Opened 2 months ago

Closed 2 months ago

#18455 closed defect (duplicate)

Crash on Mac waking from sleep

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

Description

The following bug report has been submitted:
Platform:        macOS-15.5-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 0x00000001f4165f00 (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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 59)


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{
  "uptime" : 1400000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 228771,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
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  "captureTime" : "2025-08-16 02:59:28.7298 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "6DD83723-7919-46AF-A96D-6A67A7A5828B",
  "pid" : 14735,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-08-10 16:18:06.6389 +0200",
  "procStartAbsTime" : 29146948746322,
  "procExitAbsTime" : 35311057382570,
  "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":"1F687402-3271-5C64-B8AE-19BD52A50C71","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "717FFB24-6C14-A8A5-2184-DD1E2993CA38",
  "appleIntelligenceStatus" : {"state":"available"},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "BCBBEB98-23EC-4DA9-9D53-F85E2029A0EE",
  "wakeTime" : 39515,
  "sleepWakeUUID" : "8DEB7B3D-94E5-42E9-8109-CA1DCAD7173B",
  "sip" : "enabled",
  "vmRegionInfo" : "0x64c25f908168 is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
  "exception" : {"codes":"0x0000000000000001, 0x0000e4c25f908168","rawCodes":[1,251523478094184],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e4c25f908168 -> 0x000064c25f908168 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14735},
  "vmregioninfo" : "0x64c25f908168 is not in any region.  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      UNUSED SPACE AT END",
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===== Log before crash start =====
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/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0332106_cds_0049__caprel_model.cif

Chain information for mgv-genome-0332106_cds_0049__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0332106_cds_0049__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_302458_cds_0055__caprel_model.cif

Chain information for uvig_302458_cds_0055__caprel_model.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_302458_cds_0055__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif

Chain information for
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif
#3  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif
by residue attribute pLDDT_score  

> hide #2 models

> hide #1 models

> show #2 models

> show #1 models

> color bychain

> hide #2 models

> hide #1 models

> close #3

> show #1 models

> show #2 models

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/nc_055919.1_cds_0033__caprel_model.cif

Chain information for nc_055919.1_cds_0033__caprel_model.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Color nc_055919.1_cds_0033__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_316842_cds_0025__caprel_model.cif

Chain information for uvig_316842_cds_0025__caprel_model.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_316842_cds_0025__caprel_model.cif by residue attribute pLDDT_score  

> ui tool show Matchmaker

> matchmaker #2-4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker mgv-genome-0332106_cds_0049__caprel_model.cif, chain B (#1) with
uvig_302458_cds_0055__caprel_model.cif, chain B (#2), sequence alignment score
= 1928.7  
RMSD between 266 pruned atom pairs is 0.646 angstroms; (across all 376 pairs:
7.960)  
  
Matchmaker mgv-genome-0332106_cds_0049__caprel_model.cif, chain B (#1) with
nc_055919.1_cds_0033__caprel_model.cif, chain B (#3), sequence alignment score
= 1938.9  
RMSD between 335 pruned atom pairs is 0.637 angstroms; (across all 376 pairs:
1.279)  
  
Matchmaker mgv-genome-0332106_cds_0049__caprel_model.cif, chain B (#1) with
uvig_316842_cds_0025__caprel_model.cif, chain B (#4), sequence alignment score
= 1932.3  
RMSD between 348 pruned atom pairs is 0.600 angstroms; (across all 376 pairs:
1.237)  
  

> set bgColor white

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting flat

> view

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> hide #1 models

> show #1 models

> select clear

> select :.A

Expected an objects specifier or a keyword  

> select A

Expected an objects specifier or a keyword  

> select :a

Nothing selected  

> select :A

Nothing selected  

> select :B

Nothing selected  

> color bfactor

14577 atoms, 1818 residues, atom bfactor range 19.5 to 98.7  

> color bychain

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for mgv-genome-0332106_cds_0049__caprel_model.cif_A SES
surface #1.1: minimum, -12.76, mean -2.72, maximum 8.31  
Coulombic values for mgv-genome-0332106_cds_0049__caprel_model.cif_B SES
surface #1.2: minimum, -13.27, mean 2.66, maximum 19.92  
Coulombic values for uvig_302458_cds_0055__caprel_model.cif_A SES surface
#2.1: minimum, -19.21, mean -0.24, maximum 12.50  
Coulombic values for uvig_302458_cds_0055__caprel_model.cif_B SES surface
#2.2: minimum, -13.42, mean 2.55, maximum 17.78  
Coulombic values for nc_055919.1_cds_0033__caprel_model.cif_A SES surface
#3.1: minimum, -12.67, mean -3.63, maximum 5.09  
Coulombic values for nc_055919.1_cds_0033__caprel_model.cif_B SES surface
#3.2: minimum, -13.19, mean 2.73, maximum 18.71  
Coulombic values for uvig_316842_cds_0025__caprel_model.cif_A SES surface
#4.1: minimum, -12.58, mean -2.84, maximum 7.14  
Coulombic values for uvig_316842_cds_0025__caprel_model.cif_B SES surface
#4.2: minimum, -13.20, mean 2.71, maximum 19.93  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 80

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #2/B #3/B #4/B

Alignment identifier is 1  

> select #1/B:1 #2/B:1 #3/B:1 #4/B:1

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

> select #1/B:1-234 #2/B:1-234 #3/B:1-234 #4/B:1-234

7596 atoms, 7720 bonds, 936 residues, 4 models selected  
. [ID: 1] region 4 chains [1-234] RMSD: 1.511  
  

> color (#!1-4 & sel) purple

> select #1/B:333-376 #2/B:333-376 #3/B:333-376 #4/B:333-376

1396 atoms, 1424 bonds, 176 residues, 4 models selected  

> select #1/B:234-376 #2/B:234-376 #3/B:234-376 #4/B:234-376

4556 atoms, 4624 bonds, 572 residues, 4 models selected  
. [ID: 1] region 4 chains [234-376] RMSD: 9.397  
  

> color (#!1-4 & sel) dark gray

> select clear

> select #1/B:284-376 #2/B:284-376 #3/B:284-376 #4/B:284-376

2992 atoms, 3048 bonds, 372 residues, 4 models selected  

> select #1/B #2/B #3/B #4/B

12116 atoms, 12312 bonds, 1504 residues, 4 models selected  
. [ID: 1] region 4 chains [1-376] RMSD: 5.917  
  

> select ~sel

2461 atoms, 2494 bonds, 314 residues, 4 models selected  

> color (#!1-4 & sel) orange

> transparency (#!1-4 & sel) 90

> select clear

> ui tool show Contacts

> contacts ignoreHiddenModels true color #ff1c00

195530 contacts  

> undo

> redo

> undo

> redo

> transparency 90

> select clear

> ui tool show Contacts

> contacts interModel false intraMol false ignoreHiddenModels true color
> #ff1c00

431 contacts  

> contacts interModel false intraMol false ignoreHiddenModels true color
> #ff1c00

