Opened 7 months ago

Closed 7 months ago

#17172 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-15.3.2-x86_64-i386-64bit
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 0x00007ff8481e7b00 (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.surface._surface, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 65)


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{
  "uptime" : 240000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "coalitionID" : 1003,
  "osVersion" : {
    "train" : "macOS 15.3.2",
    "build" : "24D81",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-24 09:41:52.6629 +0100",
  "codeSigningMonitor" : 0,
  "incident" : "A085D66B-232F-4CF6-9DDA-1889DCAAB909",
  "pid" : 9415,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-23 11:35:14.0950 +0100",
  "procStartAbsTime" : 194046510541388,
  "procExitAbsTime" : 241616368391841,
  "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":"C4027B15-248B-5659-BACC-6FB29543A4B7","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "8D528D7E-5C72-169F-357F-E09EC31F9564",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bootSessionUUID" : "ECAC3F3E-CD7E-4414-A068-42C10232CC05",
  "wakeTime" : 14,
  "bridgeVersion" : {"build":"22P3060","train":"9.3"},
  "sleepWakeUUID" : "BAD323D9-2941-45B6-94F8-A43071712230",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4390133760\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      105ac2000-105ac6000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":9415},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4390133760\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      105ac2000-105ac6000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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  "faultingThread" : 0,
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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 1imp

Summary of feedback from opening 1imp fetched from pdb  
---  
note | Fetching compressed mmCIF 1imp from http://files.rcsb.org/download/1imp.cif  
  
1imp title:  
Colicin E9 immunity protein IM9, NMR, 21 structures [more info...]  
  
Chain information for 1imp  
---  
Chain | Description | UniProt  
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 | IM9 | IMM9_ECOLI 1-86  
  

> hide #1.1 models

> show #1.1 models

> hide models

> show #1.1 models

> open 1fsj

Summary of feedback from opening 1fsj fetched from pdb  
---  
note | Fetching compressed mmCIF 1fsj from http://files.rcsb.org/download/1fsj.cif  
  
1fsj title:  
Crystal structure of the E9 DNAse domain [more info...]  
  
Chain information for 1fsj #2  
---  
Chain | Description | UniProt  
B C D E | COLICIN E9 | CEA9_ECOLI 2-134 202-334 402-434 602-734  
  
Non-standard residues in 1fsj #2  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  
1fsj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> hide #!1 models

Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds  

> hide #2 cartoons

> show sel cartoons

Drag select of 60 atoms, 4 pseudobonds, 55 bonds  

> hide sel atoms

Drag select of 141 atoms, 8 pseudobonds, 127 bonds  

> hide sel atoms

> select clear

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #3  
---  
Chain | Description  
Aa | No description available  
Ba | No description available  
Ca | No description available  
DA | No description available  
Da | No description available  
Db | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
EA | No description available  
FA | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.0319, step 2, values float32  

> volume #4 level 0.07

> volume #4 step 1

> hide #!4 models

> style stick

Changed 56061 atom styles  

> color #3/DA light gray

> color #3/EA dim gray

> color #3/FA dark red

> color #3/Ca rebecca purple

> color #3/Ba forest green

> color #3/Da,Db,Dc,Dd,De,Df khaki

> color #3/Aa steel blue

> color #3/Aa:232-350 dark turquoise

> hide #3 atoms

> show #3 cartoons

Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds  

> ui mousemode right "rotate selected models"

> view matrix models #2,1,0,0,82.662,0,1,0,181.25,0,0,1,114.9

> view matrix models
> #2,1,0.0013443,-0.0025868,85.9,-0.0013444,1,-6.0428e-05,181.66,0.0025868,6.3905e-05,1,96.743

> mmaker sel to #3/Aa:230-350

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 97  
RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 97 pairs:
16.295)  
  

> color #2 yellow

> color #2 byhetero

> hide #!3 models

> select subtract #2/E:700

1046 atoms, 43 bonds, 4 pseudobonds, 135 residues, 2 models selected  

> select subtract #2/E:701

1038 atoms, 39 bonds, 4 pseudobonds, 134 residues, 2 models selected  

> select subtract #2/E:702

1028 atoms, 32 bonds, 3 pseudobonds, 133 residues, 2 models selected  

> select subtract #2/E:703

1018 atoms, 25 bonds, 3 pseudobonds, 132 residues, 2 models selected  

> select subtract #2/E:719

1010 atoms, 25 bonds, 3 pseudobonds, 131 residues, 2 models selected  

> select subtract #2/E:720

999 atoms, 25 bonds, 3 pseudobonds, 130 residues, 2 models selected  

> select subtract #2/E:721

992 atoms, 25 bonds, 3 pseudobonds, 129 residues, 2 models selected  

> select subtract #2/E:722

985 atoms, 25 bonds, 3 pseudobonds, 128 residues, 2 models selected  

> select clear

> select add #2/E:700

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/E:701

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/E:702

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #2/E:703

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #2/E:719

45 atoms, 43 bonds, 5 residues, 1 model selected  

> select add #2/E:720

56 atoms, 53 bonds, 6 residues, 1 model selected  

> select add #2/E:721

63 atoms, 59 bonds, 7 residues, 1 model selected  

> select add #2/E:722

70 atoms, 65 bonds, 8 residues, 1 model selected  

> hide #!2 models

> show #!3 models

> mmaker sel to #3/Aa:300-325

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 33.3  
RMSD between 6 pruned atom pairs is 0.986 angstroms; (across all 8 pairs:
2.082)  
  

