26 messages similar to the above omitted
Chain information for Hor_194_2361_C-term.pdb #9
---
Chain | Description
A | No description available
> color #9 #f8cd47ff
> color #9 #e2ba41ff
> view clip false
> ui tool show Matchmaker
> matchmaker #9 to #8
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 5fc9, chain C (#8) with Hor_194_2361_C-term.pdb, chain A (#9),
sequence alignment score = 126.2
RMSD between 55 pruned atom pairs is 0.772 angstroms; (across all 87 pairs:
5.756)
Drag select of 1 atoms, 119 residues
> select clear
> select #8/C
913 atoms, 776 bonds, 4 pseudobonds, 255 residues, 2 models selected
> select ~sel & ##selected
2686 atoms, 2328 bonds, 14 pseudobonds, 712 residues, 2 models selected
> cartoon hide (#!8 & sel)
> hide (#!8 & sel) target a
> color sel byhetero
[Repeated 1 time(s)]
> color #8 #7f8dcdff
> color #8 #92a3ecff
> color #8 #7684bfff
> color sel byhetero
> select add #8
3599 atoms, 3104 bonds, 18 pseudobonds, 967 residues, 2 models selected
> select subtract #8
Nothing selected
> color #9#!8 byhetero
> hide #!8 models
> select add #9
855 atoms, 881 bonds, 111 residues, 1 model selected
Alignment identifier is 9/A
> show #!8 models
> select #9/A:605
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:602-605
23 atoms, 23 bonds, 4 residues, 1 model selected
> select clear
> select ::name="HIS"
860 atoms, 864 bonds, 86 residues, 9 models selected
> select #9/A:695
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:695
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:659
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:659
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:695
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:695
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select add #9
855 atoms, 881 bonds, 111 residues, 1 model selected
> hide #9 models
> select subtract #9
Nothing selected
> hide #!8 models
> show #1 models
Drag select of 5 atoms, 9 residues, 5 bonds
> hide #1 models
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #7 models
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view #6 clip false
No displayed objects specified.
> hide #!8 models
> show #9 models
> hide #9 models
> save /Users/jill/Documents/Yuki/REE_test.cxs
> show #7 models
> ui tool show Matchmaker
> matchmaker #7 to #8
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 5fc9, chain C (#8) with Hor_194_2023_REE_2361_La_rank_0.cif, chain
A (#7), sequence alignment score = 126.2
RMSD between 56 pruned atom pairs is 0.750 angstroms; (across all 87 pairs:
5.759)
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #5 to #6
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 4cvb, chain A (#6) with
fold_hor_194_ree_2023_2361_w_ca_model_0.cif, chain A (#5), sequence alignment
score = 820.5
RMSD between 325 pruned atom pairs is 1.067 angstroms; (across all 500 pairs:
6.829)
> show #!8 models
> hide #7 models
> hide #!8 models
> show #7 models
> ui tool show Matchmaker
> matchmaker #7 to #6
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 4cvb, chain A (#6) with Hor_194_2023_REE_2361_La_rank_0.cif, chain
A (#7), sequence alignment score = 801.3
RMSD between 327 pruned atom pairs is 1.067 angstroms; (across all 496 pairs:
5.729)
> color #7#!6 byhetero
> hide #7#!6 cartoons
> hide #!6 models
> show #!6 models
> select clear
> show #7#!6 cartoons
> hide #!6 models
> select add #7
5310 atoms, 5455 bonds, 707 residues, 1 model selected
Alignment identifier is 7/A
> select #7/A:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:310-312
24 atoms, 23 bonds, 3 residues, 1 model selected
> color sel cyan
> color sel byhetero
> view #7 clip false
> select clear
[Repeated 1 time(s)]
> color bfactor palette alphafold
36934 atoms, 5940 residues, 1 surfaces, atom bfactor range 2.06 to 99
> open
> /Users/jill/Downloads/protein-1-ligand-1-ligand-1/Hor_REE_1261_La_PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/protein-1-ligand-1-ligand-1/Hor_REE_1261_La_PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_REE_1261_La_PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_REE_1261_La_PQQ_rank_0.cif #10
---
Chain | Description
A | Entity A
Non-standard residues in Hor_REE_1261_La_PQQ_rank_0.cif #10
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_REE_1261_La_PQQ_rank_0.cif by residue attribute pLDDT_score
> hide #7 models
> color bfactor palette alphafold
42268 atoms, 6648 residues, 1 surfaces, atom bfactor range 2.06 to 99
> show #!8 models
> color bfactor palette alphafold
42268 atoms, 6648 residues, 1 surfaces, atom bfactor range 2.06 to 99
> hide #10 models
> show #10 models
> hide #!8 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #10 to #6
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 4cvb, chain A (#6) with Hor_REE_1261_La_PQQ_rank_0.cif, chain A
(#10), sequence alignment score = 826.8
RMSD between 307 pruned atom pairs is 1.088 angstroms; (across all 503 pairs:
8.070)
> view clip false
> select ligand
53 atoms, 56 bonds, 3 residues, 2 models selected
> select clear
> select #7/A
5309 atoms, 5455 bonds, 706 residues, 1 model selected
> select add #7
5310 atoms, 5455 bonds, 707 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #10 models
> hide #!6 models
> show #10 models
> select ligand
53 atoms, 56 bonds, 3 residues, 2 models selected
> color (#10 & sel) black
> select clear
> select Co
Nothing selected
> color #10 forest green
> undo
> select clear
> select Ca
6 atoms, 6 residues, 6 models selected
> color #10 forest green
> undo
> hide #1-2,4-5#!3,6 target m
> select Ca
6 atoms, 6 residues, 6 models selected
> color #10 forest green
> undo
> select add #6
4917 atoms, 4389 bonds, 23 pseudobonds, 1201 residues, 7 models selected
> select subtract #6
5 atoms, 5 residues, 5 models selected
> hide #1-2,4-5#!3 target m
[Repeated 1 time(s)]
> select add #5
5315 atoms, 5456 bonds, 711 residues, 5 models selected
> select add #4
9794 atoms, 10060 bonds, 1306 residues, 5 models selected
> select subtract #5
4483 atoms, 4604 bonds, 599 residues, 4 models selected
> select subtract #4
3 atoms, 3 residues, 3 models selected
> select add #3
4951 atoms, 5068 bonds, 652 residues, 3 models selected
> select subtract #3
2 atoms, 2 residues, 3 models selected
> select add #2
4833 atoms, 4964 bonds, 643 residues, 2 models selected
> select subtract #2
1 atom, 1 residue, 1 model selected
> select add #1
2686 atoms, 2747 bonds, 364 residues, 1 model selected
> select subtract #1
Nothing selected
> select Ca
6 atoms, 6 residues, 6 models selected
> select add #6
4917 atoms, 4389 bonds, 23 pseudobonds, 1201 residues, 7 models selected
> select subtract #6
5 atoms, 5 residues, 5 models selected
> select add #5
5315 atoms, 5456 bonds, 711 residues, 5 models selected
> select subtract #5
4 atoms, 4 residues, 4 models selected
> select add #4
4483 atoms, 4604 bonds, 599 residues, 4 models selected
> select add #3
9431 atoms, 9672 bonds, 1248 residues, 4 models selected
> select add #2
14262 atoms, 14636 bonds, 1889 residues, 5 models selected
> select add #1
16947 atoms, 17383 bonds, 2252 residues, 5 models selected
> select subtract #1
14261 atoms, 14636 bonds, 1888 residues, 4 models selected
> select subtract #4
9781 atoms, 10032 bonds, 1292 residues, 3 models selected
> select subtract #3
4832 atoms, 4964 bonds, 642 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #5
5311 atoms, 5456 bonds, 707 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #10
5334 atoms, 5481 bonds, 708 residues, 1 model selected
> select subtract #10
Nothing selected
> color #10 lime
> undo
> select clear
> select Co
Nothing selected
> color #10 forest green
> undo
> color #10 byhetero
> ui tool show "Side View"
> open "/Users/jill/Downloads/Hor_194_REE_2023_2361 w. sorbitol DH + Fe3, Cu2,
> PQQ/Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif"
Summary of feedback from opening /Users/jill/Downloads/Hor_194_REE_2023_2361
w. sorbitol DH + Fe3, Cu2, PQQ/Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif #11
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif #11
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color Hor_194_REE_2361_SorboseDH+Fe+Cu+PQQ_rank_0.cif by residue attribute
pLDDT_score
> hide #10 models
> view clip false
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open "/Users/jill/Downloads/Hor_194_REE_2023_2361 w. sorbitol DH + La3, Cu2,
> PQQ/pred.rank_0.cif"
Summary of feedback from opening /Users/jill/Downloads/Hor_194_REE_2023_2361
w. sorbitol DH + La3, Cu2, PQQ/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #12
---
Chain | Description
A | Entity A
Non-standard residues in pred.rank_0.cif #12
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color pred.rank_0.cif by residue attribute pLDDT_score
> hide #11 models
> save /Users/jill/Documents/Yuki/REE_test.cxs
> color #12 #6e5e7fff
> color #12 #806e93ff
> color #12 #5f516dff
> color #12 byhetero
> color #12 #7e5841ff
> color #12 #6d4c38ff
> color #12 #2d6d67ff
> color #12 #235551ff
> color #12 byhetero
> color #12 #66532aff
> color #12 byhetero
> color #12 #b99f62ff
> color #12 byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select ligand
101 atoms, 108 bonds, 5 residues, 4 models selected
> color (#12 & sel) black
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select clear
> open "/Users/jill/Downloads/Hor_194_REE_2023_95_length_260858 Ln-dep
> Gemma/Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_95_length_260858 Ln-dep
Gemma/Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif #13
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif #13
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_95_260858_Gemmati_rank_0.cif by residue attribute
pLDDT_score
> hide #12 models
> color #13 #747ec0ff
> color #13 #8894e2ff
> color #13 byhetero
> select ligand
125 atoms, 134 bonds, 6 residues, 5 models selected
> color (#13 & sel) black
> select clear
> ui tool show "Side View"
> select add #13
4514 atoms, 4651 bonds, 605 residues, 1 model selected
Alignment identifier is 13/A
> select #13/A:429-430
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #13/A:429-430
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #13/A:429-430
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #13/A:429
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/A:429
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/A:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:278-282
32 atoms, 31 bonds, 5 residues, 1 model selected
> select #13/A:279-280
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #13/A:279-280
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #13/A:279
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:279
8 atoms, 7 bonds, 1 residue, 1 model selected
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open "/Users/jill/Downloads/Hor_140_2023_10709_length_6072 nov clade +La +
> PQQ/Hor_140_2023_10709_length_6072 nov clade +La + PQQ)rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_2023_10709_length_6072 nov clade +La +
PQQ/Hor_140_2023_10709_length_6072 nov clade +La + PQQ)rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_2023_10709_length_6072 nov clade +La + PQQ)rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_140_2023_10709_length_6072 nov clade +La +
PQQ)rank_0.cif #14
---
Chain | Description
A | Entity A
Non-standard residues in Hor_140_2023_10709_length_6072 nov clade +La +
PQQ)rank_0.cif #14
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_2023_10709_length_6072 nov clade +La + PQQ)rank_0.cif by residue
attribute pLDDT_score
> hide #13 models
> view #13 clip false
> select add #13
4514 atoms, 4651 bonds, 605 residues, 1 model selected
> view #13 clip false
> color #14 #8b8fcfff
> color #14 byhetero
> color bfactor palette alphafold
67777 atoms, 9998 residues, 1 surfaces, atom bfactor range 2.06 to 99
> save /Users/jill/Documents/Yuki/REE_test.cxs
> color #14 byhetero
> select subtract #13
Nothing selected
> select add #14
10325 atoms, 10590 bonds, 1327 residues, 1 model selected
> hide #14 models
> show #14 models
Alignment identifier is 14/A
> select #14/A:1325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A:952-1325
2933 atoms, 3017 bonds, 374 residues, 1 model selected
> select #14/A:968
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #14/A:968-1325
2807 atoms, 2889 bonds, 358 residues, 1 model selected
> select #14/A:921-966
356 atoms, 364 bonds, 46 residues, 1 model selected
> select #14/A:921-1325
3171 atoms, 3262 bonds, 405 residues, 1 model selected
> save /Users/jill/Documents/Yuki/Hor-140_1079_nov+clade_C-term.pdb
> selectedOnly true
> select #14/A:920-921
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #14/A:920-921
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #14/A:920-921
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #14/A:181-921
5738 atoms, 5876 bonds, 741 residues, 1 model selected
> select #14/A:921-922
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #14/A:1-922
7142 atoms, 7314 bonds, 922 residues, 1 model selected
> save /Users/jill/Documents/Yuki/Hor-140_1079_nov+clade_N-term.pdb
> selectedOnly true
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select clear
> open "/Users/jill/Downloads/Hor_140_REE_2023_5_length_1206237_ADH-Ln-test
> with La and PQQ/Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La and
> PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La
and PQQ/Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La and
PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La and PQQ_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La
and PQQ_rank_0.cif #15
---
Chain | Description
A | Entity A
Non-standard residues in Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La
and PQQ_rank_0.cif #15
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_5_length_1206237_ADH-Ln-test with La and PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #14 models
> color bfactor palette alphafold
72181 atoms, 10573 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color #15 byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
> ui tool show "Side View"
> select ligand
173 atoms, 186 bonds, 8 residues, 7 models selected
> color (#15 & sel) black
> select clear
> color bfactor palette alphafold
72181 atoms, 10573 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color #15 byhetero
> ui tool show "Side View"
> select add #15
4404 atoms, 4527 bonds, 575 residues, 1 model selected
Alignment identifier is 15/A
> select #15/A:313
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:313
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #15/A:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel bychain
[Repeated 1 time(s)]
> color sel byhetero
> color sel lime
> color sel byhetero
> select #15/A:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:311-313
28 atoms, 28 bonds, 3 residues, 1 model selected
> select ligand
173 atoms, 186 bonds, 8 residues, 7 models selected
> color (#15 & sel) black
> select #15/A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:213-217
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #15/A:201
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:199-201
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #15/A:193-194
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #15/A:191-194
28 atoms, 28 bonds, 4 residues, 1 model selected
> select #15/A:192-193
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #15/A:192-193
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #15/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:192-193
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #15/A:240
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #15/A:239-240
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #15/A:193
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #15/A:192-193
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #15/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> select #15/A:190
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #15/A:190-195
39 atoms, 39 bonds, 6 residues, 1 model selected
> open
> /Users/jill/Downloads/fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_689/fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_689_model_0.cif
Chain information for
fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_689_model_0.cif #16
---
Chain | Description
A | .