431 contacts  

> select #1/B

3029 atoms, 3078 bonds, 376 residues, 1 model selected  

> select #1/A

734 atoms, 743 bonds, 96 residues, 1 model selected  

> color (#!1 & sel) orange

> color (#!1 & sel) yellow

> select #2/A

485 atoms, 492 bonds, 58 residues, 1 model selected  

> select #3/A

713 atoms, 725 bonds, 92 residues, 1 model selected  

> color (#!3 & sel) #ffb53cff

> color (#!3 & sel) #ffb43dff

> color (#!3 & sel) #ffb33eff

> color (#!3 & sel) #ffb648ff

> color (#!3 & sel) #ffb955ff

> color (#!3 & sel) #ffba5bff

> color (#!3 & sel) #ffbb5fff

> color (#!3 & sel) #ffbb60ff

> color (#!3 & sel) #ffbb5fff

> color (#!3 & sel) #ffbe60ff

> color (#!3 & sel) #ffc461ff

> color (#!3 & sel) #ffcc62ff

> color (#!3 & sel) #ffd363ff

> color (#!3 & sel) #ffd863ff

> color (#!3 & sel) #ffdd64ff

> color (#!3 & sel) #ffe464ff

> color (#!3 & sel) #ffe664ff

> color (#!3 & sel) #ffe965ff

> color (#!3 & sel) #ffeb65ff

> color (#!3 & sel) #ffed65ff

> color (#!3 & sel) #ffee65ff

> color (#!3 & sel) #ffef65ff

> color (#!3 & sel) #ffee65ff

> color (#!3 & sel) #ffed63ff

> color (#!3 & sel) #ffe962ff

> color (#!3 & sel) #ffe661ff

> color (#!3 & sel) #ffe460ff

> color (#!3 & sel) #ffe260ff

> color (#!3 & sel) #ffe160ff

> color (#!3 & sel) #ffe060ff

> color (#!3 & sel) #ffdc61ff

> color (#!3 & sel) #ffd862ff

> color (#!3 & sel) #ffd462ff

> color (#!3 & sel) #ffcc62ff

> color (#!3 & sel) #ffcb63ff

> color (#!3 & sel) #ffc963ff

> color (#!3 & sel) #ffc863ff

> color (#!3 & sel) #ffc763ff

> color (#!3 & sel) #ffc663ff

> color (#!3 & sel) #ffc664ff

> color (#!3 & sel) #ffc565ff

> color (#!3 & sel) #ffc266ff

> color (#!3 & sel) #ffbf67ff

> color (#!3 & sel) #ffbf68ff

> color (#!3 & sel) #ffbd68ff

> color (#!3 & sel) #ffbc69ff

> color (#!3 & sel) #ffbb6aff

> color (#!3 & sel) #ffbb6bff

> color (#!3 & sel) #ffba6cff

> color (#!3 & sel) #ffba6dff

> color (#!3 & sel) #ffbb6dff

> select clear

> transparency 80

> undo

> select #1/B:332-376 #2/B:332-376 #3/B:332-376 #4/B:332-376

1428 atoms, 1456 bonds, 180 residues, 4 models selected  

> select #1/B #2/B #3/B #4/B

12116 atoms, 12312 bonds, 1504 residues, 4 models selected  
. [ID: 1] region 4 chains [1-376] RMSD: 5.917  
  

> select ~sel

2461 atoms, 2494 bonds, 314 residues, 4 models selected  

> color (#!1-4 & sel) orange

> select clear

> transparency 90

> cartoon style xsection rectangle modeHelix default

> undo

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #5 models

> show #5 models

> hide #5 models

> open
> /Users/aegorov/Downloads/fold_funrel_check_x10/fold_funrel_check_x10_model_0.cif

Chain information for fold_funrel_check_x10_model_0.cif #6  
---  
Chain | Description  
A B C D E F G H I J | .  
  

> hide #!1 models

> hide #6 surfaces

> select add #6

34760 atoms, 35330 bonds, 4240 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> select clear

> color #6 #587f9cff

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A #6/B #6/C #6/D #6/E #6/F #6/G #6/H #6/I #6/J

Alignment identifier is 2  

> color #6 #879eaaff

> select #6/A-J:3-7

430 atoms, 430 bonds, 50 residues, 1 model selected  

> select #6/A-J:3-126

10380 atoms, 10580 bonds, 1240 residues, 1 model selected  

> select #6/A-J:45-46

160 atoms, 150 bonds, 20 residues, 1 model selected  

> select #6/A-J:45-215

14080 atoms, 14340 bonds, 1710 residues, 1 model selected  

> color sel purple

> select #6/A-J:302-308

600 atoms, 610 bonds, 70 residues, 1 model selected  

> select #6/A-J:216-308

7500 atoms, 7590 bonds, 930 residues, 1 model selected  

> color sel #aa3172ff

> color sel #aa3374ff

> color sel #aa3474ff

> color sel #aa3473ff

> color sel #aa3572ff

> color sel #aa3472ff

> color sel #aa3271ff

> color sel #aa3170ff

> color sel #aa2e6cff

> color sel #aa2c66ff

> color sel #aa2c64ff

> color sel #aa2b64ff

> color sel #aa2b65ff

> color sel #aa2a66ff

> color sel #aa2a67ff

> color sel #aa2a68ff

> color sel #aa2a69ff

> color sel #aa2b68ff

> color sel #aa2c67ff

> color sel #aa2d67ff

> color sel #aa2e67ff

> color sel #aa3069ff

> color sel #aa3169ff

> color sel #aa316aff

> color sel #aa306bff

> color sel #aa2e6eff

> color sel #aa2c70ff

> color sel #aa2874ff

> color sel #aa2775ff

> color sel #aa2676ff

> color sel #aa2577ff

> color sel #aa2677ff

> color sel #aa2775ff

> color sel #aa2774ff

> color sel #aa2873ff

> color sel #aa2870ff

> color sel #aa286fff

> color sel #aa296fff

> color sel #aa2c72ff

> color sel #aa2e76ff

> color sel #aa2f7bff

> color sel #aa2e80ff

> color sel #aa2d85ff

> color sel #aa2c8aff

> color sel #aa2b8dff

> color sel #aa2b8fff

> color sel #aa2a91ff

> color sel #aa2992ff

> color sel #aa2993ff

> color sel #aa2893ff

> color sel #aa2891ff

> color sel #aa298bff

> color sel #aa2a80ff

> color sel #aa2a7cff

> color sel #aa2a76ff

> color sel #aa2a75ff

> color sel #aa2973ff

> color sel #aa2972ff

> color sel #aa2971ff

> color sel #aa2870ff

> color sel #aa276fff

> color sel #aa276eff

> color sel #aa266eff

> color sel #aa266cff

> color sel #aa276bff

> color sel #aa2b67ff

> color sel #aa2c65ff

> color sel #aa2f63ff

> color sel #aa3064ff

> color sel #aa3265ff

> color sel #aa3365ff

> color sel #aa3466ff

> color sel #aa3566ff

> color sel #aa3565ff

> color sel #aa3461ff

> color sel #aa2f59ff

> color sel #aa2b53ff

> color sel #aa264aff

> color sel #aa2549ff

> color sel #aa2446ff

> color sel #aa213fff

> color sel #aa213bff

> color sel #aa2031ff

> color sel #aa4d22ff

> color sel #aa4926ff

> color sel #aa4627ff

> color sel #aa432aff

> color sel #aa412bff

> color sel #aa3b2fff

> color sel #aa313aff

> color sel #aa3143ff

> color sel #aa304fff

> color sel #aa3051ff

> color sel #aa3054ff

> color sel #aa3055ff

> color sel #aa3159ff

> color sel #aa3059ff

> color sel #aa305aff

> color sel #aa2f5aff

> color sel #aa2f59ff

> color sel #aa2e59ff

> color sel #aa2d59ff

> color sel #aa2c59ff

> color sel #aa2b5aff

> color sel #aa2a5bff

> color sel #aa295bff

> color sel #aa285bff

> color sel #aa275aff

> color sel #aa2759ff

> color sel #aa2659ff

> color sel #aa2759ff

> color sel #aa275aff

> color sel #aa285cff

> color sel #aa295fff

> color sel #aa2a60ff

> color sel #aa2b63ff

> color sel #aa2b64ff

> color sel #aa2c65ff

> color sel #aa2c67ff

> color sel #aa2c68ff

> color sel #aa2c69ff

> color sel #aa2c6aff

> color sel #aa2d6bff

> color sel #aa2d6dff

> color sel #aa2e6eff

> color sel #aa2e6fff

> color sel #aa2f70ff

> color sel #aa2f71ff

> color sel #aa2f72ff

> color sel #aa2f73ff

> color sel #aa3074ff

> color sel #aa3075ff

> color sel #aa3176ff

> color sel #aa3276ff

> color sel #aa3277ff

> color sel #aa2e70ff

> color sel #aa2d6eff

> select clear

> select #6/A-J:39-40

140 atoms, 130 bonds, 20 residues, 1 model selected  

> select #6/A-J:39-208

13920 atoms, 14190 bonds, 1700 residues, 1 model selected  

> color sel #aa2b35ff

> color sel #aa2c35ff

> color sel #aa3c45ff

> color sel #aa464fff

> color sel #aa5861ff

> color sel #aa646eff

> color sel #aa646fff

> color sel #aa6372ff

> color sel #aa6275ff

> color sel #aa5f7aff

> color sel #aa5f7bff

> color sel #aa5a82ff

> color sel #aa5892ff

> color sel #aa5799ff

> color sel #aa56a0ff

> color sel #aa59a4ff

> color sel #aa5ba6ff

> color sel #aa5da8ff

> color sel #a361aaff

> color sel #9e60aaff

> color sel #9c5faaff

> color sel #925baaff

> color sel #915aaaff

> color sel #8d57aaff

> color sel #8b55aaff

> color sel #8a54aaff

> color sel #8852aaff

> color sel #8853aaff

> color sel #8956aaff

> color sel #8a57aaff

> color sel #8a58aaff

> color sel #8b58aaff

> color sel #8c59aaff

> color sel #8e5aaaff

> color sel #945faaff

> color sel #9660aaff

> color sel #9661aaff

> color sel #9861aaff

> color sel #9761aaff

> color sel #9460aaff

> color sel #935faaff

> color sel #925faaff

> color sel #915eaaff

> color sel #905eaaff

> color sel #905daaff

> color sel #905caaff

> color sel #8f5caaff

> color sel #8f5baaff

> color sel #8f5aaaff

> color sel #8e5aaaff

> color sel #8e59aaff

> color sel #8c57aaff

> color sel #8b57aaff

> color sel #8b56aaff

> select clear

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> hide #6 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> open /Users/aegorov/Downloads/Unknown-12.pdb

Unknown-12.pdb title:  
job_A-AF-Q3EBB9-F1-model_v4 [more info...]  
  