> show #!2 models

> view matrix models
> #2,0.97297,-0.22873,-0.031935,103.66,0.22967,0.94372,0.23802,167.46,-0.024305,-0.23892,0.97073,110.17

> view matrix models
> #2,0.97551,-0.19874,-0.094297,106.33,0.21196,0.96388,0.16128,171.49,0.058839,-0.17731,0.98239,106.64

> view matrix models
> #2,0.97749,-0.14562,0.15266,94.724,0.17631,0.96123,-0.21202,189.82,-0.11586,0.23416,0.96527,111.65

> select clear

> select #2/E:702

10 atoms, 10 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.98567,-0.047376,0.16189,94.269,0.055707,0.99733,-0.047316,185.39,-0.15921,0.055656,0.98567,112.54

> select #2/E:700

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/E:701

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/E:702

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #2/E:703

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #2/E:704

45 atoms, 42 bonds, 5 residues, 1 model selected  

> select add #2/E:706

52 atoms, 49 bonds, 6 residues, 1 model selected  

> select add #2/E:707

60 atoms, 56 bonds, 7 residues, 1 model selected  

> select add #2/E:708

66 atoms, 61 bonds, 8 residues, 1 model selected  

> select add #2/E:709

75 atoms, 69 bonds, 9 residues, 1 model selected  

> select add #2/E:710

79 atoms, 72 bonds, 10 residues, 1 model selected  

> mmaker sel to #3/Aa:300-314

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 46.3  
RMSD between 10 pruned atom pairs is 0.499 angstroms; (across all 10 pairs:
0.499)  
  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select #3/Aa:280

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show #3/Aa:305,280,328,304

> select #3/Aa:332

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!4 models

> transparency 50

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select clear

> show #!3 models

> show #!2 models

> combine #2

> hide #!2 models

> hide #!3 models

> show #5 cartoons

> select #5/C:273

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

72 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

1047 atoms, 1071 bonds, 132 residues, 1 model selected  

> delete sel

> select #5/D:407

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #5/B:6

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

86 atoms, 84 bonds, 10 residues, 1 model selected  

> select up

2111 atoms, 2159 bonds, 266 residues, 1 model selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1fsj_E9_nuclease_HNH_like.pdb" models #5

> select #5/E:904@ZN

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select #5

1388 atoms, 1087 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@P

1387 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O2

1386 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O3

1385 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O1

1384 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O4

1383 atoms, 1083 bonds, 6 pseudobonds, 456 residues, 2 models selected  

> select subtract #5/E:904@ZN

1382 atoms, 1083 bonds, 3 pseudobonds, 455 residues, 2 models selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/zn_phosphate_from_1fsj.pdb" models #5

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined_with_water.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined_with_water.pdb
#6  
---  
Chain | Description  
Aa | No description available  
Ba | No description available  
Ca | No description available  
DA | No description available  
Da | No description available  
Db | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
EA | No description available  
FA | No description available  
  

> style stick

Changed 80248 atom styles  

> hide #6 atoms

> show #6 cartoons

> show #6/B atoms

> show #6/D atoms

> show #6/C atoms

> show #6/A atoms

> color #6/DA light gray

> color #6/EA dim gray

> color #6/FA dark red

> color #6/Ca rebecca purple

> color #6/Ba forest green

> color #6/Da,Db,Dc,Dd,De,Df khaki

> color #6/Aa steel blue

> color #6/Aa:232-350 dark turquoise

> color #6 byhetero

> show #6/Aa:305,280,328

> show #6/Aa:304,280,328

> show #!5 models

> hide #!5 models

> show #!2 models

> select #6/Aa:303

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show #!3 models

> hide #!3 models

> show #!4 models

> volume #4 level 0.09

> hide #!2 models

> show #!2 models

> hide #!4 models

> select #6/Aa:332

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> select #6/Aa:302

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/E:700

18 atoms, 16 bonds, 2 residues, 2 models selected  

> show sel atoms

> select #2/E:723

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #6/Aa:324

13 atoms, 11 bonds, 2 residues, 2 models selected  

> show sel atoms

> open 1v14

Summary of feedback from opening 1v14 fetched from pdb  
---  
note | Fetching compressed mmCIF 1v14 from http://files.rcsb.org/download/1v14.cif  
  
1v14 title:  
Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2
and dsDNA (resolution 2.9A) [more info...]  
  
