![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15630 closed defect (duplicate)
Crash changing Mac display configuration
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-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 0x00000001eb458c00 (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.surface._surface, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, chimerax.alignment_algs._sw (total: 62)
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{
"uptime" : 260000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 75408,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-18 11:11:15.9931 +0200",
"codeSigningMonitor" : 1,
"incident" : "AC904530-BA80-4376-B9AC-58D94C13672E",
"pid" : 27258,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-16 10:58:41.8850 +0200",
"procStartAbsTime" : 4591749742061,
"procExitAbsTime" : 6343215777048,
"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":"C6228A1F-62EF-52B4-877A-D6481F4E4C39","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "43732AE4-1F82-5886-841C-663749D5F8E3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "2CDCCEA9-79F8-496F-825F-61EF5D869FA4",
"sip" : "enabled",
"vmRegionInfo" : "0x3def4be8b448 is not in any region. Bytes after previous region: 67616943682633 Bytes before following region: 37455136246712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00003def4be8b448","rawCodes":[1,68097980019784],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003def4be8b448"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":27258},
"vmregioninfo" : "0x3def4be8b448 is not in any region. Bytes after previous region: 67616943682633 Bytes before following region: 37455136246712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"size" : 53248,
"uuid" : "386b0fc1-7873-3328-8e71-43269fd1b2c7",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"uuid" : "61f710be-9132-3cc2-883d-066365fba1ad",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"size" : 5083136,
"uuid" : "84b539d5-22c9-3f8c-84c8-903e9c7b8d29",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"size" : 12967936,
"uuid" : "99e0292d-7873-3968-9c9c-5955638689a5",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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"size" : 4853760,
"uuid" : "995bcbdd-5656-3d16-bfa1-0ab357c2a13e",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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"size" : 294912,
"uuid" : "502762ee-7aa7-306c-9dbd-88981a86bb78",
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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 2kzi fromDatabase pdb format mmcif
2kzi title:
Solution structure of the ZHER2 Affibody [more info...]
Chain information for 2kzi
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A | Engineered protein, ZHER2 Affibody
> set bgColor white
> close #1.1-21
> close #1
> open 2kzj fromDatabase pdb format mmcif
2kzj title:
Solution structure of the ZHER2 Affibody (alternative) [more info...]
Chain information for 2kzj
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A | Engineered protein, ZHER2 Affibody
> close #1.1-22
> color #1.23 #d6d6d6ff
> hide #!1 models
> hide #1.23 models
> open 1ot8 fromDatabase pdb format mmcif
1ot8 title:
Structure of the Ankyrin Domain of the Drosophila Notch Receptor [more
info...]
Chain information for 1ot8 #2
---
Chain | Description | UniProt
A B C | Neurogenic locus Notch protein | NOTCH_DROME 2-239
Non-standard residues in 1ot8 #2
---
MG — magnesium ion
1ot8 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> color #2 #d6d6d6ff
> view orient
> hide #!2 atoms
> hide #!2 cartoons
> select #2/A
1732 atoms, 1590 bonds, 5 pseudobonds, 370 residues, 2 models selected
> view orient
> close #2.1
> color #2 #d6d6d6ff
> ui tool show "Side View"
> view
> view orient
> select #2/A
1732 atoms, 1590 bonds, 370 residues, 1 model selected
> show sel cartoons
> color #2 #d6d6d6ff
> hide #2 models
> select add #2
5036 atoms, 4623 bonds, 1076 residues, 1 model selected
> show #2 models
> select subtract #2
Nothing selected
> hide #2 models
> open 1ttg fromDatabase pdb format mmcif
Summary of feedback from opening 1ttg fetched from pdb
---
warning | Atom H1 is not in the residue template for VAL /A:1
1ttg title:
The three-dimensional structure of the tenth type III module of fibronectin:
an insight INTO RGD-mediated interactions [more info...]
Chain information for 1ttg #3
---
Chain | Description | UniProt
A | FIBRONECTIN | FINC_HUMAN 1-94
> color #3 #d6d6d6ff
> graphics silhouettes true
> lighting soft
> hide #3 models
> open 2LUR fromDatabase pdb format mmcif
2lur title:
NMR solution structure of Kb1[ghrw;23-28] [more info...]
Chain information for 2lur
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Kalata
> close #4.1-19
> color #4.20 #d6d6d6ff
> hide #!4 models
> hide #4.20 models
> show #4.20 models
> hide #!4 models
> show #1.23 models
> hide #!1 models
> open 8AJ7 fromDatabase pdb format mmcif
8aj7 title:
Kunitz domain of Amblyomin-X [more info...]
Chain information for 8aj7 #5
---
Chain | Description
A B | Kunitz domain of Amblyomin-X
Non-standard residues in 8aj7 #5
---
EDO — 1,2-ethanediol (ethylene glycol)
8aj7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
55 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #5/A
502 atoms, 461 bonds, 109 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> color #5 #d6d6d6ff
> hide #5 models
> select add #5
1010 atoms, 919 bonds, 227 residues, 1 model selected
> open 4MVK fromDatabase pdb format mmcif
4mvk title:
Crystal structure of an engineered lipocalin (Anticalin US7) in complex with
the Alzheimer amyloid peptide fragment VFFAED [more info...]
Chain information for 4mvk #6
---
Chain | Description | UniProt
A | Neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-178
B | Amyloid peptide fragment VFFAED | A4_HUMAN 18-23
Non-standard residues in 4mvk #6
---
ACE — acetyl group
NH2 — amino group
> hide #6 atoms
> select subtract #5
Nothing selected
> show #!1 models
> show #2 models
> show #3 models
> show #!4 models
> show #5 models
> tile
6 models tiled
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> show #2 models
> hide #2 models
> show #!1 models
> show #2 models
> show #3 models
> show #!4 models
> show #5 models
> show #6 models
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> show #3 models
> hide #3 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #6 models
> show #5 models
> show #!4 models
> show #3 models
> show #2 models
> show #!1 models
> save /Users/annamb/Desktop/image1.png supersample 3
> save /Users/annamb/Desktop/image2.png supersample 3
> save /Users/annamb/Desktop/PhD-220727/Thesis/Alternative-scaffolds.cxs
> open 6ARP fromDatabase pdb format mmcif
Summary of feedback from opening 6ARP fetched from pdb
---
note | Fetching compressed mmCIF 6arp from http://files.rcsb.org/download/6arp.cif
6arp title:
Structure of a mutant Cetuximab Fab fragment [more info...]