Chain information for Unknown-12.pdb  
---  
Chain | Description  
7.1/A | No description available  
7.2/A | No description available  
  

> hide #7.1 models

> show #7.1 models

> hide #7.1 models

> hide #!7 models

> hide #!4 models

> show #7.1 models

> color #7.2 #eddb00ff

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/aegorov/Desktop/movie1.mp4

Movie saved to /Users/aegorov/Desktop/movie1.mp4  
  

> hide #!7 models

> hide #7.2 models

> hide #7.1 models

> show #!1 models

> show #5 models

> select #1/B:193 #2/B:193 #3/B:193 #4/B:193

20 atoms, 16 bonds, 4 residues, 4 models selected  

> select #1/B:193-242 #2/B:193-242 #3/B:193-242 #4/B:193-242

1604 atoms, 1640 bonds, 200 residues, 4 models selected  
. [ID: 1] region 4 chains [193-242] RMSD: 0.804  
  

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [158] RMSD: 0.240  
  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [119] RMSD: 0.315  
  

> hide #5 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> select #1/B:116-117 #2/B:116-117 #3/B:116-117 #4/B:116-117

32 atoms, 28 bonds, 8 residues, 4 models selected  

> select #1/B:116-120 #2/B:116-120 #3/B:116-120 #4/B:116-120

120 atoms, 116 bonds, 20 residues, 4 models selected  
. [ID: 1] region 4 chains [116-120] RMSD: 0.320  
  

> hide sel & #!1 surfaces

> undo

> select clear

> hide #!1 surfaces

> select #1/B:122-123 #2/B:122-123 #3/B:122-123 #4/B:122-123

72 atoms, 68 bonds, 8 residues, 4 models selected  

> select #1/B:118-123 #2/B:118-123 #3/B:118-123 #4/B:118-123

192 atoms, 188 bonds, 24 residues, 4 models selected  
. [ID: 1] region 4 chains [118-123] RMSD: 0.353  
  

> select #1/B:151 #2/B:151 #3/B:151 #4/B:151

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

> select #1/B:144-151 #2/B:144-151 #3/B:144-151 #4/B:144-151

296 atoms, 300 bonds, 32 residues, 4 models selected  
. [ID: 1] region 4 chains [144-151] RMSD: 0.297  
  

> select #1/B:298 #2/B:298 #3/B:298 #4/B:298

20 atoms, 16 bonds, 4 residues, 4 models selected  

> select #1/B:289-298 #2/B:289-298 #3/B:289-298 #4/B:289-298

336 atoms, 340 bonds, 40 residues, 4 models selected  
. [ID: 1] region 4 chains [289-298] RMSD: 11.289  
  

> select #1/B:188-189 #2/B:188-189 #3/B:188-189 #4/B:188-189

64 atoms, 60 bonds, 8 residues, 4 models selected  

> select #1/B:181-189 #2/B:181-189 #3/B:181-189 #4/B:181-189

308 atoms, 304 bonds, 36 residues, 4 models selected  
. [ID: 1] region 4 chains [181-189] RMSD: 0.271  
  

> select #1/B:122 #2/B:122 #3/B:122 #4/B:122

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

> select #1/B:115-122 #2/B:115-122 #3/B:115-122 #4/B:115-122

212 atoms, 208 bonds, 32 residues, 4 models selected  
. [ID: 1] region 4 chains [115-122] RMSD: 0.329  
  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [119] RMSD: 0.315  
  

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [158] RMSD: 0.240  
  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  

> select #1/B:119 #2/B:119 #3/B:119 #4/B:119

44 atoms, 40 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [119] RMSD: 0.315  
  

> select #1/B:119,158 #2/B:119,158 #3/B:119,158 #4/B:119,158

92 atoms, 88 bonds, 8 residues, 4 models selected  
. [ID: 1] region 4 chains [119] + 1 other block RMSD: 0.280  
  

> select #1/B:82,119,158 #2/B:82,119,158 #3/B:82,119,158 #4/B:82,119,158

136 atoms, 128 bonds, 12 residues, 4 models selected  
. [ID: 1] region 4 chains [119] + 2 other blocks RMSD: 0.475  
  

> show sel & #!1 atoms

> color sel & #!1 byhetero

> color (#!1 & sel) red

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

> label height 0.7

> label height 1

> label height 2

> select clear

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!2 models

> show #!4 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  

> select #1/B:158 #2/B:158 #3/B:158 #4/B:158

48 atoms, 48 bonds, 4 residues, 4 models selected  
. [ID: 1] region 4 chains [158] RMSD: 0.240  
  

> select #1/B:119,158 #2/B:119,158 #3/B:119,158 #4/B:119,158

92 atoms, 88 bonds, 8 residues, 4 models selected  
. [ID: 1] region 4 chains [158] + 1 other block RMSD: 0.280  
  

> select #1/B:82,119,158 #2/B:82,119,158 #3/B:82,119,158 #4/B:82,119,158

136 atoms, 128 bonds, 12 residues, 4 models selected  
. [ID: 1] region 4 chains [158] + 2 other blocks RMSD: 0.475  
  

> show sel & #!2-4 atoms

> color (#!2-4 & sel) red

> select clear

> hide #!3 models

> hide #!2 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #5 models

> close #5-7

> hide #!2 models

> show #!1 models

> show #!4 models

> show #!2 models

> show #!3 models

> close #1-4

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/ivig_1847_cds_0046__caprel_model.cif

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Color ivig_1847_cds_0046__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_2526164726_000001_2526164726_2526185787_81245-120753_cds_0030__caprel_model.cif

Chain information for
imgvr_uvig_2526164726_000001_2526164726_2526185787_81245-120753_cds_0030__caprel_model.cif
#2  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_2526164726_000001_2526164726_2526185787_81245-120753_cds_0030__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif

Chain information for
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif
#3  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300008406_000360_3300008406_ga0115224_1000119_28695-83854_cds_0050__caprel_model.cif

Chain information for
imgvr_uvig_3300008406_000360_3300008406_ga0115224_1000119_28695-83854_cds_0050__caprel_model.cif
#4  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300008406_000360_3300008406_ga0115224_1000119_28695-83854_cds_0050__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif

Chain information for
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif
#5  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif

Chain information for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif
#6  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/imgvr_uvig_3300045988_117965_3300045988_ga0495776_154133_cds_0040__caprel_model.cif

Chain information for
imgvr_uvig_3300045988_117965_3300045988_ga0495776_154133_cds_0040__caprel_model.cif
#7  
---  
Chain | Description  
A | .  
B | .  
  
Color
imgvr_uvig_3300045988_117965_3300045988_ga0495776_154133_cds_0040__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0154653_cds_0001__caprel_model.cif

Chain information for mgv-genome-0154653_cds_0001__caprel_model.cif #8  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0154653_cds_0001__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0243292_cds_0030__caprel_model.cif

Chain information for mgv-genome-0243292_cds_0030__caprel_model.cif #9  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0243292_cds_0030__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0285849_cds_0029__caprel_model.cif

Chain information for mgv-genome-0285849_cds_0029__caprel_model.cif #10  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0285849_cds_0029__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0286105_cds_0054__caprel_model.cif

Chain information for mgv-genome-0286105_cds_0054__caprel_model.cif #11  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0286105_cds_0054__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0332106_cds_0049__caprel_model.cif

Chain information for mgv-genome-0332106_cds_0049__caprel_model.cif #12  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0332106_cds_0049__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0332881_cds_0021__caprel_model.cif

Chain information for mgv-genome-0332881_cds_0021__caprel_model.cif #13  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0332881_cds_0021__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-0369858_cds_0010__caprel_model.cif

Chain information for mgv-genome-0369858_cds_0010__caprel_model.cif #14  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-0369858_cds_0010__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/mgv-
> genome-4416137_cds_0026__caprel_model.cif

Chain information for mgv-genome-4416137_cds_0026__caprel_model.cif #15  
---  
Chain | Description  
A | .  
B | .  
  
Color mgv-genome-4416137_cds_0026__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/nc_055919.1_cds_0033__caprel_model.cif

Chain information for nc_055919.1_cds_0033__caprel_model.cif #16  
---  
Chain | Description  
A | .  
B | .  
  