> hide #15 models
> select add #15
4404 atoms, 4527 bonds, 575 residues, 1 model selected
> view clip false
> select subtract #15
Nothing selected
> select add #16
1557 atoms, 1579 bonds, 212 residues, 1 model selected
Alignment identifier is 16/A
> select #16/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:181-204
192 atoms, 191 bonds, 24 residues, 1 model selected
> select #16/A:114-115
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #16/A:106-115
80 atoms, 79 bonds, 10 residues, 1 model selected
> open
> /Users/jill/Downloads/fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_686/fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_686_model_0.cif
Chain information for
fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_686_model_0.cif #17
---
Chain | Description
A | .
> hide #17 models
> select clear
> hide #16 models
> show #17 models
> hide #17 models
> show #16 models
> open "/Users/jill/Downloads/DUF2135 domain-
> containing_AF-Q9HVT4-F1-model_v4.pdb"
DUF2135 domain-containing_AF-Q9HVT4-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for DUF2135 domain-containing protein
(Q9HVT4) [more info...]
Chain information for DUF2135 domain-containing_AF-Q9HVT4-F1-model_v4.pdb #18
---
Chain | Description | UniProt
A | DUF2135 domain-containing protein | Q9HVT4_PSEAE 1-263
> ui tool show Matchmaker
> matchmaker #16 to #18
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 DUF2135 domain-containing_AF-Q9HVT4-F1-model_v4.pdb, chain A (#18)
with fold_hor_140_ree_2023_5_length_1206237_cov_93_516174_689_model_0.cif,
chain A (#16), sequence alignment score = 80
RMSD between 5 pruned atom pairs is 1.500 angstroms; (across all 167 pairs:
30.715)
> hide #16 models
> show #16 models
> hide #16 models
> select add #18
1985 atoms, 2031 bonds, 263 residues, 1 model selected
Alignment identifier is 18/A
> hide #18 models
> select subtract #18
Nothing selected
> show #16 models
> select add #16
1557 atoms, 1579 bonds, 212 residues, 1 model selected
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
——— End of log from Wed Mar 26 00:13:04 2025 ———
opened ChimeraX session
> hide #16 models
> close #17
> open "/Users/jill/Downloads/Hor_218_REE_2023_5767_length_10696 w La3+ and
> PQQ/ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and PQQ.rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_REE_2023_5767_length_10696 w La3+ and
PQQ/ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and PQQ.rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and PQQ.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and
PQQ.rank_0.cif #17
---
Chain | Description
A | Entity A
Non-standard residues in ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and
PQQ.rank_0.cif #17
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color ADH_3_Hor_218_REE_2023_5767_length_10696 w La3+ and PQQ.rank_0.cif by
residue attribute pLDDT_score
> view clip false
> color bfactor pallet alphafold
> color byattribute bfactor pallet alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor palette alphafold
80072 atoms, 11617 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color #17 byhetero
> select ligand
197 atoms, 212 bonds, 9 residues, 8 models selected
> color (#17 & sel) black
> select clear
> ui tool show "Side View"
> hide #17 cartoons
> select ligand
197 atoms, 212 bonds, 9 residues, 8 models selected
> cartoon hide (#17 & sel)
> hide (#17 & sel) target a
> show sel & #17 cartoons
> select clear
> show #17 cartoons
> select ligand
197 atoms, 212 bonds, 9 residues, 8 models selected
> show (#17 & sel) target ab
> save /Users/jill/Documents/Yuki/REE_test.cxs
Drag select of 2 residues
Alignment identifier is 17/A
> select #17/A:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:304-306
28 atoms, 28 bonds, 3 residues, 1 model selected
> color sel lime
> color sel byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_7_length_888281_cov_4.974159_462 w
> La and PQQ/Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_7_length_888281_cov_4.974159_462 w La
and PQQ/Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif #19
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif #19
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_7_length_888281_cov_4.974159_462_rank_0.cif by residue
attribute pLDDT_score
> hide #17 models
> select add #17
4349 atoms, 4470 bonds, 569 residues, 1 model selected
> select subtract #17
Nothing selected
> color bfactor palette alphafold
84646 atoms, 12202 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select add #19
4574 atoms, 4702 bonds, 585 residues, 1 model selected
Alignment identifier is 19/A
> color sel byhetero
> select ligand
221 atoms, 238 bonds, 10 residues, 9 models selected
> color (#19 & sel) black
Drag select of 1 residues
> ui tool show "Side View"
> color bfactor palette alphafold
84646 atoms, 12202 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select
> #19/A:94-101,113-115,118-123,127-132,138-143,164-166,169-173,178-183,189-194,209-211,214-218,230-234,241-246,277-279,284-289,310-315,321-326,342-345,351-356,361-366,372-377,384-388,392-395,424-426,431-438,441-445,459-464,468-475,481-487,502-506,511-516,522-527,536-541,544-551,575-581
1602 atoms, 1618 bonds, 195 residues, 1 model selected
> select clear
> color #19 byhetero
> ui tool show "Side View"
> select ligand
221 atoms, 238 bonds, 10 residues, 9 models selected
> color (#19 & sel) black
> select clear
> select #19/A:300
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #19/A:247-300
417 atoms, 435 bonds, 54 residues, 1 model selected
> select clear
> select #19/A:345
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:345-346
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #19/A:334
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:334
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #19/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:303-304
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #19/A:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:295
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #19/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
——— End of log from Wed Mar 26 15:32:57 2025 ———
opened ChimeraX session
> open "/Users/jill/Downloads/Hor_194_2023_5649_length_10772 La,
> PQQ/Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_2023_5649_length_10772 La,
PQQ/Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif #20
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif #20
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_2023_5649_length_10772 La, PQQ_rank_0.cif by residue attribute
pLDDT_score
> hide #19 models
> select add #19
4574 atoms, 4702 bonds, 585 residues, 1 model selected
> select subtract #19
Nothing selected
> select add #20
4484 atoms, 4605 bonds, 581 residues, 1 model selected
Alignment identifier is 20/A
> ui tool show "Side View"
> select clear
> color bfactor palette alphafold
89130 atoms, 12783 residues, 1 surfaces, atom bfactor range 2.06 to 99
> save /Users/jill/Documents/Yuki/REE_test.cxs
> color #20 byhetero
> select ligand
245 atoms, 264 bonds, 11 residues, 10 models selected
> color (#20 & sel) black
> select clear
> select #20/A:317
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #20/A:316-317
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #20/A:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:316-317
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> color sel lime
> color sel byhetero
[Repeated 3 time(s)]
> select clear
[Repeated 1 time(s)]
> color #20 byhetero
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:320-321
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #20/A:320-321
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #20/A:75-81,92-94,97-101,106-111,117-122,138-140,143-147,152-157,163-168,183-185,188-192,205-209,216-221,252-254,259-264,295-299,306-311,327-333,336-344,349-354,360-365,372-375,382-384,396-398,412-414,419-425,427-433,448-454,463-469,475-481,496-500,506-510,516-519,532-536,539-546,571-576
1609 atoms, 1623 bonds, 195 residues, 1 model selected
> select #20/A:319-320
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #20/A:319-320
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319,321
16 atoms, 14 bonds, 2 residues, 1 model selected
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_163 +
> La + PQQ/Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_163 + La
+ PQQ/Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif #21
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif #21
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_14_length_564673_cov_4.982306_163_rank_0.cif by residue
attribute pLDDT_score
> select add #20
4484 atoms, 4605 bonds, 581 residues, 1 model selected
> hide #20 models
> select subtract #20
Nothing selected
> select add #21
4310 atoms, 4433 bonds, 562 residues, 1 model selected
> view #20 clip false
> color bfactor palette alphafold
93440 atoms, 13345 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color sel byhetero
> select clear
> select ligand
269 atoms, 290 bonds, 12 residues, 11 models selected
> color (#21 & sel) black
> select clear
[Repeated 1 time(s)]
> ui tool show "Side View"
> select clear
> select add #21
4310 atoms, 4433 bonds, 562 residues, 1 model selected
Alignment identifier is 21/A
> select #21/A:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:212
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #21/A:212-214
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307-308
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #21/A:307-308
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #21/A:308-309
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #21/A:308-309
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #21/A:70-75,89-91,94-99,103-108,114-119,139-141,144-148,153-158,164-169,186-188,191-195,206-211,217-222,248-250,255-259,281-285,292-297,312-316,322-328,332-337,343-348,377-380,394-396,401-406,410-415,431-437,446-451,458-464,479-483,488-493,499-504,514-518,521-527,554-558
1530 atoms, 1547 bonds, 183 residues, 1 model selected
> select #21/A:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:350-396
371 atoms, 383 bonds, 47 residues, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200,305
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #21/A:200,305,307-308
29 atoms, 26 bonds, 4 residues, 1 model selected
> select #21/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:398
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:200,305
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #21/A:200,305,307
24 atoms, 21 bonds, 3 residues, 1 model selected
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_152 la
> pqq/pred.rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_152 la
pqq/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #22
---
Chain | Description
A | Entity A
Non-standard residues in pred.rank_0.cif #22
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color pred.rank_0.cif by residue attribute pLDDT_score
> close #22
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_152 la
> pqq/Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_14_length_564673_cov_4.982306_152 la
pqq/Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif #22
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif #22
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_14_length_564673_cov_4.982306_152_rank_0.cif by residue
attribute pLDDT_score
> hide #21 models
> select add #21
4310 atoms, 4433 bonds, 562 residues, 1 model selected
> view clip false
> color bfactor palette alphafold
97927 atoms, 13921 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select subtract #21
Nothing selected
> select add #22
4487 atoms, 4626 bonds, 576 residues, 1 model selected
Alignment identifier is 22/A
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
> color #22 byhetero
> select ligand
293 atoms, 316 bonds, 13 residues, 12 models selected
> color (#22 & sel) black
> select clear
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select #22/A:302
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:302
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:302-303