Chain information for 6arp #7
---
Chain | Description | UniProt
A C | Cetuximab mutant light chain,Uncharacterized protein | Q8TCD0_HUMAN 107-214
B D | Cetuximab mutant Fab heavy chain,Immunoglobulin gamma-1 heavy chain | IGG1_HUMAN 120-222
Non-standard residues in 6arp #7
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
6arp mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
172 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> close #7.1
> select #7/B
1799 atoms, 1679 bonds, 379 residues, 1 model selected
> select #7/B#7/D
3658 atoms, 3388 bonds, 791 residues, 1 model selected
> select add #7
7462 atoms, 6757 bonds, 1724 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/A
1887 atoms, 1680 bonds, 456 residues, 1 model selected
> select #7/B
1799 atoms, 1679 bonds, 379 residues, 1 model selected
Drag select of 44 atoms, 227 residues, 34 bonds
Drag select of 83 atoms, 612 residues, 65 bonds
> select add #7
7462 atoms, 6757 bonds, 1724 residues, 1 model selected
> select subtract #7
Nothing selected
Drag select of 77 atoms, 431 residues, 61 bonds
> select #7/C:27
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 77 atoms, 431 residues, 61 bonds
> select add #7
7462 atoms, 6757 bonds, 1724 residues, 1 model selected
> select subtract #7
Nothing selected
Drag select of 180 atoms, 430 residues, 143 bonds
> hide sel atoms
> hide sel cartoons
> hide sel atoms
Drag select of 77 atoms, 427 residues, 61 bonds
> hide sel atoms
> select add #7
7462 atoms, 6757 bonds, 1724 residues, 1 model selected
> select subtract #7
Nothing selected
> color #7 #d6d6d6ff
> select coil
6314 atoms, 6280 bonds, 784 residues, 7 models selected
> select add #7
11239 atoms, 10518 bonds, 2157 residues, 7 models selected
> select subtract #7
3777 atoms, 3761 bonds, 433 residues, 6 models selected
> hide #7 models
> show #7 models
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
> select add #6
4741 atoms, 4603 bonds, 691 residues, 6 models selected
> select add #5
5335 atoms, 5108 bonds, 858 residues, 6 models selected
> select add #4
5403 atoms, 5180 bonds, 864 residues, 7 models selected
> select add #3
6201 atoms, 5994 bonds, 914 residues, 7 models selected
> select add #2
9602 atoms, 9005 bonds, 1773 residues, 7 models selected
> select add #1
10372 atoms, 9784 bonds, 1820 residues, 8 models selected
> select subtract #1
9429 atoms, 8833 bonds, 1762 residues, 6 models selected
> select subtract #2
4393 atoms, 4210 bonds, 686 residues, 5 models selected
> select subtract #3
2991 atoms, 2792 bonds, 592 residues, 4 models selected
> select subtract #4
2608 atoms, 2398 bonds, 563 residues, 2 models selected
> select subtract #5
1598 atoms, 1479 bonds, 336 residues, 1 model selected
> select subtract #6
Nothing selected
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 3
Alignment identifier is 4
> select #7/D,B:61-64,73-75,86-90,162-164,193-195,207-210
316 atoms, 310 bonds, 44 residues, 1 model selected
> select
> #7/D,B:3-6,10-12,18-25,34-39,45-51,57-59,67-72,77-82,91-98,106-109,113-117,126-130,141-151,157-160,169-171,175-176,182-191,201-206,211-216
1712 atoms, 1724 bonds, 214 residues, 1 model selected
> close #7
> open " 1YYB" fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got " 1YYB"
> open " 1YYB" fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got " 1YYB"
> open 5ESQ fromDatabase pdb format mmcif
Summary of feedback from opening 5ESQ fetched from pdb
---
notes | Fetching compressed mmCIF 5esq from http://files.rcsb.org/download/5esq.cif
Fetching CCD BAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/BAL/BAL.cif
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif
5esq title:
Cetuximab Fab in complex with cyclic beta-alanine-linked meditope [more
info...]