Color nc_055919.1_cds_0033__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/samea2580206_a1_ct14209_vs1_cds_0032__caprel_model.cif

Chain information for samea2580206_a1_ct14209_vs1_cds_0032__caprel_model.cif
#17  
---  
Chain | Description  
A | .  
B | .  
  
Color samea2580206_a1_ct14209_vs1_cds_0032__caprel_model.cif by residue
attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif

Chain information for samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif #18  
---  
Chain | Description  
A | .  
B | .  
  
Color samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif

Chain information for srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif #19  
---  
Chain | Description  
A | .  
B | .  
  
Color srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif by residue
attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif

Chain information for srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif #20  
---  
Chain | Description  
A | .  
B | .  
  
Color srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/station39_mes_combined_final_node_706_length_44789_cov_5.882282_cds_0048__caprel_model.cif

Chain information for
station39_mes_combined_final_node_706_length_44789_cov_5.882282_cds_0048__caprel_model.cif
#21  
---  
Chain | Description  
A | .  
B | .  
  
Color
station39_mes_combined_final_node_706_length_44789_cov_5.882282_cds_0048__caprel_model.cif
by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/temphd_cluster_64964_cds_0014__caprel_model.cif

Chain information for temphd_cluster_64964_cds_0014__caprel_model.cif #22  
---  
Chain | Description  
A | .  
B | .  
  
Color temphd_cluster_64964_cds_0014__caprel_model.cif by residue attribute
pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_499_cds_0016__caprel_model.cif

Chain information for uvig_499_cds_0016__caprel_model.cif #23  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_499_cds_0016__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_63783_cds_0041__caprel_model.cif

Chain information for uvig_63783_cds_0041__caprel_model.cif #24  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_63783_cds_0041__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_96616_cds_0030__caprel_model.cif

Chain information for uvig_96616_cds_0030__caprel_model.cif #25  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_96616_cds_0030__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_107105_cds_0011__caprel_model.cif

Chain information for uvig_107105_cds_0011__caprel_model.cif #26  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_107105_cds_0011__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_146714_cds_0075__caprel_model.cif

Chain information for uvig_146714_cds_0075__caprel_model.cif #27  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_146714_cds_0075__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_149439_cds_0002__caprel_model.cif

Chain information for uvig_149439_cds_0002__caprel_model.cif #28  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_149439_cds_0002__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_302458_cds_0055__caprel_model.cif

Chain information for uvig_302458_cds_0055__caprel_model.cif #29  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_302458_cds_0055__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_308814_cds_0079__caprel_model.cif

Chain information for uvig_308814_cds_0079__caprel_model.cif #30  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_308814_cds_0079__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_316842_cds_0025__caprel_model.cif

Chain information for uvig_316842_cds_0025__caprel_model.cif #31  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_316842_cds_0025__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_446064_cds_0006__caprel_model.cif

Chain information for uvig_446064_cds_0006__caprel_model.cif #32  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_446064_cds_0006__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_450516_cds_0033__caprel_model.cif

Chain information for uvig_450516_cds_0033__caprel_model.cif #33  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_450516_cds_0033__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_492214__cds_0036__caprel_model.cif

Chain information for uvig_492214__cds_0036__caprel_model.cif #34  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_492214__cds_0036__caprel_model.cif by residue attribute pLDDT_score  

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/caprel/filtered_cifs/uvig_499169_cds_0013__caprel_model.cif

Chain information for uvig_499169_cds_0013__caprel_model.cif #35  
---  
Chain | Description  
A | .  
B | .  
  
Color uvig_499169_cds_0013__caprel_model.cif by residue attribute pLDDT_score  

> select
> #1/A#1/B#2/A#2/B#3/A#3/B#4/A#4/B#5/A#5/B#6/A#6/B#7/A#7/B#8/A#8/B#9/A#9/B#10/A#10/B#11/A#11/B#12/A#12/B#13/A#13/B#14/A#14/B#15/A#15/B#16/A#16/B#17/A#17/B#18/A#18/B#19/A#19/B#20/A#20/B#21/A#21/B#22/A#22/B#23/A#23/B#24/A#24/B#25/A#25/B#26/A#26/B#27/A#27/B#28/A#28/B#29/A#29/B#30/A#30/B#31/A#31/B#32/A#32/B#33/A#33/B#34/A#34/B#35/A#35/B

163749 atoms, 166631 bonds, 20306 residues, 35 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B #9/B #10/B #11/B
> #12/B #13/B #14/B #15/B #16/B #17/B #18/B #19/B #20/B #21/B #22/B #23/B
> #24/B #25/B #26/B #27/B #28/B #29/B #30/B #31/B #32/B #33/B #34/B #35/B

Alignment identifier is 1  

> select #1/B:332-376 #2/B:332-376 #3/B:332-376 #4/B:332-376 #5/B:332-376
> #6/B:332-376 #7/B:332-376 #8/B:332-376 #9/B:332-376 #10/B:332-376
> #11/B:332-376 #12/B:332-376 #13/B:332-376 #14/B:332-376 #15/B:332-376
> #16/B:332-376 #17/B:332-376 #18/B:332-376 #19/B:332-376 #20/B:332-376
> #21/B:332-376 #22/B:332-376 #23/B:332-376 #24/B:332-376 #25/B:332-376
> #26/B:332-376 #27/B:332-376 #28/B:332-376 #29/B:332-376 #30/B:332-376
> #31/B:332-376 #32/B:332-376 #33/B:332-376 #34/B:332-376 #35/B:332-376

12495 atoms, 12740 bonds, 1575 residues, 35 models selected  

> select #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B #9/B #10/B #11/B #12/B #13/B
> #14/B #15/B #16/B #17/B #18/B #19/B #20/B #21/B #22/B #23/B #24/B #25/B
> #26/B #27/B #28/B #29/B #30/B #31/B #32/B #33/B #34/B #35/B

106015 atoms, 107730 bonds, 13160 residues, 35 models selected  
. [ID: 1] region 35 chains [1-376] RMSD: 38.009  
  

> color sel dark gray

> select #1/B:237 #2/B:237 #3/B:237 #4/B:237 #5/B:237 #6/B:237 #7/B:237
> #8/B:237 #9/B:237 #10/B:237 #11/B:237 #12/B:237 #13/B:237 #14/B:237
> #15/B:237 #16/B:237 #17/B:237 #18/B:237 #19/B:237 #20/B:237 #21/B:237
> #22/B:237 #23/B:237 #24/B:237 #25/B:237 #26/B:237 #27/B:237 #28/B:237
> #29/B:237 #30/B:237 #31/B:237 #32/B:237 #33/B:237 #34/B:237 #35/B:237

210 atoms, 175 bonds, 35 residues, 35 models selected  

> select #1/B:1-237 #2/B:1-237 #3/B:1-237 #4/B:1-237 #5/B:1-237 #6/B:1-237
> #7/B:1-237 #8/B:1-237 #9/B:1-237 #10/B:1-237 #11/B:1-237 #12/B:1-237
> #13/B:1-237 #14/B:1-237 #15/B:1-237 #16/B:1-237 #17/B:1-237 #18/B:1-237
> #19/B:1-237 #20/B:1-237 #21/B:1-237 #22/B:1-237 #23/B:1-237 #24/B:1-237
> #25/B:1-237 #26/B:1-237 #27/B:1-237 #28/B:1-237 #29/B:1-237 #30/B:1-237
> #31/B:1-237 #32/B:1-237 #33/B:1-237 #34/B:1-237 #35/B:1-237

66990 atoms, 68075 bonds, 8295 residues, 35 models selected  
. [ID: 1] region 35 chains [1-237] RMSD: 39.218  
  

> color sel purple

> color sel #ed849aff

> color sel #ed71b8ff

> color sel #ed32d1ff

> color sel #ed30d0ff

> color sel #ed33e1ff

> color sel #ed31e4ff

> color sel #ed31e5ff

> color sel #cc28edff

> color sel #c624edff

> color sel #c026edff

> color sel #a636edff

> color sel #a436edff

> color sel #a639edff

> color sel #ae43edff

> color sel #b04dedff

> color sel #a556edff

> color sel #a657edff

> select #1/B:331-376 #2/B:331-376 #3/B:331-376 #4/B:331-376 #5/B:331-376
> #6/B:331-376 #7/B:331-376 #8/B:331-376 #9/B:331-376 #10/B:331-376
> #11/B:331-376 #12/B:331-376 #13/B:331-376 #14/B:331-376 #15/B:331-376
> #16/B:331-376 #17/B:331-376 #18/B:331-376 #19/B:331-376 #20/B:331-376
> #21/B:331-376 #22/B:331-376 #23/B:331-376 #24/B:331-376 #25/B:331-376
> #26/B:331-376 #27/B:331-376 #28/B:331-376 #29/B:331-376 #30/B:331-376
> #31/B:331-376 #32/B:331-376 #33/B:331-376 #34/B:331-376 #35/B:331-376