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #22/A:302-305
36 atoms, 37 bonds, 4 residues, 1 model selected
> select
> #22/A:65-72,84-86,89-94,98-103,109-114,132-134,137-141,146-151,157-162,178-180,183-186,198-203,209-214,249-251,256-261,281-285,292-297,313-319,322-330,335-341,347-354,361-364,371-373,384-387,401-403,408-414,417-422,443-446,452-460,468-473,481-483,488-492,498-503,509-514,524-528,531-538,566-572
1699 atoms, 1719 bonds, 205 residues, 1 model selected
> select #22/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:304-305
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #22/A:305-306
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #22/A:305-306
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #22/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #22/A:205
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:205
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select
> #22/A:65-72,84-86,89-94,98-103,109-114,132-134,137-141,146-151,157-162,178-180,183-186,198-203,209-214,249-251,256-261,281-285,292-297,313-319,322-330,335-341,347-354,361-364,371-373,384-387,401-403,408-414,417-422,443-446,452-460,468-473,481-483,488-492,498-503,509-514,524-528,531-538,566-572
1699 atoms, 1719 bonds, 205 residues, 1 model selected
> select #22/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel byhetero
> select #22/A:192,263
17 atoms, 15 bonds, 2 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select
> #22/A:2-17,28-32,62-64,166-169,191-193,224-226,236-239,269-271,375-377,439-441,542-555
476 atoms, 473 bonds, 61 residues, 1 model selected
> select
> #22/A:65-72,84-86,89-94,98-103,109-114,132-134,137-141,146-151,157-162,178-180,183-186,198-203,209-214,249-251,256-261,281-285,292-297,313-319,322-330,335-341,347-354,361-364,371-373,384-387,401-403,408-414,417-422,443-446,452-460,468-473,481-483,488-492,498-503,509-514,524-528,531-538,566-572
1699 atoms, 1719 bonds, 205 residues, 1 model selected
> select #22/A:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:191-192
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #22/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel byhetero
> select #22/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #22/A:192,263
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #22/A:192,263,305
25 atoms, 22 bonds, 3 residues, 1 model selected
> save /Users/jill/Documents/Yuki/REE_test.cxs
> hide #22 models
> select add #22
4487 atoms, 4626 bonds, 576 residues, 1 model selected
> select subtract #22
Nothing selected
> show #21 models
> hide #21 models
> show #20 models
> select add #20
4484 atoms, 4605 bonds, 581 residues, 1 model selected
Alignment identifier is 20/A
Destroying pre-existing alignment with identifier 20/A
Alignment identifier is 20/A
> select clear
> color #20 byhetero
> select ligand
293 atoms, 316 bonds, 13 residues, 12 models selected
> color (#20 & sel) black
> select #20/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #20/A:266,321
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #20/A:266,319,321
25 atoms, 22 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> open "/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7 La
> PQQ/Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7 La
PQQ/Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif
#23
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif #23
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_218_2023_1660_length_54156_cov_2.497566_7_rank_0.cif by residue
attribute pLDDT_score
> select add #20
4484 atoms, 4605 bonds, 581 residues, 1 model selected
> select subtract #20
Nothing selected
> hide #20 models
> select add #23
5479 atoms, 5622 bonds, 724 residues, 1 model selected
> select clear
> ui tool show "Side View"
> color bfactor palette alphafold
103406 atoms, 14645 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select add #23
5479 atoms, 5622 bonds, 724 residues, 1 model selected
Alignment identifier is 23/A
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select
> #23/A:76-83,95-97,100-104,110-114,120-124,146-148,151-155,160-165,171-176,191-193,196-200,211-216,222-227,272-275,280-285,308-313,319-324,339-346,349-356,362-367,373-378,411-413,427-429,434-441,444-448,465-467,487-494,499-506,514-517,521-525,530-535,541-546,556-560,563-569,595-601
1619 atoms, 1633 bonds, 194 residues, 1 model selected
> select #23/A:640-641
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #23/A:640-641
15 atoms, 14 bonds, 2 residues, 1 model selected
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select #23/A:598-599
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #23/A:597-599
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #23/A:644-645
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #23/A:643-645
20 atoms, 20 bonds, 3 residues, 1 model selected
> select #23/A:643
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:643-644
16 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
[Repeated 2 time(s)]
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select #23/A:639
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #23/A:639-640
18 atoms, 18 bonds, 2 residues, 1 model selected
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select #23/A:640-641
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #23/A:640-641
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select #23/A:643
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:643-644
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640,642-643
19 atoms, 17 bonds, 3 residues, 1 model selected
> select #23/A:640,642-644
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #23/A:640
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select
> #23/A:76-83,95-97,100-104,110-114,120-124,146-148,151-155,160-165,171-176,191-193,196-200,211-216,222-227,272-275,280-285,308-313,319-324,339-346,349-356,362-367,373-378,411-413,427-429,434-441,444-448,465-467,487-494,499-506,514-517,521-525,530-535,541-546,556-560,563-569,595-601
1619 atoms, 1633 bonds, 194 residues, 1 model selected
> select
> #23/A:2-21,32-43,73-75,106-108,130-135,204-206,242-252,258-260,293-296,400-402,404-407,450-455,469-471,473-484,576-578,586-589,626-639,641-644,646-648,657-659,666-673,679-681,692-712,714-716
1223 atoms, 1227 bonds, 159 residues, 1 model selected
> select #23/A:644
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #23/A:643-644
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #23/A:640,643-644
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel orange red
> hide #23 models
> select add #23
5479 atoms, 5622 bonds, 724 residues, 1 model selected
> open "/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7 +
> heme + Fe3 + La3 + PQQ/Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme
> + Fe3 + La3 + PQQrank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme +
Fe3 + La3 + PQQ/Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme + Fe3 +
La3 + PQQrank_0.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme + Fe3 + La3 +
PQQrank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme +
Fe3 + La3 + PQQrank_0.cif #24
---
Chain | Description
D | Entity D
Non-standard residues in Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme
+ Fe3 + La3 + PQQrank_0.cif #24
---
LIG1 — (LIG1)
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_218_2023_1660_length_54156_cov_2.497566_7 + heme + Fe3 + La3 +
PQQrank_0.cif by residue attribute pLDDT_score
> show #23 models
> hide #23 models
> select subtract #23
Nothing selected
> select add #24
5480 atoms, 5622 bonds, 725 residues, 1 model selected
> color bfactor palette alphafold
108886 atoms, 15370 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select ligand
341 atoms, 368 bonds, 15 residues, 14 models selected
> color (#24 & sel) black
> save /Users/jill/Documents/Yuki/REE_test.cxs
> hide #2,4-5,7,9-24#!3,6,8 target m
> select add #6
5224 atoms, 4727 bonds, 23 pseudobonds, 1209 residues, 15 models selected
> select subtract #6
312 atoms, 338 bonds, 13 residues, 13 models selected
> select add #10
5622 atoms, 5793 bonds, 720 residues, 13 models selected
> select subtract #10
288 atoms, 312 bonds, 12 residues, 12 models selected
> select add #11
5599 atoms, 5767 bonds, 720 residues, 12 models selected
> select subtract #11
264 atoms, 286 bonds, 11 residues, 11 models selected
> select add #12
5575 atoms, 5741 bonds, 719 residues, 11 models selected
> select subtract #12
240 atoms, 260 bonds, 10 residues, 10 models selected
> select add #13
4730 atoms, 4885 bonds, 614 residues, 10 models selected
> select subtract #13
216 atoms, 234 bonds, 9 residues, 9 models selected
> select add #14
10517 atoms, 10798 bonds, 1335 residues, 9 models selected
> select subtract #14
192 atoms, 208 bonds, 8 residues, 8 models selected
> select add #15
4572 atoms, 4709 bonds, 582 residues, 8 models selected
> select subtract #15
168 atoms, 182 bonds, 7 residues, 7 models selected
> select add #15
4572 atoms, 4709 bonds, 582 residues, 8 models selected
> select subtract #15
168 atoms, 182 bonds, 7 residues, 7 models selected
> select add #17
4493 atoms, 4626 bonds, 575 residues, 7 models selected
> select subtract #17
144 atoms, 156 bonds, 6 residues, 6 models selected
> select add #19
4694 atoms, 4832 bonds, 590 residues, 6 models selected
> select subtract #19
120 atoms, 130 bonds, 5 residues, 5 models selected
> select add #20
4580 atoms, 4709 bonds, 585 residues, 5 models selected
> select subtract #20
96 atoms, 104 bonds, 4 residues, 4 models selected
> select add #21
4382 atoms, 4511 bonds, 565 residues, 4 models selected
> select subtract #21
72 atoms, 78 bonds, 3 residues, 3 models selected
> select add #22
4535 atoms, 4678 bonds, 578 residues, 3 models selected
> select subtract #22
48 atoms, 52 bonds, 2 residues, 2 models selected
> select add #23
5503 atoms, 5648 bonds, 725 residues, 2 models selected
> select subtract #23
24 atoms, 26 bonds, 1 residue, 1 model selected
> select add #24
5480 atoms, 5622 bonds, 725 residues, 1 model selected
> select subtract #24
Nothing selected
> show #23 models
> color #23 byhetero
> select ligand
341 atoms, 368 bonds, 15 residues, 14 models selected
> color (#23 & sel) black
> select #23/A:620
7 atoms, 7 bonds, 1 residue, 1 model selected
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 +
> La + PQQ/pred.rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La
+ PQQ/pred.rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #25
---
Chain | Description
A | Entity A
Non-standard residues in pred.rank_0.cif #25
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color pred.rank_0.cif by residue attribute pLDDT_score
> close #25
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 +
> La + PQQ/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La +
> PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La
+ PQQ/Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La +
PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La + PQQ_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La
+ PQQ_rank_0.cif #25
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_REE_2023_13_length_739503_cov_36.909420_441 +
La + PQQ_rank_0.cif #25
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_13_length_739503_cov_36.909420_441 + La +
PQQ_rank_0.cif by residue attribute pLDDT_score
> hide #23 models
> select add #23
5479 atoms, 5622 bonds, 724 residues, 1 model selected
> select subtract #23
Nothing selected
> color #25 #d1a53cff
> color #25 #ab8731ff
> color #25 byhetero
> color bfactor palette alphafold
114239 atoms, 16077 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color #25 byhetero
> ui tool show "Side View"
> view #23 clip false
> select add #25
5353 atoms, 5502 bonds, 707 residues, 1 model selected
Alignment identifier is 25/A
> select #25/A:585-630
328 atoms, 337 bonds, 46 residues, 1 model selected
> select #25/A:585-635
361 atoms, 371 bonds, 51 residues, 1 model selected
> select #25/A:634
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #25/A:633-634
16 atoms, 16 bonds, 2 residues, 1 model selected
> color sel red
> select #25/A:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #25/A:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select clear