Chain information for 5esq #7
---
Chain | Description
A C | Cetuximab Fab light chain
B D | Cetuximab Fab heavy chain
E F | Cyclic beta-alanine-linked meditope
Non-standard residues in 5esq #7
---
BAL — β-alanine
PO4 — phosphate ion
5esq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> tile
1 model tiled
> hide #!7 surfaces
> hide #!7 cartoons
> show #!7 cartoons
> style #!7 stick
Changed 7064 atom styles
> style #!7 stick
Changed 7064 atom styles
> style #!7 sphere
Changed 7064 atom styles
> style #!7 sphere
Changed 7064 atom styles
> nucleotides #!7 atoms
> style nucleic & #!7 stick
Changed 0 atom styles
> style #!7 ball
Changed 7064 atom styles
> style #!7 sphere
Changed 7064 atom styles
> style #!7 sphere
Changed 7064 atom styles
> style #!7 ball
Changed 7064 atom styles
> style #!7 stick
Changed 7064 atom styles
> nucleotides #!7 atoms
> style nucleic & #!7 stick
Changed 0 atom styles
> nucleotides #!7 tube/slab shape box
> hide #!7 atoms
Drag select of 436 residues, 2 pseudobonds
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> select #7/B
1717 atoms, 1681 bonds, 1 pseudobond, 296 residues, 2 models selected
> color #7.1 #929292ff models
> color #7.1 #919191ff models
> color #7 darkgrey
> color #7 #5e5e5eff
> color #7 #797979ff
> color #7 #d6d6d6ff
> select add #7.1
1717 atoms, 1681 bonds, 3 pseudobonds, 296 residues, 2 models selected
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
Destroying pre-existing alignment with identifier 1.23/A
Alignment identifier is 1.23/A
Alignment identifier is 3
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Destroying pre-existing alignment with identifier 4.20/A
Alignment identifier is 4.20/A
Alignment identifier is 4
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
Destroying pre-existing alignment with identifier 6/B
Alignment identifier is 6/B
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
> select #7/B,D:26
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #7/B,D:26-30
72 atoms, 72 bonds, 10 residues, 1 model selected
> select #7/B,D:52
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #7/B,D:52-56
72 atoms, 74 bonds, 10 residues, 1 model selected
> select #7/B,D:99
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/B,D:99-108
192 atoms, 200 bonds, 20 residues, 1 model selected
> select #7/B,D:52
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #7/B,D:52-55
56 atoms, 58 bonds, 8 residues, 1 model selected
> select #7/B,D:52-56
72 atoms, 74 bonds, 10 residues, 1 model selected
> select #7/B,D:99-108
192 atoms, 200 bonds, 20 residues, 1 model selected
> select #7/B,D:52-55
56 atoms, 58 bonds, 8 residues, 1 model selected
> select #7/B,D:26
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #7/B,D:26-30
72 atoms, 72 bonds, 10 residues, 1 model selected
> color sel #ff2600ff
> select #7/B,D:52-53
40 atoms, 42 bonds, 4 residues, 1 model selected
> select #7/B,D:52-56
72 atoms, 74 bonds, 10 residues, 1 model selected
> color sel red
> select #7/B,D:99
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/B,D:99-108
192 atoms, 200 bonds, 20 residues, 1 model selected
> color sel red
> select #7/B,D:26
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #7/B,D:26-31
88 atoms, 88 bonds, 12 residues, 1 model selected
> color sel blue
> select #7/B,D:52-53
40 atoms, 42 bonds, 4 residues, 1 model selected
> select #7/B,D:52-56
72 atoms, 74 bonds, 10 residues, 1 model selected
> color sel blue
> select #7/B,D:99
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/B,D:99-108
192 atoms, 200 bonds, 20 residues, 1 model selected
> color sel blue
> select #7/A,C:24
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A,C:24-33
138 atoms, 136 bonds, 20 residues, 1 model selected
> color sel medium blue
> select #7/A,C:50
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #7/A,C:50-55
92 atoms, 92 bonds, 12 residues, 1 model selected
> color sel medium blue
> select #7/A,C:89
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #7/A,C:89-96
140 atoms, 144 bonds, 16 residues, 1 model selected
> color sel medium blue
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
> color #7 #0433ffff
> color #7 #0096ffff
> color #7 #0433ffff
> color #7 #7a81ffff
> undo
> save /Users/annamb/Desktop/image2.png supersample 3
> select clear
Drag select of 4 residues
> select #7/A,C:32
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A,C:26-32
96 atoms, 94 bonds, 14 residues, 1 model selected
> color sel cornflower blue
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
> color #7 #0433ffff
> color #7 #0433fffa
> color #7 #0433ffea
> color #7 #0433ffc9
> color #7 #0433ffbf
> color #7 #0433ffb4
> color #7 #0433ffab
> color #7 #0433ffa3
> color #7 #0433ff9c
> color #7 #0433ff99
> color #7 #0433ff98
> color #7 #0433ff96
> color #7 #0433ff92
> color #7 #0433ff8d
> color #7 #0433ff89
> color #7 #0433ff87
> color #7 #0433ff86
> color #7 #0433ff84
> color #7 #0433ff7e
> color #7 #0433ff7d
> color #7 #0433ff7b
> color #7 #0433ff7a
> color #7 #0433ff78
> color #7 #0433ff76
> color #7 #0433ff75
> undo
> color #7 #d6d6d6ff
> select #7/B,D:26
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #7/B,D:26-30
72 atoms, 72 bonds, 10 residues, 1 model selected
> select #7/B,D:26-30,52-56
144 atoms, 146 bonds, 20 residues, 1 model selected
> select #7/B,D:26-30,52-56,99-108
336 atoms, 346 bonds, 40 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #0433ffff
> color sel #0433fffc
> color sel #0433fffb
> color sel #0433ffe5
> color sel #0433ffe0
> color sel #0433ffdb
> color sel #0433ffd6
> color sel #0433ffd1
> color sel #0433ffcf
> color sel #0433ffce
> color sel #0433ffcd
> color sel #0433ffcc
> color sel #0433ffcb
> color sel #0433ffca
> color sel #0433ffc9
> color sel #0433ffc8
> color sel #0433ffc4
> color sel #0433ffc2
> color sel #0433ffbe
> color sel #0433ffba
> color sel #0433ffb9
> color sel #0433ffb8
> color sel #0433ffb6
> color sel #0433ffb4
> color sel #0433ffb3
> color sel #0433ffb2
> color sel #0433ffae
> color sel #0433ffab
> color sel #0433ffa9
> color sel #0433ffa6
> color sel #0433ffa3
> color sel #0433ffa2
> color sel #0433ffa0
> color sel #0433ff9e
> color sel #0433ff9d
> color sel #0433ff9c
> color sel #0433ff9a
> color sel #0433ff99
> color sel #0433ff98
> color sel #0433ff97
> color sel #0433ff96
> color sel #0433ff95
> color sel #0433ff91
> color sel #0433ff8f
> color sel #0433ff8d
> color sel #0433ff8c
> color sel #0433ff8b
> color sel #0433ff89
> color sel #0433ff88
> color sel #0433ff86
> color sel #0433ff84
> color sel #0433ff83
> color sel #0433ff82
> color sel #0433ff81