12775 atoms, 13020 bonds, 1610 residues, 35 models selected  

> select #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B #9/B #10/B #11/B #12/B #13/B
> #14/B #15/B #16/B #17/B #18/B #19/B #20/B #21/B #22/B #23/B #24/B #25/B
> #26/B #27/B #28/B #29/B #30/B #31/B #32/B #33/B #34/B #35/B

106015 atoms, 107730 bonds, 13160 residues, 35 models selected  
. [ID: 1] region 35 chains [1-376] RMSD: 38.009  
  

> select ~sel

57734 atoms, 58901 bonds, 7146 residues, 35 models selected  

> color sel orange

> select clear

> select #1/B:375-376 #2/B:375-376 #3/B:375-376 #4/B:375-376 #5/B:375-376
> #6/B:375-376 #7/B:375-376 #8/B:375-376 #9/B:375-376 #10/B:375-376
> #11/B:375-376 #12/B:375-376 #13/B:375-376 #14/B:375-376 #15/B:375-376
> #16/B:375-376 #17/B:375-376 #18/B:375-376 #19/B:375-376 #20/B:375-376
> #21/B:375-376 #22/B:375-376 #23/B:375-376 #24/B:375-376 #25/B:375-376
> #26/B:375-376 #27/B:375-376 #28/B:375-376 #29/B:375-376 #30/B:375-376
> #31/B:375-376 #32/B:375-376 #33/B:375-376 #34/B:375-376 #35/B:375-376

525 atoms, 490 bonds, 70 residues, 35 models selected  

> select #1/B:375-376 #2/B:375-376 #3/B:375-376 #4/B:375-376 #5/B:375-376
> #6/B:375-376 #7/B:375-376 #8/B:375-376 #9/B:375-376 #10/B:375-376
> #11/B:375-376 #12/B:375-376 #13/B:375-376 #14/B:375-376 #15/B:375-376
> #16/B:375-376 #17/B:375-376 #18/B:375-376 #19/B:375-376 #20/B:375-376
> #21/B:375-376 #22/B:375-376 #23/B:375-376 #24/B:375-376 #25/B:375-376
> #26/B:375-376 #27/B:375-376 #28/B:375-376 #29/B:375-376 #30/B:375-376
> #31/B:375-376 #32/B:375-376 #33/B:375-376 #34/B:375-376 #35/B:375-376

525 atoms, 490 bonds, 70 residues, 35 models selected  
. [ID: 1] region 35 chains [375-376] RMSD: 42.014  
  

> select #1/B:82 #2/B:82 #3/B:82 #4/B:82 #5/B:82 #6/B:82 #7/B:82 #8/B:82
> #9/B:82 #10/B:82 #11/B:82 #12/B:82 #13/B:82 #14/B:82 #15/B:82 #16/B:82
> #17/B:82 #18/B:82 #19/B:82 #20/B:82 #21/B:82 #22/B:82 #23/B:82 #24/B:82
> #25/B:82 #26/B:82 #27/B:82 #28/B:82 #29/B:82 #30/B:82 #31/B:82 #32/B:82
> #33/B:82 #34/B:82 #35/B:82

385 atoms, 350 bonds, 35 residues, 35 models selected  

> select #1/B:82 #2/B:82 #3/B:82 #4/B:82 #5/B:82 #6/B:82 #7/B:82 #8/B:82
> #9/B:82 #10/B:82 #11/B:82 #12/B:82 #13/B:82 #14/B:82 #15/B:82 #16/B:82
> #17/B:82 #18/B:82 #19/B:82 #20/B:82 #21/B:82 #22/B:82 #23/B:82 #24/B:82
> #25/B:82 #26/B:82 #27/B:82 #28/B:82 #29/B:82 #30/B:82 #31/B:82 #32/B:82
> #33/B:82 #34/B:82 #35/B:82

385 atoms, 350 bonds, 35 residues, 35 models selected  
. [ID: 1] region 35 chains [82] RMSD: 26.711  
  

> select #1/B:82,119 #2/B:82,119 #3/B:82,119 #4/B:82,119 #5/B:82,119
> #6/B:82,119 #7/B:82,119 #8/B:82,119 #9/B:82,119 #10/B:82,119 #11/B:82,119
> #12/B:82,119 #13/B:82,119 #14/B:82,119 #15/B:82,119 #16/B:82,119
> #17/B:82,119 #18/B:82,119 #19/B:82,119 #20/B:82,119 #21/B:82,119
> #22/B:82,119 #23/B:82,119 #24/B:82,119 #25/B:82,119 #26/B:82,119
> #27/B:82,119 #28/B:82,119 #29/B:82,119 #30/B:82,119 #31/B:82,119
> #32/B:82,119 #33/B:82,119 #34/B:82,119 #35/B:82,119

770 atoms, 700 bonds, 70 residues, 35 models selected  
. [ID: 1] region 35 chains [82] + 1 other block RMSD: 26.520  
  

> select #1/B:82,119,158 #2/B:82,119,158 #3/B:82,119,158 #4/B:82,119,158
> #5/B:82,119,158 #6/B:82,119,158 #7/B:82,119,158 #8/B:82,119,158
> #9/B:82,119,158 #10/B:82,119,158 #11/B:82,119,158 #12/B:82,119,158
> #13/B:82,119,158 #14/B:82,119,158 #15/B:82,119,158 #16/B:82,119,158
> #17/B:82,119,158 #18/B:82,119,158 #19/B:82,119,158 #20/B:82,119,158
> #21/B:82,119,158 #22/B:82,119,158 #23/B:82,119,158 #24/B:82,119,158
> #25/B:82,119,158 #26/B:82,119,158 #27/B:82,119,158 #28/B:82,119,158
> #29/B:82,119,158 #30/B:82,119,158 #31/B:82,119,158 #32/B:82,119,158
> #33/B:82,119,158 #34/B:82,119,158 #35/B:82,119,158

1190 atoms, 1120 bonds, 105 residues, 35 models selected  
. [ID: 1] region 35 chains [82] + 2 other blocks RMSD: 26.649  
  