> color #25 byhetero
> select main
112632 atoms, 115677 bonds, 14819 residues, 25 models selected
> select main
112632 atoms, 115677 bonds, 14819 residues, 25 models selected
> select ligand
365 atoms, 394 bonds, 16 residues, 15 models selected
> color (#25 & sel) black
> select clear
> ui tool show "Side View"
> open
> "/Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39 +
> La +PQQ/pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La
> +PQQ.rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39 + La
+PQQ/pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La +PQQ.rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La +PQQ.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La
+PQQ.rank_0.cif #26
---
Chain | Description
A | Entity A
Non-standard residues in pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La
+PQQ.rank_0.cif #26
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color pHor_140_REE_2023_548_length_84259_cov_2.557018_39+La +PQQ.rank_0.cif by
residue attribute pLDDT_score
> hide #25 models
> color bfactor palette alphafold
119695 atoms, 16802 residues, 1 surfaces, atom bfactor range 2.06 to 99
> ui tool show "Side View"
[Repeated 1 time(s)]
> color #26 byhetero
> select ligand
389 atoms, 420 bonds, 17 residues, 16 models selected
> color (#26 & sel) black
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open
> /Users/jill/Downloads/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_related/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_related/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
#27
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
#27
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum_lavamentivorans_rel_rank_0.cif
by residue attribute pLDDT_score
> hide #26 models
> select add #27
5697 atoms, 5855 bonds, 741 residues, 1 model selected
> color bfactor palette alphafold
125392 atoms, 17543 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select clear
> color #27 byhetero
> select ligand
413 atoms, 446 bonds, 18 residues, 17 models selected
> color (#27 & sel) black
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
> open
> /Users/jill/Downloads/Hor_194_REE_2023_5762_length_17088_cov_1.688698_3/Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_5762_length_17088_cov_1.688698_3/Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif #28
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif #28
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_5762_length_17088_cov_1.688698_3_rank_0.cif by residue
attribute pLDDT_score
> hide #27 models
> color bfactor palette alphafold
131056 atoms, 18285 residues, 1 surfaces, atom bfactor range 2.06 to 99
> save /Users/jill/Documents/Yuki/REE_test.cxs
> color #28 byhetero
> select ligand
437 atoms, 472 bonds, 19 residues, 18 models selected
> color (#28 & sel) black
> save /Users/jill/Documents/Yuki/REE_test.cxs
> select clear
> save /Users/jill/Documents/Yuki/REE_test.cxs
> hide #28 models
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24 +
> La + PQQ/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24 + La
+ PQQ/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif #29
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif #29
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif by residue
attribute pLDDT_score
> color bfactor palette alphafold
136698 atoms, 19007 residues, 1 surfaces, atom bfactor range 2.06 to 99
> ui tool show "Side View"
[Repeated 1 time(s)]
> color #29 byhetero
> select ligand
461 atoms, 498 bonds, 20 residues, 19 models selected
> color (#29 & sel) black
> select clear
> select add #29
5642 atoms, 5814 bonds, 722 residues, 1 model selected
Alignment identifier is 29/A
> select #29/A:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:214-215
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #29/A:214-218
41 atoms, 41 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select clear
> select #29/A:206
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:206
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:115-116
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #29/A:115-116
13 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:130
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:130
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #29/A:38-39
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #29/A:35-39
38 atoms, 37 bonds, 5 residues, 1 model selected
> select #29/A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:19-26
60 atoms, 61 bonds, 8 residues, 1 model selected
> select #29/A:360
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:351-360
85 atoms, 88 bonds, 10 residues, 1 model selected
> select #29/A:187
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #29/A:181-187
55 atoms, 55 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:328
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #29/A:321-328
66 atoms, 68 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #29/A:549
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #29/A:549-561
87 atoms, 89 bonds, 13 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:548
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #29/A:542-548
56 atoms, 56 bonds, 7 residues, 1 model selected
> select #29/A:585
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:578-585
66 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #29/A:566
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #29/A:566-576
92 atoms, 96 bonds, 11 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #29/A:565-566
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #29/A:552-566
94 atoms, 96 bonds, 15 residues, 1 model selected
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> select #29/A:86-87
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #29/A:86-90
44 atoms, 46 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #29/A:463-464
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #29/A:456-464
74 atoms, 76 bonds, 9 residues, 1 model selected
> show sel atoms
> hide sel atoms
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_test.cxs
Alignment identifier is 29/A
> select #29/A:407-408
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #29/A:406-408
14 atoms, 13 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel atoms
> open "/Users/jill/Downloads/Hor_194_REE_2023_987_length_69075_cov_3.080786_3
> + La + PQQ/Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La +
> PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La +
PQQ/Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La + PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La + PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La +
PQQ_rank_0.cif #30
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La
+ PQQ_rank_0.cif #30
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_987_length_69075_cov_3.080786_3 + La + PQQ_rank_0.cif
by residue attribute pLDDT_score
> select add #29
5642 atoms, 5814 bonds, 722 residues, 1 model selected
> hide #29 models
> select subtract #29
Nothing selected
> select add #30
5422 atoms, 5591 bonds, 700 residues, 1 model selected
> color bfactor palette alphafold
142120 atoms, 19707 residues, 1 surfaces, atom bfactor range 2.06 to 99
> select clear
> view #29 clip false
[Repeated 2 time(s)]
> view
> save /Users/jill/Documents/Yuki/REE_test.cxs
Drag select of 37 atoms, 43 residues, 41 bonds
> view sel
> select clear
[Repeated 1 time(s)]Drag select of 13 atoms, 17 residues, 12 bonds
> view sel
> color sel byhetero
> select clear
> select ligand
485 atoms, 524 bonds, 21 residues, 20 models selected
> color (#30 & sel) black
> select clear
[Repeated 1 time(s)]
> view
Drag select of 11 atoms, 5 residues, 10 bonds
> view sel
> select clear
> color #30 byhetero
> save /Users/jill/Documents/Yuki/REE_test.cxs
——— End of log from Mon Mar 31 01:45:17 2025 ———
opened ChimeraX session
> hide #30 models
> open
> /Users/jill/Downloads/fold_2025_03_31_01_24hor_140_2023_10709_length_6072_cov_11_268124_2_w_ca/fold_2025_03_31_01_24hor_140_2023_10709_length_6072_cov_11_268124_2_w_ca_model_0.cif
Chain information for
fold_2025_03_31_01_24hor_140_2023_10709_length_6072_cov_11_268124_2_w_ca_model_0.cif
#31
---
Chain | Description
A | .
> color bfactor palette alphafold
152422 atoms, 21033 residues, 1 surfaces, atom bfactor range 2.06 to 99
> open 3Q7M
Summary of feedback from opening 3Q7M fetched from pdb
---
note | Fetching compressed mmCIF 3q7m from http://files.rcsb.org/download/3q7m.cif
3q7m title:
The crystal structure of BamB from the BAM complex in spacegroup I222 [more
info...]
Chain information for 3q7m #32
---
Chain | Description | UniProt
A | Lipoprotein yfgL | YFGL_ECOLI 21-392
> ui tool show Matchmaker
> matchmaker #31 to #32
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 3q7m, chain A (#32) with
fold_2025_03_31_01_24hor_140_2023_10709_length_6072_cov_11_268124_2_w_ca_model_0.cif,
chain A (#31), sequence alignment score = 436.3
RMSD between 151 pruned atom pairs is 1.216 angstroms; (across all 326 pairs:
6.761)
> view clip false
> hide #!32 models
> hide #31 models
> show #31 models
> select add #31
10302 atoms, 10565 bonds, 1326 residues, 1 model selected
Alignment identifier is 31/A
> select clear
> select #31/A:1281-1325
366 atoms, 375 bonds, 45 residues, 1 model selected
> select #31/A:1051-1325
2136 atoms, 2195 bonds, 275 residues, 1 model selected
> select ::name="CYS"
1404 atoms, 1191 bonds, 234 residues, 31 models selected
> show sel & #31 atoms
> color sel & #31 byhetero
> select ::name="HIS"
3460 atoms, 3471 bonds, 346 residues, 32 models selected
> show sel & #31 atoms
> hide #31 models
> show #15 models
> hide #15 models
> show #18 models
> select ::name="ASP"
10122 atoms, 8943 bonds, 1266 residues, 32 models selected
> show sel & #18 atoms
> hide #18 models
> show #19 models
> hide #19 models
> show #31 models
> select clear
> select add #31
10302 atoms, 10565 bonds, 1326 residues, 1 model selected
> select #31/A:1215
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 2 atoms, 8 residues, 1 bonds
> select clear
> color #31 byhetero
Drag select of 3 atoms, 2 residues, 2 bonds
> select #31/A:1276
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #31/A:640-1276
4908 atoms, 5032 bonds, 637 residues, 1 model selected
Drag select of 1 residues
> select add #31
10302 atoms, 10565 bonds, 1326 residues, 1 model selected
> select subtract #31
Nothing selected
> open "/Users/jill/Downloads/Hor_140_2023_10709_length_6072_cov_11.268124_2 +
> La + PQQ/Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_2023_10709_length_6072_cov_11.268124_2 + La +
PQQ/Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif #33
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif #33
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_2023_10709_length_6072_cov_11.268124_2_rank_0.cif by residue
attribute pLDDT_score
> hide #31 models
> bfactor palette alphafold
Unknown command: bfactor palette alphafold
> color bfactor palette alphafold
165613 atoms, 23035 residues, 1 surfaces, atom bfactor range 2.06 to 99
> color #33 byhetero
> open "/Users/jill/Downloads/Hor_218_2023_10700_length_10099_cov_4.864922_9 +
> PQQ + La/Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_10700_length_10099_cov_4.864922_9 + PQQ +
La/Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif #34
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif #34
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif by residue
attribute pLDDT_score
> hide #33 models
> color bfactor palette alphafold
172082 atoms, 23825 residues, 1 surfaces, atom bfactor range 2.06 to 99
> view clip false
> view #34 clip false
Drag select of 48 atoms, 41 residues, 47 bonds
> view sel
> select clear
Drag select of 15 atoms, 6 residues, 15 bonds
> view sel
> select clear
[Repeated 1 time(s)]
> color #34 byhetero
> open 3qde
Summary of feedback from opening 3qde fetched from pdb
---
note | Fetching compressed mmCIF 3qde from http://files.rcsb.org/download/3qde.cif
3qde title:
The structure of Cellobiose phosphorylase from Clostridium thermocellum in
complex with phosphate [more info...]