> color sel #0433ff80
> color sel #0433ff8a
> color sel #0433ff8e
> color sel #0433ff91
> color sel #0433ff96
> color sel #0433ff9f
> color sel #0433ffa9
> color sel #0433ffae
> color sel #0433ffb2
> color sel #0433ffb4
> color sel #0433ffb6
> color sel #0433ffb5
> color sel #0433ffb3
> color sel #0433ffaf
> color sel #0433ffa7
> color sel #0433ff9c
> color sel #0433ff97
> color sel #0433ff8e
> color sel #0433ff89
> color sel #0433ff86
> color sel #0433ff84
> color sel #0433ff83
> color sel #0433ff82
> color sel #0433ff81
> color sel #0433ff80
> color sel #0433ffff
> color sel #0433ff7f
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
> select #7/A,C:24
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A,C:24-32
122 atoms, 120 bonds, 18 residues, 1 model selected
> select #7/A,C:24-32
122 atoms, 120 bonds, 18 residues, 1 model selected
> select #7/A,C:33
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A,C:24-33
138 atoms, 136 bonds, 20 residues, 1 model selected
> select #7/A,C:24-33,50-56
242 atoms, 240 bonds, 34 residues, 1 model selected
> select #7/A,C:24-33,50-56
242 atoms, 240 bonds, 34 residues, 1 model selected
> select #7/A,C:24-34,50-56
262 atoms, 262 bonds, 36 residues, 1 model selected
> select #7/A,C:24-34,50-56,89-99
446 atoms, 452 bonds, 58 residues, 1 model selected
> select #7/A,C:24-34,50-56,89-99
446 atoms, 452 bonds, 58 residues, 1 model selected
> select #7/A,C:24-34,50-56,89-99
446 atoms, 452 bonds, 58 residues, 1 model selected
> select #7/A,C:24-34,50-56,89-99
446 atoms, 452 bonds, 58 residues, 1 model selected
> select #7/A,C:24-34,50-56,89-99
446 atoms, 452 bonds, 58 residues, 1 model selected
> color sel #0433ffff
> color sel #0433ff7d
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
> select #7/A,C:98
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #7/A,C:98-99
30 atoms, 30 bonds, 4 residues, 1 model selected
> color sel #d6d6d6ff
> select add #7
7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected
> select subtract #7
Nothing selected
> save /Users/annamb/Desktop/image3.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/annamb/Downloads/g12-scfv.cif "/Users/annamb/Downloads/a12
> scfv.cif" "/Users/annamb/Downloads/zwt scfv.cif" "/Users/annamb/Downloads/B8
> scfv.cif"
Summary of feedback from opening /Users/annamb/Downloads/g12-scfv.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening /Users/annamb/Downloads/a12 scfv.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening /Users/annamb/Downloads/zwt scfv.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening /Users/annamb/Downloads/B8 scfv.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for g12-scfv.cif #8
---
Chain | Description
A | No description available
B | No description available
Chain information for a12 scfv.cif #9
---
Chain | Description
A | No description available
B | No description available
Chain information for zwt scfv.cif #10
---
Chain | Description
A | No description available
B | No description available
Chain information for B8 scfv.cif #11
---
Chain | Description
A | No description available
B | No description available
> hide #!7 models
> hide #7.1 models
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
Drag select of 44 residues
> lighting full
> lighting soft
> lighting full
> lighting simple
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> show #9 models
> show #8 models
> hide #9 models
> select add #8
2560 atoms, 2344 bonds, 334 residues, 4 models selected
> select add #9
4729 atoms, 4693 bonds, 618 residues, 4 models selected
> select add #10
6983 atoms, 7044 bonds, 911 residues, 4 models selected
> select add #11
9205 atoms, 9415 bonds, 1200 residues, 4 models selected
> select subtract #10
6904 atoms, 7064 bonds, 900 residues, 3 models selected
> select subtract #11
4590 atoms, 4693 bonds, 600 residues, 2 models selected
> select subtract #9
2293 atoms, 2344 bonds, 300 residues, 1 model selected
> select subtract #8
Nothing selected
Drag select of 237 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean
-0.31, maximum 10.39
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide sel surfaces
Drag select of 45 residues
Drag select of 58 residues
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for g12-scfv.cif_A SES surface #8.2: minimum, -11.02, mean
-0.52, maximum 11.29
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> mlp sel
Map values for surface "g12-scfv.cif_A SES surface": minimum -25.35, mean
-5.344, maximum 21.49
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide sel surfaces
> show sel cartoons
> undo
Drag select of g12-scfv.cif_A SES surface, 64491 of 65098 triangles, 58
residues
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel cartoons
> coulombic sel
Coulombic values for g12-scfv.cif_A SES surface #8.2: minimum, -11.02, mean
-0.52, maximum 11.29
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> show sel cartoons
> hide sel surfaces
> mlp
Map values for surface "g12-scfv.cif_A SES surface": minimum -25.74, mean
-5.336, maximum 21.68
Map values for surface "g12-scfv.cif_B SES surface": minimum -31.49, mean
-7.968, maximum 21.93
Map values for surface "1ot8_A SES surface": minimum -28.65, mean -5.892,
maximum 21.99
Map values for surface "1ot8_B SES surface": minimum -30.87, mean -5.953,
maximum 22.58
Map values for surface "1ot8_C SES surface": minimum -28.35, mean -6.257,
maximum 22.53
Map values for surface "2kzj_A SES surface": minimum -22.95, mean -3.088,
maximum 24.28
Map values for surface "2lur_A SES surface": minimum -29.24, mean -3.03,
maximum 23.4
Map values for surface "1ttg_A SES surface": minimum -26.79, mean -3.597,
maximum 24.88
Map values for surface "8aj7_A SES surface": minimum -27.38, mean -6.131,
maximum 19.71
Map values for surface "8aj7_B SES surface": minimum -24.39, mean -6.308,
maximum 18.93
Map values for surface "5esq_A SES surface": minimum -27.12, mean -7.066,
maximum 22.84
Map values for surface "5esq_B SES surface": minimum -31.19, mean -5.59,
maximum 22.58
Map values for surface "5esq_C SES surface": minimum -29.43, mean -7.12,
maximum 22.82
Map values for surface "5esq_D SES surface": minimum -30.44, mean -5.523,
maximum 22.3
Map values for surface "5esq_E SES surface": minimum -22.98, mean -2.931,
maximum 22.4
Map values for surface "5esq_F SES surface": minimum -28.34, mean 9.21,
maximum 120.1
Map values for surface "4mvk_A SES surface": minimum -25.36, mean -4.806,
maximum 21.44
Map values for surface "4mvk_B SES surface": minimum -24.34, mean -3.061,
maximum 22.37
Map values for surface "a12 scfv.cif_A SES surface": minimum -26.74, mean