> show sel atoms

> color sel red

> select clear

> ui tool show Matchmaker

> matchmaker #3-35 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif,
chain B (#3), sequence alignment score = 1878  
RMSD between 256 pruned atom pairs is 0.671 angstroms; (across all 376 pairs:
16.373)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300008406_000360_3300008406_ga0115224_1000119_28695-83854_cds_0050__caprel_model.cif,
chain B (#4), sequence alignment score = 1850.7  
RMSD between 258 pruned atom pairs is 0.760 angstroms; (across all 376 pairs:
12.310)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif,
chain B (#5), sequence alignment score = 1867.5  
RMSD between 256 pruned atom pairs is 0.710 angstroms; (across all 376 pairs:
12.086)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif,
chain B (#6), sequence alignment score = 1863.3  
RMSD between 238 pruned atom pairs is 0.657 angstroms; (across all 376 pairs:
12.162)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300045988_117965_3300045988_ga0495776_154133_cds_0040__caprel_model.cif,
chain B (#7), sequence alignment score = 1918.2  
RMSD between 345 pruned atom pairs is 0.468 angstroms; (across all 376 pairs:
1.547)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0154653_cds_0001__caprel_model.cif, chain B (#8), sequence alignment
score = 1857.3  
RMSD between 234 pruned atom pairs is 0.980 angstroms; (across all 376 pairs:
15.394)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0243292_cds_0030__caprel_model.cif, chain B (#9), sequence alignment
score = 1846.5  
RMSD between 247 pruned atom pairs is 0.814 angstroms; (across all 376 pairs:
13.019)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0285849_cds_0029__caprel_model.cif, chain B (#10), sequence alignment
score = 1868.1  
RMSD between 245 pruned atom pairs is 0.767 angstroms; (across all 376 pairs:
12.218)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0286105_cds_0054__caprel_model.cif, chain B (#11), sequence alignment
score = 1870.5  
RMSD between 256 pruned atom pairs is 0.751 angstroms; (across all 376 pairs:
12.124)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0332106_cds_0049__caprel_model.cif, chain B (#12), sequence alignment
score = 1855.5  
RMSD between 254 pruned atom pairs is 0.779 angstroms; (across all 376 pairs:
12.277)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0332881_cds_0021__caprel_model.cif, chain B (#13), sequence alignment
score = 1867.5  
RMSD between 254 pruned atom pairs is 0.783 angstroms; (across all 376 pairs:
12.331)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0369858_cds_0010__caprel_model.cif, chain B (#14), sequence alignment
score = 1881.9  
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 376 pairs:
12.346)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-4416137_cds_0026__caprel_model.cif, chain B (#15), sequence alignment
score = 1878.3  
RMSD between 242 pruned atom pairs is 0.779 angstroms; (across all 376 pairs:
12.695)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
nc_055919.1_cds_0033__caprel_model.cif, chain B (#16), sequence alignment
score = 1877.7  
RMSD between 261 pruned atom pairs is 0.697 angstroms; (across all 376 pairs:
11.635)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
samea2580206_a1_ct14209_vs1_cds_0032__caprel_model.cif, chain B (#17),
sequence alignment score = 1881.3  
RMSD between 257 pruned atom pairs is 0.721 angstroms; (across all 376 pairs:
11.819)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif, chain B (#18), sequence
alignment score = 1867.5  
RMSD between 254 pruned atom pairs is 0.739 angstroms; (across all 376 pairs:
11.723)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif, chain B (#19), sequence
alignment score = 1865.1  
RMSD between 245 pruned atom pairs is 0.747 angstroms; (across all 376 pairs:
15.883)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif, chain B (#20), sequence
alignment score = 1874.7  
RMSD between 260 pruned atom pairs is 0.704 angstroms; (across all 376 pairs:
12.206)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
station39_mes_combined_final_node_706_length_44789_cov_5.882282_cds_0048__caprel_model.cif,
chain B (#21), sequence alignment score = 1921.5  
RMSD between 365 pruned atom pairs is 0.486 angstroms; (across all 376 pairs:
0.982)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
temphd_cluster_64964_cds_0014__caprel_model.cif, chain B (#22), sequence
alignment score = 1870.5  
RMSD between 257 pruned atom pairs is 0.683 angstroms; (across all 376 pairs:
12.097)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_499_cds_0016__caprel_model.cif, chain B (#23), sequence alignment score =
1871.1  
RMSD between 257 pruned atom pairs is 0.737 angstroms; (across all 376 pairs:
12.012)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_63783_cds_0041__caprel_model.cif, chain B (#24), sequence alignment score
= 1870.5  
RMSD between 258 pruned atom pairs is 0.716 angstroms; (across all 376 pairs:
12.134)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_96616_cds_0030__caprel_model.cif, chain B (#25), sequence alignment score
= 1866.9  
RMSD between 246 pruned atom pairs is 0.803 angstroms; (across all 376 pairs:
12.253)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_107105_cds_0011__caprel_model.cif, chain B (#26), sequence alignment
score = 1871.1  
RMSD between 259 pruned atom pairs is 0.698 angstroms; (across all 376 pairs:
12.110)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_146714_cds_0075__caprel_model.cif, chain B (#27), sequence alignment
score = 1877.7  
RMSD between 262 pruned atom pairs is 0.678 angstroms; (across all 376 pairs:
12.035)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_149439_cds_0002__caprel_model.cif, chain B (#28), sequence alignment
score = 1898.4  
RMSD between 344 pruned atom pairs is 0.423 angstroms; (across all 376 pairs:
1.392)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_302458_cds_0055__caprel_model.cif, chain B (#29), sequence alignment
score = 1880.7  
RMSD between 243 pruned atom pairs is 0.840 angstroms; (across all 376 pairs:
16.329)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_308814_cds_0079__caprel_model.cif, chain B (#30), sequence alignment
score = 1870.5  
RMSD between 250 pruned atom pairs is 0.750 angstroms; (across all 376 pairs:
12.077)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_316842_cds_0025__caprel_model.cif, chain B (#31), sequence alignment
score = 1877.7  
RMSD between 255 pruned atom pairs is 0.740 angstroms; (across all 376 pairs:
12.366)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_446064_cds_0006__caprel_model.cif, chain B (#32), sequence alignment
score = 1918.2  
RMSD between 334 pruned atom pairs is 0.451 angstroms; (across all 376 pairs:
1.512)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_450516_cds_0033__caprel_model.cif, chain B (#33), sequence alignment
score = 1881.3  
RMSD between 263 pruned atom pairs is 0.671 angstroms; (across all 376 pairs:
11.768)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_492214__cds_0036__caprel_model.cif, chain B (#34), sequence alignment
score = 1871.1  
RMSD between 262 pruned atom pairs is 0.631 angstroms; (across all 376 pairs:
6.545)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_499169_cds_0013__caprel_model.cif, chain B (#35), sequence alignment
score = 1903.2  
RMSD between 352 pruned atom pairs is 0.462 angstroms; (across all 376 pairs:
1.235)  
  

> matchmaker #3-35 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif,
chain B (#3), sequence alignment score = 1878  
RMSD between 256 pruned atom pairs is 0.671 angstroms; (across all 376 pairs:
16.373)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300008406_000360_3300008406_ga0115224_1000119_28695-83854_cds_0050__caprel_model.cif,
chain B (#4), sequence alignment score = 1850.7  
RMSD between 258 pruned atom pairs is 0.760 angstroms; (across all 376 pairs:
12.310)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif,
chain B (#5), sequence alignment score = 1867.5  
RMSD between 256 pruned atom pairs is 0.710 angstroms; (across all 376 pairs:
12.086)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif,
chain B (#6), sequence alignment score = 1863.3  
RMSD between 238 pruned atom pairs is 0.657 angstroms; (across all 376 pairs:
12.162)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
imgvr_uvig_3300045988_117965_3300045988_ga0495776_154133_cds_0040__caprel_model.cif,
chain B (#7), sequence alignment score = 1918.2  
RMSD between 345 pruned atom pairs is 0.468 angstroms; (across all 376 pairs:
1.547)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0154653_cds_0001__caprel_model.cif, chain B (#8), sequence alignment
score = 1857.3  
RMSD between 234 pruned atom pairs is 0.980 angstroms; (across all 376 pairs:
15.394)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0243292_cds_0030__caprel_model.cif, chain B (#9), sequence alignment
score = 1846.5  
RMSD between 247 pruned atom pairs is 0.814 angstroms; (across all 376 pairs:
13.019)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0285849_cds_0029__caprel_model.cif, chain B (#10), sequence alignment
score = 1868.1  
RMSD between 245 pruned atom pairs is 0.767 angstroms; (across all 376 pairs:
12.218)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0286105_cds_0054__caprel_model.cif, chain B (#11), sequence alignment
score = 1870.5  
RMSD between 256 pruned atom pairs is 0.751 angstroms; (across all 376 pairs:
12.124)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0332106_cds_0049__caprel_model.cif, chain B (#12), sequence alignment
score = 1855.5  
RMSD between 254 pruned atom pairs is 0.779 angstroms; (across all 376 pairs:
12.277)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0332881_cds_0021__caprel_model.cif, chain B (#13), sequence alignment
score = 1867.5  
RMSD between 254 pruned atom pairs is 0.783 angstroms; (across all 376 pairs:
12.331)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-0369858_cds_0010__caprel_model.cif, chain B (#14), sequence alignment
score = 1881.9  
RMSD between 254 pruned atom pairs is 0.784 angstroms; (across all 376 pairs:
12.346)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with mgv-
genome-4416137_cds_0026__caprel_model.cif, chain B (#15), sequence alignment
score = 1878.3  
RMSD between 242 pruned atom pairs is 0.779 angstroms; (across all 376 pairs:
12.695)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
nc_055919.1_cds_0033__caprel_model.cif, chain B (#16), sequence alignment
score = 1877.7  
RMSD between 261 pruned atom pairs is 0.697 angstroms; (across all 376 pairs:
11.635)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
samea2580206_a1_ct14209_vs1_cds_0032__caprel_model.cif, chain B (#17),
sequence alignment score = 1881.3  
RMSD between 257 pruned atom pairs is 0.721 angstroms; (across all 376 pairs:
11.819)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif, chain B (#18), sequence
alignment score = 1867.5  
RMSD between 254 pruned atom pairs is 0.739 angstroms; (across all 376 pairs:
11.723)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif, chain B (#19), sequence
alignment score = 1865.1  
RMSD between 245 pruned atom pairs is 0.747 angstroms; (across all 376 pairs:
15.883)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif, chain B (#20), sequence
alignment score = 1874.7  
RMSD between 260 pruned atom pairs is 0.704 angstroms; (across all 376 pairs:
12.206)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
station39_mes_combined_final_node_706_length_44789_cov_5.882282_cds_0048__caprel_model.cif,
chain B (#21), sequence alignment score = 1921.5  
RMSD between 365 pruned atom pairs is 0.486 angstroms; (across all 376 pairs:
0.982)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
temphd_cluster_64964_cds_0014__caprel_model.cif, chain B (#22), sequence
alignment score = 1870.5  
RMSD between 257 pruned atom pairs is 0.683 angstroms; (across all 376 pairs:
12.097)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_499_cds_0016__caprel_model.cif, chain B (#23), sequence alignment score =
1871.1  
RMSD between 257 pruned atom pairs is 0.737 angstroms; (across all 376 pairs:
12.012)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_63783_cds_0041__caprel_model.cif, chain B (#24), sequence alignment score
= 1870.5  
RMSD between 258 pruned atom pairs is 0.716 angstroms; (across all 376 pairs:
12.134)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_96616_cds_0030__caprel_model.cif, chain B (#25), sequence alignment score
= 1866.9  
RMSD between 246 pruned atom pairs is 0.803 angstroms; (across all 376 pairs:
12.253)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_107105_cds_0011__caprel_model.cif, chain B (#26), sequence alignment
score = 1871.1  
RMSD between 259 pruned atom pairs is 0.698 angstroms; (across all 376 pairs:
12.110)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_146714_cds_0075__caprel_model.cif, chain B (#27), sequence alignment
score = 1877.7  
RMSD between 262 pruned atom pairs is 0.678 angstroms; (across all 376 pairs:
12.035)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_149439_cds_0002__caprel_model.cif, chain B (#28), sequence alignment
score = 1898.4  
RMSD between 344 pruned atom pairs is 0.423 angstroms; (across all 376 pairs:
1.392)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_302458_cds_0055__caprel_model.cif, chain B (#29), sequence alignment
score = 1880.7  
RMSD between 243 pruned atom pairs is 0.840 angstroms; (across all 376 pairs:
16.329)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_308814_cds_0079__caprel_model.cif, chain B (#30), sequence alignment
score = 1870.5  
RMSD between 250 pruned atom pairs is 0.750 angstroms; (across all 376 pairs:
12.077)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_316842_cds_0025__caprel_model.cif, chain B (#31), sequence alignment
score = 1877.7  
RMSD between 255 pruned atom pairs is 0.740 angstroms; (across all 376 pairs:
12.366)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_446064_cds_0006__caprel_model.cif, chain B (#32), sequence alignment
score = 1918.2  
RMSD between 334 pruned atom pairs is 0.451 angstroms; (across all 376 pairs:
1.512)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_450516_cds_0033__caprel_model.cif, chain B (#33), sequence alignment
score = 1881.3  
RMSD between 263 pruned atom pairs is 0.671 angstroms; (across all 376 pairs:
11.768)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_492214__cds_0036__caprel_model.cif, chain B (#34), sequence alignment
score = 1871.1  
RMSD between 262 pruned atom pairs is 0.631 angstroms; (across all 376 pairs:
6.545)  
  