Chain information for 3qde #35
---
Chain | Description | UniProt
A B | Cellobiose phosphorylase | Q8VP44_CLOTM 1-811
Non-standard residues in 3qde #35
---
144 — tris-hydroxymethyl-methyl-ammonium
PO4 — phosphate ion
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #34 to #35
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 3qde, chain A (#35) with
Hor_218_2023_10700_length_10099_cov_4.864922_9_rank_0.cif, chain A (#34),
sequence alignment score = 2140
RMSD between 679 pruned atom pairs is 0.947 angstroms; (across all 779 pairs:
1.867)
> view clip false
Drag select of 191 residues
> view sel
> select clear
> select #35/B
6948 atoms, 6747 bonds, 1185 residues, 1 model selected
> cartoon hide sel
> hide sel target a
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Tue Apr 1 10:02:02 2025 ———
opened ChimeraX session
> open "/Users/jill/Downloads/H
> or_140_REE_2023_825_length_58097_cov_14.251647_16+ La +
> PQQ/Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif"
Summary of feedback from opening /Users/jill/Downloads/H
or_140_REE_2023_825_length_58097_cov_14.251647_16+ La +
PQQ/Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif #36
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif #36
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_825_length_58097_cov_14.251647_16+La+PQQ_rank_0.cif by
residue attribute pLDDT_score
> hide #35 models
> hide #34 models
> select add #35
13844 atoms, 13494 bonds, 2318 residues, 1 model selected
> select add #36
18185 atoms, 17945 bonds, 2902 residues, 2 models selected
> select subtract #35
4341 atoms, 4451 bonds, 584 residues, 1 model selected
> view clip false
> color bfactor palette alphafold
190267 atoms, 26727 residues, 1 surfaces, atom bfactor range 2.06 to 104
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> select clear
> color #36 byhetero
> select ligand
583 atoms, 624 bonds, 28 residues, 24 models selected
> color (#36 & sel) black
> select clear
[Repeated 1 time(s)]
> select add #36
4341 atoms, 4451 bonds, 584 residues, 1 model selected
Alignment identifier is 36/A
> select #36/A:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:323-324
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #36/A:204
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #36/A:204-209
50 atoms, 52 bonds, 6 residues, 1 model selected
> select #36/A:318
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:318
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #36/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #36/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel lime
> color sel byhetero
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:321,323
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:206,323
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #36/A:206,321,323
24 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel atoms
> show #35 models
> show #29 models
> select add #29
5666 atoms, 5835 bonds, 725 residues, 2 models selected
> hide #35 models
> hide #36 models
> select add #36
9983 atoms, 10265 bonds, 1306 residues, 2 models selected
> color sel & #29 byhetero
> select ligand
583 atoms, 624 bonds, 28 residues, 24 models selected
> color (#29 & sel) black
> select clear
> ui mousemode right "tape measure"
> select #29/B:1@LA1_1
1 atom, 1 residue, 1 model selected
> select #29/A:325@CG
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> select clear
> distance #29/B:1@LA1_1 #29/A:325@CG
Distance between Hor_194_REE_2023_1074_length_65262_cov_9.538512_24_rank_0.cif
#29/B LIG2 1 LA1_1 and /A ASP 325 CG: 4.494Å
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> hide #29 models
> hide #!37 models
> hide #37.1 models
> show #30 models
> color #30 byhetero
> select ligand
583 atoms, 624 bonds, 28 residues, 24 models selected
> color (#30 & sel) black
Drag select of 1 residues
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> view #30 clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> "/Users/jill/Downloads/Hor_140_REE_2023_345_length_112773_cov_820.380102_67+
> La+PQQ/Hor_140_REE_2023_345_length_112773_cov_820.380102_67+
> La+PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_345_length_112773_cov_820.380102_67+
La+PQQ/Hor_140_REE_2023_345_length_112773_cov_820.380102_67+ La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_345_length_112773_cov_820.380102_67+ La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_140_REE_2023_345_length_112773_cov_820.380102_67+
La+PQQ_rank_0.cif #38
---
Chain | Description
A | Entity A
Non-standard residues in Hor_140_REE_2023_345_length_112773_cov_820.380102_67+
La+PQQ_rank_0.cif #38
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_345_length_112773_cov_820.380102_67+ La+PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #30 models
> color bfactor palette alphafold
195097 atoms, 27352 residues, 1 surfaces, atom bfactor range 2.06 to 104
> color #38 byhetero
Drag select of 47 atoms, 34 residues, 48 bonds
> view sel
Drag select of 3 atoms, 5 residues, 1 bonds
> view sel
> ui tool show "Side View"
Drag select of 1 atoms, 3 residues
> view sel
> select ligand
607 atoms, 650 bonds, 29 residues, 25 models selected
> color (#38 & sel) black
> select clear
Drag select of 1 atoms, 1 residues
> view sel
> select clear
> color bfactor palette alphafold
195097 atoms, 27352 residues, 1 surfaces, atom bfactor range 2.06 to 104
> color #38 byhetero
> view clip false
Drag select of 4 atoms, 4 residues, 1 bonds
> view sel
Drag select of 2 atoms
> view sel
> view clip false
Drag select of 19 atoms, 14 residues, 18 bonds
> view sel
Drag select of 4 atoms, 3 residues, 2 bonds
> view sel
> ui tool show "Side View"
Drag select of 3 atoms, 1 residues, 3 bonds
Drag select of 7 atoms, 3 residues, 4 bonds
> view sel
> select clear
> select add #38
4830 atoms, 4968 bonds, 625 residues, 1 model selected
Alignment identifier is 38/A
> select #38/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel lime
> color sel byhetero
> select #38/A:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #38/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel lime
> color sel byhetero
> select #38/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> open
> /Users/jill/Downloads/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif #39
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif #39
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #38 models
> color bfactor palette alphafold
199882 atoms, 27979 residues, 1 surfaces, atom bfactor range 2.06 to 104
> color #39 byhetero
> view clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> mlp #39
Map values for surface
"Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif_A SES
surface": minimum -28.89, mean -4.867, maximum 21.77
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #!39
Map values for surface
"Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif_A SES
surface": minimum -28.89, mean -4.867, maximum 21.77
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!39 surfaces
Drag select of 8 atoms, 9 residues, 7 bonds
> view sel
Drag select of 9 atoms, 9 residues, 8 bonds
> view sel
Drag select of 6 atoms, 3 residues, 6 bonds
> view sel
> ui tool show "Side View"
Drag select of 5 atoms, 3 residues, 4 bonds
> view sel
Drag select of 1 atoms, 1 bonds
> view sel
> view clip false
Drag select of 10 atoms, 8 residues, 8 bonds
> view sel
Drag select of 11 atoms, 11 residues, 8 bonds
> view sel
Drag select of 8 atoms, 8 residues, 8 bonds
> view sel
Drag select of 4 atoms, 2 residues, 3 bonds
> view sel
> select clear
> select ligand
631 atoms, 676 bonds, 30 residues, 26 models selected
> color (#!39 & sel) black
> select clear
> color #!39 byhetero
> select add #39
4785 atoms, 4925 bonds, 627 residues, 1 model selected
Alignment identifier is 39/A
> select #39/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #39/A:359-360
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #39/A:359-360
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #39/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> show sel atoms
> color (#!39 & sel) lime
> color sel byhetero
> select #39/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:357
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> color (#!39 & sel) lime
> color sel byhetero
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> view #39 clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> "/Users/jill/Downloads/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ
> 2/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ
2/Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif #40
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif #40
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_332_length_115426_cov_1344.395944_98+La+PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #!39 models
> select add #39
4785 atoms, 4925 bonds, 627 residues, 2 models selected
> color bfactor palette alphafold
204667 atoms, 28606 residues, 2 surfaces, atom bfactor range 2.06 to 104
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Wed Apr 2 07:26:28 2025 ———
opened ChimeraX session
> open
> "/Users/jill/Downloads/Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
> +La+PQQ_MSA/Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
> +La+PQQ_MSA_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
+La+PQQ_MSA/Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
+La+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_1429_length_53470_cov_2.906586_5 +La+PQQ_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
+La+PQQ_MSA_rank_0.cif #41
---
Chain | Description
A | Entity A
Non-standard residues in Hor_194_REE_2023_1429_length_53470_cov_2.906586_5
+La+PQQ_MSA_rank_0.cif #41
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_1429_length_53470_cov_2.906586_5 +La+PQQ_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #40 models
> select add #39
4785 atoms, 4925 bonds, 627 residues, 1 model selected
> select subtract #39
Nothing selected
> color bfactor palette alphafold
209170 atoms, 29203 residues, 2 surfaces, atom bfactor range 2.06 to 104
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> color #41 byhetero
> ui tool show "Side View"
> select ligand
679 atoms, 728 bonds, 32 residues, 28 models selected
> color (#41 & sel) black
> select clear
Drag select of 4 atoms, 7 bonds
> view sel
Drag select of 38 atoms, 9 residues, 39 bonds
> view sel
> select clear
> view #39 clip false
> view
Drag select of 45 atoms, 46 residues, 48 bonds
Drag select of 20 atoms, 23 residues, 19 bonds
> view sel
> select clear
> ui tool show "Side View"
Drag select of 6 atoms, 8 residues, 4 bonds
> view sel
> select clear
> select add #41
4503 atoms, 4629 bonds, 597 residues, 1 model selected
Alignment identifier is 41/A
> select ::name="ASP"
13370 atoms, 11807 bonds, 1672 residues, 40 models selected
> select #41/A:285-286
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #41/A:282-286
39 atoms, 38 bonds, 5 residues, 1 model selected
> select ::name="ASP"
13370 atoms, 11807 bonds, 1672 residues, 40 models selected
> select #41/A:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:248-251
31 atoms, 31 bonds, 4 residues, 1 model selected
> show #4 models
> select add #4
4511 atoms, 4635 bonds, 600 residues, 2 models selected
> hide #41 models
> select add #41
8983 atoms, 9233 bonds, 1193 residues, 2 models selected
> select subtract #41
4480 atoms, 4604 bonds, 596 residues, 1 model selected
> view #41 clip false
> color sel byhetero
> view #41 clip false
> hide #4 models
> select subtract #4
Nothing selected
> show #41 models
> select add #41
4503 atoms, 4629 bonds, 597 residues, 1 model selected
> view #41 clip false
[Repeated 1 time(s)]
> view
> open
> /Users/jill/Downloads/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif #42
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif #42
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif
by residue attribute pLDDT_score
> select subtract #41
Nothing selected
> hide #41 models
> color bfactor palette alphafold
214504 atoms, 29911 residues, 2 surfaces, atom bfactor range 2.06 to 104
Drag select of 24 atoms, 27 residues, 26 bonds
> view sel
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif #42/A
GLU 706 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif_A SES
surface #42.1: minimum, -18.92, mean -3.34, maximum 16.32
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color sel byhetero
> select clear
> color #!42 byhetero
> select ligand
703 atoms, 754 bonds, 33 residues, 29 models selected
> color (#!42 & sel) black
> select clear
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> view clip false
> open
> /Users/jill/Downloads/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ/Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif #43
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif #43
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+Cu+La+PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #!42 models
> color bfactor palette alphafold
219839 atoms, 30620 residues, 3 surfaces, atom bfactor range 2.06 to 104
> close #5
> close #4
> close #3
> close #2
> close #1
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Drag select of 6 atoms, 5 residues, 10 bonds
> view sel
> color sel byhetero
> select clear
> color #43 byhetero
> select ligand
727 atoms, 780 bonds, 34 residues, 30 models selected
> color (#43 & sel) black
> select clear
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> /Users/jill/Downloads/Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La/Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La/Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif #1
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif #1
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_140_REE_2023_48_length_379761_cov_10.181736_15+PQQ+La_rank_0.cif by
residue attribute pLDDT_score
> hide #43 models
> color bfactor palette alphafold
202436 atoms, 28304 residues, 2 surfaces, atom bfactor range 2.06 to 104
> view clip false
> view
Drag select of 17 atoms, 29 residues, 15 bonds
> view sel
Drag select of 12 atoms, 21 residues, 10 bonds
> view sel
> select clear
> select ligand
751 atoms, 806 bonds, 35 residues, 31 models selected
> color (#1 & sel) black
> select clear
> color #1 byhetero
> select ligand
751 atoms, 806 bonds, 35 residues, 31 models selected
> color (#1 & sel) black
> select clear
> select add #1
4855 atoms, 4989 bonds, 643 residues, 1 model selected
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Wed Apr 2 18:08:08 2025 ———
opened ChimeraX session
> hide #1 models
> select subtract #1
Nothing selected
> open
> /Users/jill/Downloads/Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA/Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA/Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif #2
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif #2
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color
Hor_140_REE_2023_3837_length_12104_cov_1311.846623_2+La+PQQ_MSA_rank_0.cif by
residue attribute pLDDT_score
> color bfactor palette alphafold
207416 atoms, 28955 residues, 2 surfaces, atom bfactor range 2.06 to 104
> ui tool show "Side View"
> color #2 byhetero
Drag select of 27 atoms, 13 residues, 30 bonds
> view sel
> select ligand
775 atoms, 832 bonds, 36 residues, 32 models selected
> color (#2 & sel) black
> select #2/A:536
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #2 models
> show #41 models
> select add #41
4509 atoms, 4634 bonds, 598 residues, 2 models selected
> view #41 clip false
> select clear
> view
> open
> /Users/jill/Downloads/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif #3
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif #3
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif by
residue attribute pLDDT_score
> hide #41 models
> color bfactor palette alphafold
212649 atoms, 29637 residues, 2 surfaces, atom bfactor range 2.06 to 104
> coulombic #3
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif #3/A PRO
680 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+La+PQQ_rank_0.cif_A SES
surface #3.1: minimum, -22.86, mean -2.27, maximum 16.08