-4.741, maximum 22.4
Map values for surface "a12 scfv.cif_B SES surface": minimum -30.71, mean
-7.968, maximum 22.05
Map values for surface "B8 scfv.cif_A SES surface": minimum -26.49, mean
-4.081, maximum 21.48
Map values for surface "B8 scfv.cif_B SES surface": minimum -31.1, mean -8,
maximum 23.07
Map values for surface "zwt scfv.cif_A SES surface": minimum -25.59, mean
-5.122, maximum 21.77
Map values for surface "zwt scfv.cif_B SES surface": minimum -29.5, mean
-7.889, maximum 22.17
> hide #7.2 models
> hide #7.3 models
> hide #7.4 models
> hide #7.5 models
> hide #7.6 models
> hide #7.7 models
> select add #8
2293 atoms, 2344 bonds, 300 residues, 2 models selected
> select subtract #8
2 models selected
> hide #2.3 models
> hide #2.2 models
> hide #2.1 models
> show #!8 cartoons
> hide #!8 surfaces
Drag select of 241 residues
Drag select of 232 residues
> hide sel cartoons
Drag select of 2 residues
Drag select of 6 residues
> hide sel cartoons
> select #8/B:101
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> color (#!8 & sel) byhetero
> coulombic sel
Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean
-0.31, maximum 10.39
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean
-0.31, maximum 10.39
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide sel surfaces
Drag select of 58 residues
> show sel atoms
> mlp sel
Map values for surface "g12-scfv.cif_A SES surface": minimum -25.52, mean
-5.35, maximum 22.03
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> color (#!8 & sel) byelement
> undo
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel bychain
> color sel byhetero
> color sel byelement
> color sel bynucleotide
> hide #!8 models
> select add #8
2293 atoms, 2344 bonds, 300 residues, 2 models selected
> show #!8 models
> hide sel cartoons
> show sel cartoons
> hbonds sel reveal true
584 hydrogen bonds found
> hide sel atoms
> show sel atoms
> select subtract #8
2 models selected
Drag select of 985 atoms, 232 residues, 832 bonds, 192 pseudobonds
> select subtract #8/B:184@CD2
1750 atoms, 830 bonds, 192 pseudobonds, 232 residues, 3 models selected
> select #8/B:184@CD2
1 atom, 1 residue, 1 model selected
Drag select of 877 atoms, 212 residues, 738 bonds, 171 pseudobonds
> hide sel atoms
> undo
> hbonds /a:nad restrict cross log true reveal true
Atom specifier selects no atoms
> delete solvent
> hide protein
> hbonds sidechain restrict both reveal true color yellow radius .08
593 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
139 hydrogen bonds found
> coulombic sel
Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean
-0.31, maximum 10.39
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "g12-scfv.cif_B SES surface": minimum -31.29, mean
-7.972, maximum 21.71
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean
-0.31, maximum 10.39
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color #8.1 #ff2600ff
> color #8.2 #0433ffff
> hide #!8 models
> hide #7.8 models
> show #!8 models
> select add #8
2293 atoms, 2344 bonds, 57 pseudobonds, 300 residues, 4 models selected
> select subtract #8
2 models selected
> color #8 #941100ff
> color #8.2 #0433ffff
> select add #8.2
460 atoms, 58 residues, 1 model selected
> select subtract #8.2
1 model selected
> hide #!8 models
> select add #8.1
1833 atoms, 242 residues, 1 model selected
> show #!8 models
> color #8.1 #0022a7ff
> color (#!8 & sel) blue
> select subtract #8.1
1 model selected
Drag select of 247 atoms, 210 residues, 211 bonds, 36 pseudobonds
> hide sel atoms
> select subtract #8.1
1 model selected
> hide #!8 models
> show #!10 models
> hide #!10 surfaces
> hide #!10 models
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 8/A
Alignment identifier is 6
Alignment identifier is 9/A
Alignment identifier is 10/A
Alignment identifier is 11/A
> select #10/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #10/A
468 atoms, 475 bonds, 7 pseudobonds, 58 residues, 3 models selected
> select #10/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/A
468 atoms, 475 bonds, 7 pseudobonds, 58 residues, 3 models selected
> select #9/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A
464 atoms, 473 bonds, 6 pseudobonds, 58 residues, 3 models selected
> select #8/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A
460 atoms, 468 bonds, 7 pseudobonds, 58 residues, 3 models selected
Alignment identifier is 8/A
> show #!11 models
Alignment identifier is 8/A
> hide #8.1 models
> hide #8.2 models
> hide #10.1 models
> hide #10.2 models
> hide #!11 models
> hide #12 models
> hide #13 models
> show #!11 models
> select add #12
460 atoms, 468 bonds, 594 pseudobonds, 58 residues, 4 models selected
> select add #13
460 atoms, 468 bonds, 732 pseudobonds, 58 residues, 4 models selected
> select subtract #12
460 atoms, 468 bonds, 139 pseudobonds, 58 residues, 3 models selected
> select subtract #13
460 atoms, 468 bonds, 58 residues, 2 models selected
> select add #8
2293 atoms, 2344 bonds, 57 pseudobonds, 300 residues, 4 models selected
> select subtract #8
2 models selected
> select add #8.1
1833 atoms, 242 residues, 1 model selected
> select subtract #8.1
1 model selected
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 8/A
Alignment identifier is 6
Alignment identifier is 9/A
Alignment identifier is 10/A
Alignment identifier is 11/A
> select #11/A:1
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/A
481 atoms, 495 bonds, 8 pseudobonds, 58 residues, 3 models selected
> hide sel surfaces
> show #8.2 models
> hide #8.2 models
> show #8.1 models
> hide #!8 models
> hide #8.1 models
> hide #11.1 models
> hide #!11 models
> show #!8 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
139 hydrogen bonds found
> show #8.1 models
> show #8.2 models
> hbonds #!8 reveal true
471 hydrogen bonds found
> hide #11.2 models
> select add #11
2314 atoms, 2371 bonds, 9 pseudobonds, 300 residues, 3 models selected
> select subtract #11.1
1833 atoms, 1876 bonds, 7 pseudobonds, 242 residues, 4 models selected
> select add #11
2314 atoms, 2371 bonds, 9 pseudobonds, 300 residues, 3 models selected
> select subtract #11.2
481 atoms, 495 bonds, 2 pseudobonds, 58 residues, 4 models selected
> select subtract #11.1
1 model selected
> select add #8
2293 atoms, 2344 bonds, 284 pseudobonds, 300 residues, 3 models selected
> select add #12
2293 atoms, 2344 bonds, 481 pseudobonds, 300 residues, 5 models selected
> select add #13
2293 atoms, 2344 bonds, 610 pseudobonds, 300 residues, 5 models selected
> hide #!8 models
> hide #8.1 models
> hide #8.2 models