Matchmaker ivig_1847_cds_0046__caprel_model.cif, chain B (#1) with
uvig_499169_cds_0013__caprel_model.cif, chain B (#35), sequence alignment
score = 1903.2  
RMSD between 352 pruned atom pairs is 0.462 angstroms; (across all 376 pairs:
1.235)  
  

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> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/json_files_homologs_caprel/CCZ70856.1__caprel.json

Failed opening file
/Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/json_files_homologs_caprel/CCZ70856.1__caprel.json:  
Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open
/Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/json_files_homologs_caprel/CCZ70856.1__caprel.json
format pae structure #1  

> hide #31 models

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> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> view #1 clip false

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #15 models

> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> show #1 models

> hide #1 models

> show #2 models

> log metadata #2

The model has no metadata

> log chains #2

Chain information for
imgvr_uvig_2526164726_000001_2526164726_2526185787_81245-120753_cds_0030__caprel_model.cif
#2  
---  
Chain | Description  
A | .  
B | .  
  

> hide #2 models

> show #3 models

> log metadata #3

The model has no metadata

> log chains #3

Chain information for
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif
#3  
---  
Chain | Description  
A | .  
B | .  
  

> hide #3 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #3 models

> log metadata #3

The model has no metadata

> log chains #3

Chain information for
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif
#3  
---  
Chain | Description  
A | .  
B | .  
  

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> log metadata #5

The model has no metadata

> log chains #5

Chain information for
imgvr_uvig_3300025711_000255_3300025711_ga0207696_1000048_102954-133738_cds_0029__caprel_model.cif
#5  
---  
Chain | Description  
A | .  
B | .  
  

> hide #5 models

> show #6 models

> log metadata #6

The model has no metadata

> log chains #6

Chain information for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif
#6  
---  
Chain | Description  
A | .  
B | .  
  

> log metadata #6

The model has no metadata

> log chains #6

Chain information for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif
#6  
---  
Chain | Description  
A | .  
B | .  
  

> hide #6 models

> show #7 models

> hide #7 models

> show #6 models

> log metadata #6

The model has no metadata

> log chains #6

Chain information for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif
#6  
---  
Chain | Description  
A | .  
B | .  
  

> hide #6 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> log metadata #9

The model has no metadata

> log chains #9

Chain information for mgv-genome-0243292_cds_0030__caprel_model.cif #9  
---  
Chain | Description  
A | .  
B | .  
  

> log metadata #9

The model has no metadata

> log chains #9

Chain information for mgv-genome-0243292_cds_0030__caprel_model.cif #9  
---  
Chain | Description  
A | .  
B | .  
  

> hide #9 models

> show #10 models

> log metadata #10

The model has no metadata

> log chains #10

Chain information for mgv-genome-0285849_cds_0029__caprel_model.cif #10  
---  
Chain | Description  
A | .  
B | .  
  

> hide #10 models

> show #11 models

> log metadata #11

The model has no metadata

> log chains #11

Chain information for mgv-genome-0286105_cds_0054__caprel_model.cif #11  
---  
Chain | Description  
A | .  
B | .  
  

> show #12 models

> hide #11 models

> hide #12 models

> show #13 models

> log metadata #13

The model has no metadata

> log chains #13

Chain information for mgv-genome-0332881_cds_0021__caprel_model.cif #13  
---  
Chain | Description  
A | .  
B | .  
  

> hide #13 models

> show #14 models

> log metadata #14

The model has no metadata

> log chains #14

Chain information for mgv-genome-0369858_cds_0010__caprel_model.cif #14  
---  
Chain | Description  
A | .  
B | .  
  

> hide #14 models

> show #15 models

> log metadata #15

The model has no metadata

> log chains #15

Chain information for mgv-genome-4416137_cds_0026__caprel_model.cif #15  
---  
Chain | Description  
A | .  
B | .  
  

> hide #15 models

> show #16 models

> log metadata #16

The model has no metadata

> log chains #16

Chain information for nc_055919.1_cds_0033__caprel_model.cif #16  
---  
Chain | Description  
A | .  
B | .  
  

> hide #16 models

> show #17 models

> hide #17 models

> show #18 models

> log metadata #18

The model has no metadata

> log chains #18

Chain information for samn00715152_b1_ct5_vs2_cds_0015__caprel_model.cif #18  
---  
Chain | Description  
A | .  
B | .  
  

> hide #18 models

> show #19 models

> log metadata #19

The model has no metadata

> log chains #19

Chain information for srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif #19  
---  
Chain | Description  
A | .  
B | .  
  

> hide #19 models

> show #20 models

> show #20 target m

> hide #20 models

> show #19 models

> hide #19 models

> show #20 models

> hide #20 models

> show #19 models

> hide #19 models

> show #20 models

> hide #20 models

> show #19 models

> hide #19 models

> show #20 models

> hide #20 models

> show #19 models

> hide #19 models

> show #20 models

> log metadata #20

The model has no metadata

> log chains #20

Chain information for srs147664_a1_ct51078_vs1_cds_0026__caprel_model.cif #20  
---  
Chain | Description  
A | .  
B | .  
  

> hide #20 models

> show #21 models

> hide #21 models

> show #22 models

> hide #22 models

> show #23 models

> hide #23 models

> show #24 models

> hide #24 models

> show #25 models

> hide #25 models

> show #26 models

> log metadata #26

The model has no metadata

> log chains #26

Chain information for uvig_107105_cds_0011__caprel_model.cif #26  
---  
Chain | Description  
A | .  
B | .  
  

> hide #26 models

> show #27 models

> hide #27 models

> show #28 models

> hide #28 models

> show #29 models

> log metadata #29

The model has no metadata

> log chains #29

Chain information for uvig_302458_cds_0055__caprel_model.cif #29  
---  
Chain | Description  
A | .  
B | .  
  