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 surfaces
> color #!3 byhetero
> select ligand
799 atoms, 858 bonds, 37 residues, 33 models selected
> color (#!3 & sel) black
> select clear
> open
> /Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ/Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ/Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif
#4
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif #4
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_2023_672_length_76081_cov_3.399795_22_rank_0.cif by residue
attribute pLDDT_score
> hide #!3 models
> color bfactor palette alphafold
217994 atoms, 30349 residues, 3 surfaces, atom bfactor range 2.06 to 104
> select add #4
5345 atoms, 5485 bonds, 712 residues, 1 model selected
Alignment identifier is 4/A
> select #4/A:710
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:536-710
1307 atoms, 1340 bonds, 175 residues, 1 model selected
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-111
831 atoms, 847 bonds, 111 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #4/A:710
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:700-710
72 atoms, 72 bonds, 11 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select ::name="HIS"
5030 atoms, 5047 bonds, 503 residues, 41 models selected
> select #4/A:479
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:475-479
36 atoms, 36 bonds, 5 residues, 1 model selected
> color sel red
> color sel byhetero
> select clear
> color #4 byhetero
> select ligand
823 atoms, 884 bonds, 38 residues, 34 models selected
> color (#4 & sel) black
> select clear
> ui tool show "Side View"
Drag select of 3 atoms, 3 residues, 2 bonds
> select clear
> select
> #4/A:61-67,78-80,83-87,93-97,103-107,121-125,128-135,138-142,158-160,181-183,186-189,203-208,214-219,247-249,254-258,280-285,291-296,312-318,321-329,335-339,349-353,367-371,420-422,442-448,452-454,456-458,561-563,583-589,594-600,630-633,641-646,652-657,667-671,674-682,693-699
1552 atoms, 1561 bonds, 186 residues, 1 model selected
> select ::name="ASP"
13826 atoms, 12203 bonds, 1729 residues, 41 models selected
> select #4/A:306-307
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/A:301-307
59 atoms, 58 bonds, 7 residues, 1 model selected
> select #4/A:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #4/A:310
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:303-310
63 atoms, 64 bonds, 8 residues, 1 model selected
> select #4/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #4/A:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:304,306
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> show sel atoms
> hide #4 models
> select add #4
5345 atoms, 5485 bonds, 712 residues, 1 model selected
> select subtract #4
Nothing selected
> show #!3 models
> select add #3
5233 atoms, 5388 bonds, 682 residues, 1 model selected
Alignment identifier is 3/A
> select ::name="HIS"
5030 atoms, 5047 bonds, 503 residues, 41 models selected
> hide #2,4,7,9-31,33-36,38,40-41,43#!3,6,8,32,37,39,42 target m
[Repeated 1 time(s)]
> select add #1
9775 atoms, 9925 bonds, 1135 residues, 44 models selected
> select subtract #1
4920 atoms, 4936 bonds, 492 residues, 43 models selected
> select add #2
9800 atoms, 9936 bonds, 1133 residues, 43 models selected
> select add #3
14893 atoms, 15184 bonds, 1801 residues, 43 models selected
> select subtract #3
9660 atoms, 9796 bonds, 1119 residues, 42 models selected
> select add #4
14945 atoms, 15220 bonds, 1825 residues, 41 models selected
> select subtract #4
9600 atoms, 9735 bonds, 1113 residues, 40 models selected
> select add #6
14502 atoms, 14114 bonds, 23 pseudobonds, 2308 residues, 41 models selected
> select subtract #6
9590 atoms, 9725 bonds, 1112 residues, 39 models selected
> select add #7
14750 atoms, 15029 bonds, 1804 residues, 39 models selected
> select subtract #7
9440 atoms, 9574 bonds, 1097 residues, 38 models selected
> select add #8
12919 atoms, 12558 bonds, 18 pseudobonds, 2052 residues, 39 models selected
> select subtract #8
9320 atoms, 9454 bonds, 1085 residues, 37 models selected
> select add #9
10155 atoms, 10315 bonds, 1194 residues, 37 models selected
> select subtract #9
9300 atoms, 9434 bonds, 1083 residues, 36 models selected
> select add #10
14484 atoms, 14764 bonds, 1776 residues, 36 models selected
> select subtract #10
9150 atoms, 9283 bonds, 1068 residues, 35 models selected
> select add #11
14335 atoms, 14613 bonds, 1762 residues, 35 models selected
> select subtract #11
9000 atoms, 9132 bonds, 1053 residues, 34 models selected
> select add #12
14185 atoms, 14462 bonds, 1747 residues, 34 models selected
> select subtract #12
8850 atoms, 8981 bonds, 1038 residues, 33 models selected
> select add #13
13244 atoms, 13512 bonds, 1631 residues, 33 models selected
> select subtract #13
8730 atoms, 8861 bonds, 1026 residues, 32 models selected
> select add #14
18835 atoms, 19229 bonds, 2331 residues, 32 models selected
> select subtract #14
8510 atoms, 8639 bonds, 1004 residues, 31 models selected
> select add #15
12844 atoms, 13096 bonds, 1572 residues, 31 models selected
> select subtract #15
8440 atoms, 8569 bonds, 997 residues, 30 models selected
> select add #16
9977 atoms, 10128 bonds, 1207 residues, 30 models selected
> select subtract #16
8420 atoms, 8549 bonds, 995 residues, 29 models selected
> select add #17
12679 atoms, 12929 bonds, 1555 residues, 29 models selected
> select subtract #17
8330 atoms, 8459 bonds, 986 residues, 28 models selected
> select add #18
10285 atoms, 10460 bonds, 1246 residues, 28 models selected
> select subtract #18
8300 atoms, 8429 bonds, 983 residues, 27 models selected
> select add #19
12764 atoms, 13021 bonds, 1557 residues, 27 models selected
> select subtract #19
8190 atoms, 8319 bonds, 972 residues, 26 models selected
> select add #20
12604 atoms, 12854 bonds, 1546 residues, 26 models selected
> select subtract #20
8120 atoms, 8249 bonds, 965 residues, 25 models selected
> select add #21
12320 atoms, 12572 bonds, 1516 residues, 25 models selected
> select subtract #21
8010 atoms, 8139 bonds, 954 residues, 24 models selected
> select add #22
12427 atoms, 12695 bonds, 1523 residues, 24 models selected
> select subtract #22
7940 atoms, 8069 bonds, 947 residues, 23 models selected
> select add #23
13319 atoms, 13591 bonds, 1661 residues, 23 models selected
> select subtract #23
7840 atoms, 7969 bonds, 937 residues, 22 models selected
> select add #24
13220 atoms, 13491 bonds, 1652 residues, 22 models selected
> select subtract #24
7740 atoms, 7869 bonds, 927 residues, 21 models selected
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Thu Apr 3 14:02:35 2025 ———
opened ChimeraX session
> select subtract #2
2760 atoms, 2768 bonds, 276 residues, 18 models selected
> show #4 models
> select add #4
8105 atoms, 8253 bonds, 988 residues, 19 models selected
> select clear
> open
> /Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ/Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ/Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
#5
---
Chain | Description
E | Entity E
Non-standard residues in
Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
#5
---
LIG1 — (LIG1)
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color
Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif
by residue attribute pLDDT_score
> hide #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color bfactor palette alphafold
223390 atoms, 31058 residues, 3 surfaces, atom bfactor range 2.06 to 104
Drag select of 85 atoms, 62 residues, 83 bonds
> view sel
> select clear
> view clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
Drag select of 56 atoms, 51 residues, 59 bonds
> view sel
> select clear
> select add #5
5396 atoms, 5548 bonds, 709 residues, 1 model selected
Alignment identifier is 5/E
> select #5/E:634
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/E:630-634
35 atoms, 35 bonds, 5 residues, 1 model selected
> select #5/E:630-634
35 atoms, 35 bonds, 5 residues, 1 model selected
> select #5/E:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/E:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/E:634
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/E:633-634
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/E:633-634
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/E:630-631,633-634
28 atoms, 27 bonds, 4 residues, 1 model selected
> select #5/E:630-631,633-634
28 atoms, 27 bonds, 4 residues, 1 model selected
> select #5/E:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/E:630-631
12 atoms, 11 bonds, 2 residues, 1 model selected
> select
> #5/E:2-19,33-38,67-69,124-129,227-229,234-242,247-249,281-283,393-395,397-400,467-476,567-574,616-629,631-634,636-638,647-649,656-665,669-671,682-704
1040 atoms, 1042 bonds, 136 residues, 1 model selected
> select #5/E:634
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/E:633-634
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/E:630,633-634
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel byhetero
> view sel
> color sel orange
> color sel byhetero
> view clip false
Drag select of 26 atoms, 35 residues, 25 bonds
> view sel
Drag select of 74 atoms, 28 residues, 75 bonds
> view sel
> hide #5 models
> select add #5
5396 atoms, 5548 bonds, 709 residues, 1 model selected
> select subtract #5
Nothing selected
> show #5 models
> color #5 #47ef98ff
> color #5 #3bc77fff
> color #5 #36b573ff
> color #5 #2e9b63ff
> color #5 byhetero
Drag select of 79 atoms, 54 residues, 78 bonds
> view sel
Drag select of 49 atoms, 15 residues, 54 bonds
> view sel
Drag select of 53 atoms, 10 residues, 59 bonds
> view sel
> select ligand
889 atoms, 956 bonds, 40 residues, 35 models selected
> color (#5 & sel) dim gray
> color (#5 & sel) black
> select clear
> select #5/E:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/E:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/E:630,633-634
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel hot pink
> color sel byhetero
> ui tool show "Side View"
> hide #5 models
> select add #5
5396 atoms, 5548 bonds, 709 residues, 1 model selected
> show #1 models
> select subtract #5
Nothing selected
> select add #1
4855 atoms, 4989 bonds, 643 residues, 1 model selected
Alignment identifier is 1/A
> select ::name="HIS"
5120 atoms, 5137 bonds, 512 residues, 42 models selected
> hide #1 models
> select add #1
9865 atoms, 10015 bonds, 1144 residues, 45 models selected
> select subtract #1
5010 atoms, 5026 bonds, 501 residues, 44 models selected
> show #2 models
Alignment identifier is 6/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 9/A
Alignment identifier is 13/A
Alignment identifier is 3
Alignment identifier is 15/A
Alignment identifier is 16/A
Alignment identifier is 18/A
Alignment identifier is 17/A
Alignment identifier is 19/A
Alignment identifier is 20/A
Alignment identifier is 21/A
Alignment identifier is 22/A
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 26/A
Alignment identifier is 27/A
Alignment identifier is 28/A
Alignment identifier is 29/A
Alignment identifier is 30/A
Alignment identifier is 32/A
Alignment identifier is 34/A
Alignment identifier is 6
Alignment identifier is 36/A
Alignment identifier is 38/A
Alignment identifier is 7
Alignment identifier is 41/A
Alignment identifier is 2/A
Alignment identifier is 3/A
Alignment identifier is 4/A
> select clear
> select add #2
4980 atoms, 5101 bonds, 651 residues, 1 model selected
> select clear
> select ::name="CYS"
2136 atoms, 1807 bonds, 356 residues, 41 models selected
> select clear
> hide #2 models
> show #!3 models
> select add #3
5233 atoms, 5388 bonds, 682 residues, 1 model selected
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
> select ::name="CYS"
2136 atoms, 1807 bonds, 356 residues, 41 models selected
> select clear
> show #4 models
> hide #!3 models
> select add #4
5345 atoms, 5485 bonds, 712 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 4/A
> select ::name="CYS"
2136 atoms, 1807 bonds, 356 residues, 41 models selected
> select clear
> hide #4 models
> show #5 models
> select add #5
5396 atoms, 5548 bonds, 709 residues, 1 model selected
Alignment identifier is 5/E
> select ::name="CYS"
2136 atoms, 1807 bonds, 356 residues, 41 models selected
> show #!3 models
> hide #5 models
> select clear
> select add #3
5233 atoms, 5388 bonds, 682 residues, 1 model selected
Alignment identifier is 3/A
> select ::name="CYS"
2136 atoms, 1807 bonds, 356 residues, 41 models selected
> select clear
> open
> /Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif #44
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif #44
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
by residue attribute pLDDT_score
> hide #!3 models
> select add #44
5388 atoms, 5531 bonds, 714 residues, 1 model selected
Alignment identifier is 44/A
> hide #44 models
> select subtract #44
Nothing selected
> open
> /Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2/Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif #45
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif #45
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color Hor_194_2023_672_length_76081_cov_3.399795_22+La+PQQ+Heme+Fe2_rank_0.cif
by residue attribute pLDDT_score
> close #44
> color bfactor palette alphafold
228778 atoms, 31772 residues, 3 surfaces, atom bfactor range 2.06 to 104
> view clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> select add #45
5388 atoms, 5531 bonds, 714 residues, 1 model selected
Alignment identifier is 45/A
> select ::name="CYS"
2148 atoms, 1817 bonds, 358 residues, 42 models selected
> select #45/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:478-479
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #45/A:475
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:475
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #45/A:475,478-479
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel red
Drag select of 52 atoms, 30 residues, 55 bonds
> view sel
> color sel byhetero
[Repeated 1 time(s)]
> select clear
> color #45 byhetero
> select ligand
955 atoms, 1028 bonds, 42 residues, 36 models selected
> color (#45 & sel) black
Drag select of 1 residues
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Fri Apr 4 07:40:37 2025 ———
opened ChimeraX session
> show #!3 models
> select add #45
5388 atoms, 5531 bonds, 714 residues, 1 model selected
> hide #45 models
> select subtract #45
Nothing selected
> view #3 clip false
[Repeated 1 time(s)]
> open
> "/Users/jill/Downloads/Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ
> 2/Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ
2/Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif #44
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif #44
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_194_2023_14220_length_4386_cov_0.457384_4+La+PQQ_rank_0.cif by
residue attribute pLDDT_score
> hide #!3 models
> color bfactor palette alphafold
234259 atoms, 32478 residues, 3 surfaces, atom bfactor range 2.06 to 104
> color #44 byhetero
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> view clip false
> select ligand
979 atoms, 1054 bonds, 43 residues, 37 models selected
> color (#44 & sel) black
> select clear
> open
> /Users/jill/Downloads/Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ/Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ/Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif #46
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif #46
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_218_2023_1018_length_76770_cov_1.825085_50+La+PQQ_rank_0.cif by
residue attribute pLDDT_score
> hide #44 models
> color bfactor palette alphafold
239133 atoms, 33102 residues, 3 surfaces, atom bfactor range 2.06 to 104
> view clip false
> color #46 byhetero
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
[Repeated 1 time(s)]
——— End of log from Fri Apr 4 19:43:53 2025 ———
opened ChimeraX session
> open 1KB0
Summary of feedback from opening 1KB0 fetched from pdb
---
note | Fetching compressed mmCIF 1kb0 from http://files.rcsb.org/download/1kb0.cif
1kb0 title:
Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas
testosteroni [more info...]