> select subtract #8
128 pseudobonds, 3 models selected
> select add #8.1
1833 atoms, 128 pseudobonds, 242 residues, 2 models selected
> select subtract #8.1
128 pseudobonds, 2 models selected
> show #!11 models
> select add #12
599 pseudobonds, 2 models selected
> show #!8 models
> hide #!11 models
> show #12 models
> show #13 models
> select subtract #12
128 pseudobonds, 1 model selected
> select add #13
139 pseudobonds, 1 model selected
> select subtract #13
Nothing selected
Drag select of 495 atoms, 238 residues, 415 bonds, 213 pseudobonds
> select add #13
1814 atoms, 415 bonds, 343 pseudobonds, 240 residues, 5 models selected
> select subtract #13
1814 atoms, 415 bonds, 204 pseudobonds, 240 residues, 4 models selected
> select add #12
1814 atoms, 415 bonds, 471 pseudobonds, 240 residues, 4 models selected
> select subtract #12
1814 atoms, 415 bonds, 240 residues, 3 models selected
> select add #11
4128 atoms, 2786 bonds, 9 pseudobonds, 540 residues, 5 models selected
> select subtract #11
1814 atoms, 415 bonds, 240 residues, 5 models selected
Drag select of 271 atoms, 147 residues, 227 bonds, 132 pseudobonds
> hide #!8 models
> show #!8 models
> select add #8
2293 atoms, 2344 bonds, 284 pseudobonds, 300 residues, 5 models selected
> select subtract #8.1
460 atoms, 468 bonds, 58 pseudobonds, 58 residues, 5 models selected
> select subtract #8.2
1 model selected
Drag select of 275 atoms, 158 residues, 232 bonds, 133 pseudobonds
> select subtract #8.1
1 model selected
> ~hbonds
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
143 hydrogen bonds found
> hbonds #!8 reveal true
464 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
143 hydrogen bonds found
> hbonds /a:nad restrict cross log true reveal true
Atom specifier selects no atoms
> delete solvent
> hide protein
> hbonds sidechain restrict both reveal true color yellow radius .08
606 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
Drag select of 221 atoms, 187 residues, 180 bonds, 33 pseudobonds
> hide sel atoms
> select subtract #8.1
1 model selected
> color #8 #d6d6d6ff
> color #8 silver
> color #8 darkgrey
> color #8 #d6d6d6ff
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
Alignment identifier is 1.23/A
Alignment identifier is 1
Alignment identifier is 3/A
Alignment identifier is 4.20/A
Alignment identifier is 2
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 8/A
Alignment identifier is 6
Alignment identifier is 9/A
Alignment identifier is 10/A
Alignment identifier is 11/A
> select #8/A:7-18,24-36,38-54
334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6-7
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:7-18,24-36,38-54
334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:7-18,24-36,38-54
334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:9
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:9-11
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6-7
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6-7
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:9
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:9-13
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:9
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:9-11
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #8/A:6,9-11
35 atoms, 34 bonds, 4 residues, 1 model selected
> select #8/A:6,9-11,13-14
47 atoms, 45 bonds, 6 residues, 1 model selected
> select #8/A:6,9-11,13-14,18
59 atoms, 57 bonds, 7 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,30
70 atoms, 68 bonds, 8 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,30
81 atoms, 79 bonds, 9 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,30
81 atoms, 79 bonds, 9 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,30,32
87 atoms, 84 bonds, 10 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,30,32
87 atoms, 84 bonds, 10 residues, 1 model selected
> select #8/A:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:30-31
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:6,9-11
35 atoms, 34 bonds, 4 residues, 1 model selected
> select #8/A:6,9-11,13-14
47 atoms, 45 bonds, 6 residues, 1 model selected
> select #8/A:6,9-11,13-14,18
59 atoms, 57 bonds, 7 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25
70 atoms, 68 bonds, 8 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,32
76 atoms, 73 bonds, 9 residues, 1 model selected
> select #8/A:6,9-11,13-14,18,25,32,35
84 atoms, 80 bonds, 10 residues, 1 model selected
> color (#!8 & sel) cornflower blue
> show sel atoms
> select #8/A:6,9-11,13-14,17-18,25,32,35
95 atoms, 91 bonds, 11 residues, 1 model selected
> select #8/A:6,9-11,13-14,17-18,24-25,32,35
105 atoms, 102 bonds, 12 residues, 1 model selected
> select #8/A:6,9-11,13-14,17-18,24-25,27-28,32,35
122 atoms, 118 bonds, 14 residues, 1 model selected
> color (#!8 & sel) cornflower blue
> select subtract #8.2
1 model selected
> hide #!8 models
> show #!9 models
> hide #!9 surfaces
Drag select of 269 atoms, 220 residues, 222 bonds, 28 pseudobonds
> hide sel atoms
> show sel atoms
> select add #9
2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected
> select subtract #9
2 models selected
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
145 hydrogen bonds found
Drag select of 910 atoms, 221 residues, 768 bonds, 28 pseudobonds
> select add #9
2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected
> select subtract #9
2 models selected
> select clear
Drag select of 757 atoms, 188 residues, 636 bonds, 23 pseudobonds
> hide sel atoms
> color #9 #d6d6d6ff
> select add #9
2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected
> select subtract #9
2 models selected
> select #9/A:6
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:6
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:6,9-11
36 atoms, 35 bonds, 4 residues, 1 model selected
> select #9/A:6,9-11,13-14
52 atoms, 51 bonds, 6 residues, 1 model selected
> select #9/A:6,9-11,13-14,17-18
77 atoms, 77 bonds, 8 residues, 1 model selected
> select #9/A:6,9-11,13-14,17-18,24-25
95 atoms, 95 bonds, 10 residues, 1 model selected
> select #9/A:6,9-11,13-14,17-18,24-25,27-28
112 atoms, 111 bonds, 12 residues, 1 model selected
> select #9/A:6,9-11,13-14,17-18,24-25,27-28,32
119 atoms, 117 bonds, 13 residues, 1 model selected
> select #9/A:6,9-11,13-14,17-18,24-25,27-28,32,35
126 atoms, 123 bonds, 14 residues, 1 model selected
> color (#!9 & sel) cornflower blue
> select add #9
2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected
> select subtract #9
2 models selected
> show #!8 models
> tile
2 models tiled
> lighting simple