> hide #29 models

> show #30 models

> hide #30 models

> show #31 models

> log metadata #31

The model has no metadata

> log chains #31

Chain information for uvig_316842_cds_0025__caprel_model.cif #31  
---  
Chain | Description  
A | .  
B | .  
  

> hide #31 models

> show #32 models

> hide #32 models

> show #33 models

> hide #33 models

> show #34 models

> log metadata #34

The model has no metadata

> log chains #34

Chain information for uvig_492214__cds_0036__caprel_model.cif #34  
---  
Chain | Description  
A | .  
B | .  
  

> hide #34 models

> show #35 models

> hide #35 models

> show #15 models

> hide #15 models

> show #26 models

> hide #26 models

> show #26 models

> hide #26 models

> show #30 models

> hide #30 models

> show #31 models

> hide #31 models

> show #35 models

> hide #35 models

> show #31 models

> hide #31 models

> show #1 models

> show #1 target m

> log metadata #1

The model has no metadata

> log chains #1

Chain information for ivig_1847_cds_0046__caprel_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> hide #1 models

> show #1 models

> hide #1 models

> show #28 models

> hide #28 models

> show #11 models

> hide #11 models

> show #35 models

> log metadata #35

The model has no metadata

> log chains #35

Chain information for uvig_499169_cds_0013__caprel_model.cif #35  
---  
Chain | Description  
A | .  
B | .  
  

> hide #35 models

> show #30 models

> hide #30 models

> show #22 models

> hide #22 models

> show #30 models

> hide #30 models

> show #33 models

> hide #33 models

> show #30 models

> hide #30 models

> show #34 models

> hide #34 models

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/cifs_of_homologs/hml48345.1__prel_model.cif

Chain information for hml48345.1__prel_model.cif #36  
---  
Chain | Description  
A | .  
B | .  
  
Color hml48345.1__prel_model.cif by residue attribute pLDDT_score  

> select add #36

2591 atoms, 2645 bonds, 315 residues, 1 model selected  

> color sel bychain

> hide #36 models

> show #36 models

> select subtract #36

Nothing selected  

> hide #36 models

> show #35 models

> hide #35 models

> show #34 models

> hide #34 models

> show #34 models

> hide #34 models

> show #35 models

> hide #35 models

> show #26 models

> hide #26 models

> open
> /Users/aegorov/Desktop/LU_Lab_Projects/anti_defences/cifs_of_homologs/wp_238702502.1__prel_model.cif

Chain information for wp_238702502.1__prel_model.cif #37  
---  
Chain | Description  
A | .  
B | .  
  
Color wp_238702502.1__prel_model.cif by residue attribute pLDDT_score  

> select add #37

3314 atoms, 3376 bonds, 403 residues, 1 model selected  

> color sel bychain

> select subtract #37

Nothing selected  

> hide #37 models

> show #30 models

> hide #30 models

> show #29 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> close #36-37

> hide #29 models

> show #29 models

> coulombic #29

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for uvig_302458_cds_0055__caprel_model.cif_A SES surface
#29.1: minimum, -19.21, mean -0.24, maximum 12.50  
Coulombic values for uvig_302458_cds_0055__caprel_model.cif_B SES surface
#29.2: minimum, -13.42, mean 2.55, maximum 17.78  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #29 80

> transparency #29 20

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> transparency #29 90

> lighting flat

> transparency #29 100

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #1 models

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ivig_1847_cds_0046__caprel_model.cif_A SES surface #1.1:
minimum, -16.61, mean -1.28, maximum 8.11  
Coulombic values for ivig_1847_cds_0046__caprel_model.cif_B SES surface #1.2:
minimum, -13.25, mean 2.89, maximum 18.62  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting flat

> transparency #1 100

> transparency #1 10

> hide #!1 models

> show #23 models

> hide #23 models

> show #35 models

> ui tool show "Side View"

> coulombic #35

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for uvig_499169_cds_0013__caprel_model.cif_A SES surface
#35.1: minimum, -10.46, mean 0.13, maximum 9.87  
Coulombic values for uvig_499169_cds_0013__caprel_model.cif_B SES surface
#35.2: minimum, -13.88, mean 2.96, maximum 21.57  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #35 100

> transparency #35 10

> hide #!35 models

> show #34 models

> coulombic #34

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for uvig_492214__cds_0036__caprel_model.cif_A SES surface
#34.1: minimum, -12.43, mean -1.81, maximum 8.22  
Coulombic values for uvig_492214__cds_0036__caprel_model.cif_B SES surface
#34.2: minimum, -13.19, mean 2.49, maximum 17.21  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #34 100

> transparency #34 90

> transparency #34 10

> transparency #34 20

> hide #!34 models

> show #19 models

> coulombic #19

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif_A
SES surface #19.1: minimum, -19.14, mean -2.87, maximum 8.52  
Coulombic values for srs019073_a1_ct115055_vs1_cds_0041__caprel_model.cif_B
SES surface #19.2: minimum, -13.01, mean 2.48, maximum 18.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #19 100

> transparency #19 10

> hide #!19 models

> show #31 models

> coulombic #31

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for uvig_316842_cds_0025__caprel_model.cif_A SES surface
#31.1: minimum, -12.58, mean -2.84, maximum 7.14  
Coulombic values for uvig_316842_cds_0025__caprel_model.cif_B SES surface
#31.2: minimum, -13.20, mean 2.71, maximum 19.93  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #31 100

> transparency #31 10

> hide #!31 models

> show #15 models

> coulombic #15

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for mgv-genome-4416137_cds_0026__caprel_model.cif_A SES
surface #15.1: minimum, -19.01, mean -4.14, maximum 9.02  
Coulombic values for mgv-genome-4416137_cds_0026__caprel_model.cif_B SES
surface #15.2: minimum, -13.71, mean 2.79, maximum 20.60  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #15 100

> transparency #15 10

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #16 models

> coulombic #16

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for nc_055919.1_cds_0033__caprel_model.cif_A SES surface
#16.1: minimum, -12.67, mean -3.63, maximum 5.09  
Coulombic values for nc_055919.1_cds_0033__caprel_model.cif_B SES surface
#16.2: minimum, -13.19, mean 2.73, maximum 18.71  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #16 100

> transparency #16 10

> hide #!16 models

> show #3 models

> hide #3 models

> show #3 models

> color #3 bychain

> undo

> coulombic #3

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif_A
SES surface #3.1: minimum, -10.77, mean -0.37, maximum 9.46  
Coulombic values for
imgvr_uvig_3300008005_000900_3300008005_ga0100385_1000007_127851-178635_cds_0030__caprel_model.cif_B
SES surface #3.2: minimum, -13.30, mean 2.46, maximum 15.78  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #3 100

> transparency #3 10

> hide #!3 models

> show #9 models

> coulombic #9

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for mgv-genome-0243292_cds_0030__caprel_model.cif_A SES
surface #9.1: minimum, -16.17, mean -3.80, maximum 10.94  
Coulombic values for mgv-genome-0243292_cds_0030__caprel_model.cif_B SES
surface #9.2: minimum, -13.38, mean 2.61, maximum 21.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #9 100

> transparency #9 10

> hide #!9 models

> show #11 models

> coulombic #11

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for mgv-genome-0286105_cds_0054__caprel_model.cif_A SES
surface #11.1: minimum, -8.37, mean 1.07, maximum 9.36  
Coulombic values for mgv-genome-0286105_cds_0054__caprel_model.cif_B SES
surface #11.2: minimum, -20.76, mean 2.68, maximum 19.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #11 100

> transparency #11 10

> transparency #11 100

> show #10 models

> hide #!11 models

> hide #10 models

> show #7 models

> hide #7 models

> show #6 models

> coulombic #6

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif_A
SES surface #6.1: minimum, -30.74, mean -0.42, maximum 14.74  
Coulombic values for
imgvr_uvig_3300045988_012104_3300045988_ga0495776_015938_cds_0072__caprel_model.cif_B
SES surface #6.2: minimum, -18.41, mean 2.68, maximum 20.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency #6 70

> transparency #6 100


===== 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/aegorov/Downloads/fold_huge_pin_ecoli/fold_huge_pin_ecoli_model_0.cif
> format mmcif

Chain information for fold_huge_pin_ecoli_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> close




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: Z15J003AGRU/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 35 days, 6 hours, 19 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG UltraFine:
          Resolution: 4096 x 2304
          UI Looks like: 2048 x 1152 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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 pett, 2 months ago

Component: UnassignedWindow Toolkit
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionCrash on Mac waking from sleep

comment:2 by pett, 2 months ago

Resolution: duplicate
Status: assignedclosed
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