Chain information for 1kb0 #47
---
Chain | Description | UniProt
A | quinohemoprotein alcohol dehydrogenase | QHED_COMTE 1-677
Non-standard residues in 1kb0 #47
---
CA — calcium ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEC — heme C
PQQ — pyrroloquinoline quinone
TFB — tetrahydrofuran-2-carboxylic acid
TRO — 2-hydroxy-tryptophan
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #46 models
> view clip false
> ui tool show "Side View"
> select ligand
1096 atoms, 1175 bonds, 4 pseudobonds, 50 residues, 40 models selected
> color (#!47 & sel) black
> select clear
> view clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> show #5 models
> select add #5
5396 atoms, 5548 bonds, 709 residues, 1 model selected
> select subtract #5
Nothing selected
> ui tool show Matchmaker
> matchmaker #5 to #47
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 1kb0, chain A (#47) with
Hor_194_REE_2023_13_length_739503_cov_36.909420_441+Heme+Fe+La+PQQ_rank_0.cif,
chain E (#5), sequence alignment score = 1759.4
RMSD between 476 pruned atom pairs is 0.884 angstroms; (across all 653 pairs:
4.829)
> color #5 #ffbc24ff
> color #47 #2a4986ff
> color #47 #3862b4ff
> open "/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7
> +La+PQQ+Heme+Fe2/Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7
+La+PQQ+Heme+Fe2/Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif
#48
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif #48
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color Hor_218_2023_1660_length_54156+La+PQQ+Hem+Fe2_rank_0.cif by residue
attribute pLDDT_score
> hide #5 models
> color bfactor palette alphafold
250893 atoms, 35521 residues, 3 surfaces, atom bfactor range 2.06 to 104
> hide #!47 models
> view #47 clip false
[Repeated 1 time(s)]
> color #48 byhetero
> select ligand
1162 atoms, 1247 bonds, 4 pseudobonds, 52 residues, 41 models selected
> color (#48 & sel) black
> select clear
[Repeated 1 time(s)]Drag select of 2 residues
Drag select of 43 atoms, 34 residues, 39 bonds
> view sel
> select clear
Drag select of 1 residues
> select #48/A:288
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #48/A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 2 atoms, 7 residues, 1 bonds
> view sel
> color sel byhetero
Drag select of 6 residues
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> /Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
#49
---
Chain | Description
B | Entity B
Non-standard residues in
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
#49
---
LIG1 — (LIG1)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+La+Fe2+PQQ+Heme_MSA_rank_0.cif
by residue attribute pLDDT_score
> select add #48
5522 atoms, 5668 bonds, 726 residues, 1 model selected
> hide #48 models
> select subtract #48
Nothing selected
> color bfactor palette alphafold
256392 atoms, 36248 residues, 3 surfaces, atom bfactor range 2.06 to 104
> ui tool show "Side View"
> show #48 models
> hide #49 models
> hide #48 models
> show #1 models
> select add #1
4855 atoms, 4989 bonds, 643 residues, 1 model selected
Alignment identifier is 1/A
> select ::name="CYS"
2274 atoms, 1928 bonds, 379 residues, 47 models selected
> hide #1 models
> show #11 models
> select clear
> select add #11
5335 atoms, 5481 bonds, 709 residues, 1 model selected
> select clear
> select add #11
5335 atoms, 5481 bonds, 709 residues, 1 model selected
Alignment identifier is 11/A
> save /Users/jill/Documents/Yuki/194_HOR_REE_2023_Sorbose_361_36335.pdb
Atom names longer than 4 characters; truncating
> select clear
> hide #11 models
> show #9 models
> hide #9 models
> open 1kv9
Summary of feedback from opening 1kv9 fetched from pdb
---
note | Fetching compressed mmCIF 1kv9 from http://files.rcsb.org/download/1kv9.cif
1kv9 title:
Structure at 1.9 A Resolution of a Quinohemoprotein Alcohol Dehydrogenase from
Pseudomonas putida HK5 [more info...]
Chain information for 1kv9 #50
---
Chain | Description | UniProt
A | TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE | Q8GR64_PSEPU 1-668
Non-standard residues in 1kv9 #50
---
ACN — acetone
CA — calcium ion
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEC — heme C
PQQ — pyrroloquinoline quinone
> ui tool show Matchmaker
> matchmaker #!42 to #50
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 1kv9, chain A (#50) with
Hor_194_REE_2023_2361_length_36335_cov_1.961417_3+La+PQQ_MSA_rank_0.cif, chain
A (#42), sequence alignment score = 856.4
RMSD between 348 pruned atom pairs is 1.055 angstroms; (across all 553 pairs:
8.988)
> show #!42 models
> color #42 #b49a1aff
> color #42 #c4a91cff
> color #50 #3e73d3ff
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Mon Apr 7 13:04:37 2025 ———
opened ChimeraX session
> hide #!42 models
> hide #!50 models
> open
> /Users/jill/Downloads/Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA/Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-
> rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA/Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-
rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-
rank_0.cif #51
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-rank_0.cif #51
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color Hor_194_REE_2023_5762_length_17088+La+Fe2+PQQ+Heme_MSA-rank_0.cif by
residue attribute pLDDT_score
> color bfactor palette alphafold
268027 atoms, 38394 residues, 3 surfaces, atom bfactor range 2.06 to 104
Drag select of 14 atoms, 12 residues, 11 bonds
> view sel
> select clear
> color #51 byhetero
> select ligand
1386 atoms, 1486 bonds, 8 pseudobonds, 61 residues, 45 models selected
> color (#51 & sel) black
> select clear
[Repeated 1 time(s)]
> view clip false
> open
> /Users/jill/Downloads/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA/Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif #52
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif #52
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color
Hor_194_REE_2023_67_length_325079_cov_25.702670_209+LA+PQQ_MSA_rank_0.cif by
residue attribute pLDDT_score
> hide #51 models
> color bfactor palette alphafold
273260 atoms, 39076 residues, 3 surfaces, atom bfactor range 2.06 to 104
> select add #52
5233 atoms, 5388 bonds, 682 residues, 1 model selected
Alignment identifier is 52/A
> select ::name="HIS"
6150 atoms, 6168 bonds, 615 residues, 51 models selected
> select ::name="CYS"
2346 atoms, 1991 bonds, 391 residues, 50 models selected
Drag select of 19 atoms, 25 residues, 16 bonds
> view sel
> color sel byhetero
> select clear
> view
Drag select of 1 atoms, 3 residues, 1 bonds
> view sel
> color sel byhetero
[Repeated 1 time(s)]
> select ligand
1410 atoms, 1512 bonds, 8 pseudobonds, 62 residues, 46 models selected
> color (#52 & sel) black
> select clear
[Repeated 1 time(s)]
> color #52 byhetero
> ui tool show "Side View"
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> hide #52 models
> show #49 models
> select add #49
5499 atoms, 5645 bonds, 727 residues, 1 model selected
> color sel byhetero
Drag select of 4 atoms, 3 residues, 1 bonds
> view sel
> select ligand
1410 atoms, 1512 bonds, 8 pseudobonds, 62 residues, 46 models selected
> color (#49 & sel) black
> open
> /Users/jill/Downloads/Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA/Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA/Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif #53
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif #53
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #49 models
> color bfactor palette alphafold
278476 atoms, 39767 residues, 3 surfaces, atom bfactor range 2.06 to 104
> coulombic #53
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif #53/A
ARG 689 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
Hor_218_REE_2023_376_length_108999_cov_9.976890_57_PQQ_La_MSA_rank_0.cif_A SES
surface #53.1: minimum, -28.52, mean -1.66, maximum 12.23
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!53 surfaces
> color #!53 byhetero
> view clip false
Drag select of 7 atoms, 13 residues, 10 bonds
> view sel
Drag select of 9 atoms, 7 residues, 7 bonds
> view sel
> select clear
> select ligand
1434 atoms, 1538 bonds, 8 pseudobonds, 63 residues, 47 models selected
> color (#!53 & sel) black
> select clear
> ui tool show "Side View"
> select add #53
5216 atoms, 5387 bonds, 691 residues, 1 model selected
Alignment identifier is 53/A
> select ::name="ASP"
17602 atoms, 15524 bonds, 2201 residues, 52 models selected
> select #53/A:353
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:353-358
57 atoms, 59 bonds, 6 residues, 1 model selected
> color (#!53 & sel) lime
> color sel byhetero
> undo
[Repeated 1 time(s)]
> select #53/A:356-357
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #53/A:356-357
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #53/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356-357
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356,358-359
24 atoms, 22 bonds, 3 residues, 1 model selected
> select
> #53/A:65-71,103-106,111-115,122-127,156-159,171-176,181-186,201-203,227-229,232-235,252-256,262-266,299-301,306-310,332-337,343-348,364-370,373-381,387-391,401-405,419-423,471-473,487-489,494-500,504-510,539-545,561-567,572-578,617-620,627-632,638-643,653-657,660-667,680-685
1531 atoms, 1543 bonds, 185 residues, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356,358
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!53 & sel) lime
> color sel byhetero
> select #53/A:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!53 & sel) lime
> color sel byhetero
> select #53/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #53/A:356,358
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #53/A:241,356,358
24 atoms, 21 bonds, 3 residues, 1 model selected
> open
> /Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
> w_Fe_PQQ_MSA/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
> w_Fe_PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
w_Fe_PQQ_MSA/Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
w_Fe_PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-w_Fe_PQQ_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
w_Fe_PQQ_MSA_rank_0.cif #54
---
Chain | Description
B | Entity B
Non-standard residues in
Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-w_Fe_PQQ_MSA_rank_0.cif
#54
---
LIG1 — (LIG1)
LIG3 — (LIG3)
Color Hor_140_REE_2023_548_length_84259_cov_2.557018_39+heme-
w_Fe_PQQ_MSA_rank_0.cif by residue attribute pLDDT_score
> hide #!53 models
> select add #53
5216 atoms, 5387 bonds, 691 residues, 2 models selected
> select subtract #53
1 model selected
> color bfactor palette alphafold
283974 atoms, 40492 residues, 4 surfaces, atom bfactor range 2.06 to 104
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open "/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7
> +La+PQQ+Heme+Fe2_MSA/Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif"
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_2023_1660_length_54156_cov_2.497566_7
+La+PQQ+Heme+Fe2_MSA/Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif
#55
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif
#55
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_218_2023_1660_length_54156_cov_2.497566_7+La+PQQ+Heme+Fe2_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #!54 models
> color bfactor palette alphafold
289496 atoms, 41218 residues, 4 surfaces, atom bfactor range 2.06 to 104
> color #55 byhetero
[Repeated 1 time(s)]Drag select of 13 atoms, 17 residues, 9 bonds
> view sel
> select clear
> select main
283883 atoms, 291678 bonds, 4 pseudobonds, 37105 residues, 56 models selected
> select clear
Drag select of 28 atoms, 24 residues, 30 bonds
Drag select of 12 atoms, 3 residues, 10 bonds
Drag select of 1 residues
Drag select of 22 atoms, 10 residues, 17 bonds
> view sel
> select clear
> ui tool show "Side View"
> select ligand
1566 atoms, 1682 bonds, 8 pseudobonds, 67 residues, 49 models selected
> color (#55 & sel) black
> select clear
> open
> /Users/jill/Downloads/Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA/Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA/Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