> select clear
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #8.1 models
> show #8.2 models
> lighting soft
> select #8/A:6,9-11,13-14,17-18,24-25,27-28,32,35
122 atoms, 118 bonds, 14 residues, 1 model selected
> label (#!8 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select subtract #8.2
1 model selected
Drag select of 3 atoms, 2 residues, 4 bonds
> select #8/A:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
Drag select of 3 atoms, 1 residues, 3 bonds
> color (#!8 & sel) cornflower blue
> label (#!8 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select subtract #8.2
1 model selected
> hide #8.1 models
> hide #8.2 models
> hide #8.3 models
> show #!9 models
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> hide #!8 models
> hide #!9 models
> show #!11 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
> color #11 #d6d6d6ff
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
Drag select of 263 atoms, 228 residues, 217 bonds, 31 pseudobonds
> hide sel atoms
> select add #11
2314 atoms, 2371 bonds, 44 pseudobonds, 300 residues, 4 models selected
> select subtract #11
2 models selected
> select #11/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!11 & sel) cornflower blue
No visible atoms, bonds, or surfaces selected
> select add #12
606 pseudobonds, 1 model selected
> select subtract #12
Nothing selected
> color #12 #fffb00ff models
> undo
> select #11/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!11 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
Drag select of 2 residues
> select add #11
2314 atoms, 2371 bonds, 44 pseudobonds, 300 residues, 5 models selected
> select subtract #11
2 models selected
> show #!9 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> select #9/A:6
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:6
10 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 3 atoms, 2 residues, 3 bonds
> select add #9/A:6
27 atoms, 13 bonds, 3 residues, 2 models selected
> select #9/A:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:4-47
359 atoms, 367 bonds, 2 pseudobonds, 44 residues, 2 models selected
> color (#!9 & sel) #d6d6d6ff
> select add #12
359 atoms, 367 bonds, 606 pseudobonds, 44 residues, 3 models selected
> select subtract #12
359 atoms, 367 bonds, 44 residues, 2 models selected
> select subtract #9.1
1 model selected
> select #9/A:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:7,17
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #9/A:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:9,17
20 atoms, 18 bonds, 2 residues, 1 model selected
> color (#!9 & sel) cornflower blue
> select subtract #9.1
1 model selected
> hide #!9 models
> show #!8 models
> select #8/A:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select #8/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select #8/A:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #8/A:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select #8/A:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select #8/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select clear
> select #8/A:18@CG
1 atom, 1 residue, 1 model selected
> select #8/A:18
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select #8/A:14
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:13
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:11
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 5 atoms, 6 residues, 4 bonds
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> select subtract #8.2
1 model selected
Drag select of 15 atoms, 7 residues, 12 bonds, 2 pseudobonds
> select add #12
49 atoms, 12 bonds, 606 pseudobonds, 7 residues, 3 models selected
> select subtract #12
49 atoms, 12 bonds, 7 residues, 2 models selected
> select #8/A:6
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #c0c0c0ff
> color (#!8 & sel) #d6d6d6ff
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!8 models
> select #11/A:21-22
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #11/A:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #11/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
138 hydrogen bonds found
> hbonds sel reveal true
2 hydrogen bonds found
> select add #11.2
1844 atoms, 10 bonds, 243 residues, 2 models selected
> select subtract #11.1
1833 atoms, 242 residues, 3 models selected
> select subtract #11.2
1 model selected
> show #11.1 models
> show #11.2 models
> hide #!9 models
> hide #9.1 models
> hide #9.2 models
> hide #!11 surfaces
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
141 hydrogen bonds found
> hbonds #!11 reveal true
412 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
136 hydrogen bonds found
> ~hbonds
> hbonds #!11 reveal true
443 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
136 hydrogen bonds found
Drag select of 427 atoms, 226 residues, 363 bonds, 186 pseudobonds
> select subtract #11.2
1 model selected
Drag select of 364 atoms, 206 residues, 305 bonds, 165 pseudobonds
> hide sel atoms
> undo
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
136 hydrogen bonds found
> show #!10 models
> hide #!10 models
> show #!9 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
138 hydrogen bonds found
> select add #12
443 pseudobonds, 1 model selected
> select add #13
581 pseudobonds, 2 models selected
> select subtract #12
138 pseudobonds, 1 model selected
> select subtract #13
Nothing selected
> select add #12
443 pseudobonds, 1 model selected
> select subtract #12
Nothing selected
> hide #11.1 models
> hide #11.2 models
> ~hbonds
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
138 hydrogen bonds found
> hide #!9 models
> hide #!11 models
> show #!8 models
> hbonds #!8 reveal true
407 hydrogen bonds found
> show #!9 models
> hide #!9 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
144 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
145 hydrogen bonds found
> hide #12 models
> show #12 models
> ~hbonds
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
> hbonds #!8 reveal true
389 hydrogen bonds found
> interModel true
Unknown command: interModel true
> interfaces #!8 & ~solvent
1 buried areas: B A 910
> tile off
> hbonds #!8 reveal true
423 hydrogen bonds found
Drag select of 797 atoms, 300 residues, 669 bonds, 284 pseudobonds
> hide sel atoms
> close #12
> select add #13
2293 atoms, 669 bonds, 142 pseudobonds, 300 residues, 4 models selected
> select subtract #13
2293 atoms, 669 bonds, 300 residues, 3 models selected
> close #13
> hide #11.3 models
> show #11.3 models
> select add #8
2293 atoms, 2344 bonds, 300 residues, 4 models selected
> select subtract #8
2 models selected
> hide #!11 models
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
> hbonds #!8 reveal true
423 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
> hbonds /a:nad restrict cross log true reveal true
Atom specifier selects no atoms
> delete solvent
> hide protein
> hbonds sidechain restrict both reveal true color yellow radius .08
531 hydrogen bonds found
> hbonds sidechain restrict both saltOnly true name "salt bridges" color
> magenta radius .1
142 hydrogen bonds found
Drag select of 3 atoms, 4 residues, 1 pseudobonds
> select clear
> show #!9 models
> show #!11 models
> tile
3 models tiled
> hide #12 models
> show #12 models
> hide #13 models
> show #13 models
Drag select of 6 pseudobonds
> select clear
Drag select of 43 atoms, 29 residues, 36 bonds, 4 pseudobonds
Drag select of 32 atoms, 26 residues, 24 bonds, 8 pseudobonds
> select add #12
207 atoms, 24 bonds, 148 pseudobonds, 31 residues, 5 models selected
> select subtract #12
207 atoms, 24 bonds, 6 pseudobonds, 31 residues, 4 models selected
> select add #13
207 atoms, 24 bonds, 531 pseudobonds, 31 residues, 4 models selected
> select subtract #13
207 atoms, 24 bonds, 31 residues, 3 models selected
> select subtract #8.2
15 atoms, 4 bonds, 5 residues, 3 models selected
> select subtract #8.1
1 model selected
Drag select of 5 pseudobonds
> select clear
Drag select of 5 pseudobonds
Drag select of 25 atoms, 19 residues, 21 bonds, 7 pseudobonds
> select clear
Drag select of 1 atoms, 5 pseudobonds
> hide (#!8 & sel) target a
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> hide #!11 models
> lighting soft
> hide #!9 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!11 models
> show #!9 models
> show #!8 models
> hide #!11 models
> lighting soft
> hide #!9 models
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> undo
Drag select of 23 atoms, 16 residues, 19 bonds, 1 pseudobonds
> select subtract #8.1
1 model selected
> show #!9 models
> select #8/A:24
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:24
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #941100ff
> select #8/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #ff2600ff
> color (#!8 & sel) #941100ff
> select #8/A:9
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #ff2600ff
> color (#!8 & sel) #941100ff
> select clear
> select #8/A:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #945200ff
> color (#!8 & sel) #941100ff
> select #8/A:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #945200ff
> color (#!8 & sel) #941100ff
> select #8/B:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0096ffff
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff7f
> select #8/B:226@CG
1 atom, 1 residue, 1 model selected
> select #8/B:184
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff80
> select #8/B:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff7e
> color (#!8 & sel) #0433ff7d
> select #8/B:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff7d
> select clear
> select #8/B:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff7c
> select #8/B:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!8 & sel) #0433ffff
> color (#!8 & sel) #0433ff81
> hide #!9 models
> show #!9 models
> select #9/A:9
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color (#!9 & sel) #941100ff
> select #9/A:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!9 & sel) #ff2600ff
> color (#!9 & sel) #941100ff
> select #9/B:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!9 & sel) #0433ffff
> color (#!9 & sel) #0433ff80
> color (#!9 & sel) #0433ff7f
> select #9/B:184
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!9 & sel) #0433ffff
> color (#!9 & sel) #0433ff79
> show #!11 models
> hide #!8 models
> select #11/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!11 & sel) #941100ff
> select #11/B:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/B:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/B:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!11 & sel) #0433ffff
> color (#!11 & sel) #0433ff7e
> select #11/B:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!11 & sel) #0433ffff
> color (#!11 & sel) #0433ff82
Drag select of 212 atoms, 214 residues, 180 bonds, 28 pseudobonds
> hide sel atoms
> show #!8 models
Drag select of 181 atoms, 173 residues, 150 bonds, 30 pseudobonds
> hide sel atoms
Drag select of 24 atoms, 49 residues, 19 bonds
> hide sel atoms
Drag select of 2 atoms, 2 residues, 2 bonds
> hide sel atoms
Drag select of 3 atoms, 2 residues, 2 bonds
> hide sel atoms
Drag select of 3 atoms, 2 residues, 6 bonds
> hide sel atoms
Drag select of 3 atoms, 163 residues, 4 bonds
> hide sel atoms
> select clear
Drag select of 10 atoms, 6 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 25 atoms, 60 residues, 17 bonds, 4 pseudobonds
Drag select of 5 residues
Drag select of 4 atoms, 69 residues, 2 bonds
> hide sel atoms
Drag select of 1 atoms, 1 residues, 1 bonds
Drag select of 2 atoms, 4 residues, 1 bonds
> hide sel atoms
Drag select of 14 residues
> select add #8
2292 atoms, 2343 bonds, 57 pseudobonds, 300 residues, 5 models selected
> select subtract #8
2 models selected
Drag select of 23 atoms, 234 residues, 23 bonds
Drag select of 204 residues
> hide sel atoms
Drag select of 8 atoms, 17 residues, 6 bonds
> hide sel atoms
Drag select of 17 atoms, 60 residues, 16 bonds
> hide sel atoms
Drag select of 137 atoms, 175 residues, 115 bonds, 23 pseudobonds
> hide sel atoms
Drag select of 11 atoms, 63 residues, 7 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 32 atoms, 50 residues, 27 bonds, 3 pseudobonds
Drag select of 3 residues
Drag select of 15 atoms, 67 residues, 13 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 4 atoms, 28 residues, 3 bonds
> hide sel atoms
Drag select of 6 atoms, 42 residues, 5 bonds
> hide sel atoms
Drag select of 4 atoms, 58 residues, 3 bonds
> hide sel atoms
===== 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
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX43KS/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 12 days, 17 hours, 32 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
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 HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 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 , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing Mac display configuration |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Qt 6.6 bug crashing _NSViewHierarchyDidChangeBackingProperties in probably when pluggin in external display.