#56
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
#56
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_194_REE_2023_987_length_69075_cov_3.080786_3+La+PQQ+heme+Fe_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #55 models
> view #55 clip false
> color bfactor palette alphafold
294961 atoms, 41920 residues, 4 surfaces, atom bfactor range 2.06 to 104
> color #56 byhetero
> select ligand
1632 atoms, 1754 bonds, 8 pseudobonds, 69 residues, 50 models selected
> color (#56 & sel) black
> select clear
Drag select of 24 atoms, 11 residues, 20 bonds
> view sel
> select clear
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> /Users/jill/Downloads/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA/Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
#57
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
#57
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_194_REE_2023_1117_length_63779_cov_15.972334_28_Parvibaculum-63_102+La+PQQ+Heme+Fe_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #56 models
> color bfactor palette alphafold
300701 atoms, 42663 residues, 4 surfaces, atom bfactor range 2.06 to 104
> view #56 clip false
[Repeated 1 time(s)]
> view
Drag select of 19 atoms, 20 residues, 16 bonds
> view sel
> select clear
Drag select of 12 atoms, 12 residues, 8 bonds
> view sel
> select clear
> color #57 byhetero
> select ligand
1698 atoms, 1826 bonds, 8 pseudobonds, 71 residues, 51 models selected
> color (#57 & sel) black
> select clear
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> hide #57 models
> show #25 models
> color #25 byhetero
> select add #25
5353 atoms, 5502 bonds, 707 residues, 1 model selected
Alignment identifier is 25/A
> select #25/A:327
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:327
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:325,327
16 atoms, 14 bonds, 2 residues, 1 model selected
> open
> /Users/jill/Downloads/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA/Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
#58
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
#58
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #25 models
> select add #25
5353 atoms, 5502 bonds, 707 residues, 1 model selected
> color bfactor palette alphafold
306386 atoms, 43387 residues, 4 surfaces, atom bfactor range 2.06 to 104
> color #58 byhetero
> mlp #58
Map values for surface
"Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif_A
SES surface": minimum -28.82, mean -4.461, maximum 23.65
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Side View"
> hide #!58 surfaces
> mlp #!58
Map values for surface
"Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif_A
SES surface": minimum -28.82, mean -4.461, maximum 23.65
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!58 surfaces
> mlp #!58
Map values for surface
"Hor_194_REE_2023_1074_length_65262_cov_9.538512_24+La+PQQ+Fe+Heme_MSA_rank_0.cif_A
SES surface": minimum -28.82, mean -4.461, maximum 23.65
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!58 surfaces
> rainbow #!58
> color bfactor palette alphafold
306386 atoms, 43387 residues, 5 surfaces, atom bfactor range 2.06 to 104
> select ligand
1764 atoms, 1898 bonds, 8 pseudobonds, 73 residues, 52 models selected
> color (#!58 & sel) black
> color sel & #!58 byhetero
> undo
> select clear
> color #!58 byhetero
> select ligand
1764 atoms, 1898 bonds, 8 pseudobonds, 73 residues, 52 models selected
> color (#!58 & sel) black
> select clear
[Repeated 4 time(s)]Alignment identifier is 6/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 9/A
Alignment identifier is 13/A
Alignment identifier is 3
Alignment identifier is 15/A
Alignment identifier is 16/A
Alignment identifier is 18/A
Alignment identifier is 17/A
Alignment identifier is 19/A
Alignment identifier is 20/A
Alignment identifier is 21/A
Alignment identifier is 22/A
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 32/A
Alignment identifier is 34/A
Alignment identifier is 11
Alignment identifier is 36/A
Alignment identifier is 38/A
Alignment identifier is 12
Alignment identifier is 41/A
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 13
Alignment identifier is 14
Alignment identifier is 44/A
Alignment identifier is 46/A
Alignment identifier is 47/A
Alignment identifier is 50/A
Alignment identifier is 53/A
> select add #58
5685 atoms, 5860 bonds, 724 residues, 3 models selected
Alignment identifier is 58/A
> select #50/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #50/A:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #50/A:345
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #50/A:77-345
2078 atoms, 2134 bonds, 269 residues, 1 model selected
> select add #50
5928 atoms, 5343 bonds, 13 pseudobonds, 1402 residues, 2 models selected
> select subtract #50
Nothing selected
> select add #58
5685 atoms, 5860 bonds, 724 residues, 3 models selected
Destroying pre-existing alignment with identifier 58/A
Alignment identifier is 58/A
Destroying pre-existing alignment with identifier 58/A
Alignment identifier is 58/A
> select #58/A:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #58/A:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!58 & sel) lime
> color sel byhetero
> select #58/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #58/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!58 & sel) lime
> select #58/A:203,325
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> color sel byhetero
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
——— End of log from Mon Apr 7 18:37:09 2025 ———
opened ChimeraX session
> open
> /Users/jill/Downloads/Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA/Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA/Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
#59
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
#59
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_140_REE_2023_31_length_482572_cov_9.005970_240+La+PQQ+Fe+Heme_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #!58 models
> olor bfactor palette alphafold
Unknown command: olor bfactor palette alphafold
> color bfactor palette alphafold
311909 atoms, 44101 residues, 5 surfaces, atom bfactor range 2.06 to 104
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> open
> /Users/jill/Downloads/PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA/PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA/PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
#60
---
Chain | Description
A | Entity A
Non-standard residues in
PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
#60
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
PQQ_ADH_Type_4_Quinohemoproteins_WP_022977371.1_La+PQQ+Heme+Fe_MSA_rank_0.cif
by residue attribute pLDDT_score
> select add #58
5685 atoms, 5860 bonds, 724 residues, 1 model selected
> select subtract #58
1 model selected
> hide #59 models
> color bfactor palette alphafold
317506 atoms, 44838 residues, 5 surfaces, atom bfactor range 2.06 to 104
> color #60 byhetero
> select ligand
1896 atoms, 2042 bonds, 8 pseudobonds, 77 residues, 54 models selected
> color (#60 & sel) black
> select clear
> ui tool show "Side View"
> open
> /Users/jill/Downloads/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
#61
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
#61
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ+Fe+Heme_MSA_rank_0.cif
by residue attribute pLDDT_score
> hide #60 models
> color bfactor palette alphafold
323781 atoms, 45661 residues, 5 surfaces, atom bfactor range 2.06 to 104
> view clip false
> color #61 byhetero
> select ligand
1962 atoms, 2114 bonds, 8 pseudobonds, 79 residues, 55 models selected
> color (#61 & sel) black
Drag select of 1 residues
> select clear
> select add #61
6275 atoms, 6440 bonds, 823 residues, 1 model selected
Alignment identifier is 61/A
> select clear
> select #61/A:362
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:362
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select #61/A:474
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:474
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:474,476
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> color sel lime
> color sel byhetero
> select #61/A:434
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:434
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> open
> /Users/jill/Downloads/glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA/glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA/glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
Unable to fetch template for 'LIG5': will connect using distance criteria
glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for
glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif #62
---
Chain | Description
A | Entity A
Non-standard residues in
glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif #62
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
LIG5 — (LIG5)
Color glucoseDH_sp_P15877_DHG_ECOLI_+La+PQQ+Fe+Heme_MSA_rank_0.cif by residue
attribute pLDDT_score
> select add #61
6275 atoms, 6440 bonds, 823 residues, 1 model selected
> hide #61 models
> select subtract #61
Nothing selected
> select add #62
6187 atoms, 6372 bonds, 800 residues, 1 model selected
> color bfactor palette alphafold
329968 atoms, 46461 residues, 5 surfaces, atom bfactor range 2.06 to 104
> view #61 clip false
Drag select of 198 atoms, 529 residues, 189 bonds
> view sel
> select clear
> color #62 byhetero
> select clear
Drag select of 19 atoms, 12 residues, 18 bonds
> view sel
> hide sel cartoons
> select clear
Drag select of 15 atoms, 7 residues, 12 bonds
> view sel
> select clear
> select ligand
2028 atoms, 2186 bonds, 8 pseudobonds, 81 residues, 56 models selected
> color (#62 & sel) black
> select clear
> open
> /Users/jill/Downloads/glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA/glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA/glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif #63
---
Chain | Description
A | Entity A
Non-standard residues in glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif
#63
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif by residue attribute
pLDDT_score
> hide #62 models
> color bfactor palette alphafold
336112 atoms, 47259 residues, 5 surfaces, atom bfactor range 2.06 to 104
> view clip false
> save /Users/jill/Documents/Yuki/REE_binding_test_2023.cxs
> mlp #63
Map values for surface "glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif_A
SES surface": minimum -31.03, mean -3.82, maximum 25.2
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!63 surfaces
> coulombic #!63
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif #63/A LYS 796 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for glucoseDH_sp_P15877_DHG_ECOLI+La+PQQ_MSA_rank_0.cif_A SES
surface #63.1: minimum, -36.12, mean -2.95, maximum 16.49
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!63 surfaces
> color #!63 byhetero
> ui tool show "Side View"
> select ligand
2052 atoms, 2212 bonds, 8 pseudobonds, 82 residues, 57 models selected
> color (#!63 & sel) black
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jill/Downloads/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif
Summary of feedback from opening
/Users/jill/Downloads/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA/Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif
title:
Chai-1 predicted structure [more info...]
Chain information for
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif #1
---
Chain | Description
A | Entity A
Non-standard residues in
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif #1
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color
Hor_218_REE_2023_5_length_1114490_cov_34.010974_824+La+PQQ_MSA_rank_0.cif by
residue attribute pLDDT_score
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.6.1 (21G217)
Kernel Version: Darwin 21.6.0
Time since boot: 12 days 47 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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