Chain information for 1v14 #7  
---  
Chain | Description | UniProt  
A B C D | COLICIN E9 | CEA9_ECOLI 2-134  
E F G H I J K L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' |   
  
Non-standard residues in 1v14 #7  
---  
MG — magnesium ion  
  
1v14 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> hide #!2 models

> hide #!6 models

> view

> select add #7

5341 atoms, 5524 bonds, 73 pseudobonds, 623 residues, 5 models selected  

> select clear

> select add #7

5328 atoms, 5513 bonds, 73 pseudobonds, 621 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select add #7/G:8

19 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #7/H:12

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select add #7/J:11

62 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #7/I:8

81 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #7/C:80

87 atoms, 92 bonds, 5 residues, 1 model selected  

> select add #7/B:123

94 atoms, 98 bonds, 6 residues, 1 model selected  

> select add #7/E:5

114 atoms, 119 bonds, 7 residues, 1 model selected  

> select add #7/F:12

135 atoms, 142 bonds, 8 residues, 1 model selected  

> select add #7/A:53

146 atoms, 153 bonds, 9 residues, 1 model selected  

> select up

1143 atoms, 1247 bonds, 77 residues, 1 model selected  

> select up

3979 atoms, 4147 bonds, 438 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #7/D:100

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #7/D:101

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #7/D:102

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #7/D:103

32 atoms, 29 bonds, 4 residues, 1 model selected  

> select add #7/D:104

40 atoms, 36 bonds, 5 residues, 1 model selected  

> select add #7/D:105

49 atoms, 44 bonds, 6 residues, 1 model selected  

> select add #7/D:106

56 atoms, 51 bonds, 7 residues, 1 model selected  

> select add #7/D:107

64 atoms, 58 bonds, 8 residues, 1 model selected  

> show #!6 models

> mmaker sel to #6/Aa:300-310

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
(#6) with 1v14, chain D (#7), sequence alignment score = 23.8  
RMSD between 8 pruned atom pairs is 0.406 angstroms; (across all 8 pairs:
0.406)  
  

> color #7 yellow

> color #7 byhetero

> select clear

> select #7/K:6

19 atoms, 20 bonds, 1 residue, 1 model selected  

> show #!4 models

> hide #!4 models

> show #!4 models

> show sel atoms

> select #7/K:5

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> view sel

> select #7/D:5

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide #!4 models

> select #7/D:102

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #7/D:6

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select subtract #7/D:6

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #7/D:5

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select add #7/D:103

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select add #7/D:100

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #7/D:127

45 atoms, 42 bonds, 5 residues, 1 model selected  

> show sel atoms

> style stick

Changed 85576 atom styles  

> select add #7/K:4

66 atoms, 65 bonds, 6 residues, 1 model selected  

> select #7/K:5

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #7/K:6

39 atoms, 41 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select clear

> show #!4 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7

> hide #!4 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> show #7 cartoons

> view

> select #7/H:12

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #7/G:8

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select add #7/F:13

60 atoms, 64 bonds, 3 residues, 1 model selected  

> select add #7/E:7

82 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #7/A:102

92 atoms, 98 bonds, 5 residues, 1 model selected  

> select add #7/J:12

113 atoms, 121 bonds, 6 residues, 1 model selected  

> select add #7/I:7

135 atoms, 145 bonds, 7 residues, 1 model selected  

> select add #7/C:78

141 atoms, 150 bonds, 8 residues, 1 model selected  

> select up

956 atoms, 1055 bonds, 56 residues, 1 model selected  

> select up

2934 atoms, 3079 bonds, 306 residues, 1 model selected  

> select up

2956 atoms, 3079 bonds, 328 residues, 1 model selected  

> select up

5328 atoms, 5513 bonds, 621 residues, 1 model selected  

> select down

2956 atoms, 3079 bonds, 328 residues, 1 model selected  

> delete sel

> select #7/B:89

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select up

1045 atoms, 1068 bonds, 132 residues, 1 model selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7

> hide #!7 models

> open 1emv

Summary of feedback from opening 1emv fetched from pdb  
---  
note | Fetching compressed mmCIF 1emv from http://files.rcsb.org/download/1emv.cif  
  
1emv title:  
Crystal structure of colicin E9 DNAse domain with its cognate immunity protein
IM9 (1.7 angstroms) [more info...]  
  
Chain information for 1emv #8  
---  
Chain | Description | UniProt  
A | IMMUNITY PROTEIN IM9 | IMM9_ECOLI 1-86  
B | COLICIN E9 | CEA9_ECOLI 2-134  
  
Non-standard residues in 1emv #8  
---  
PO4 — phosphate ion  
  

> view

> select #8/A:71

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

121 atoms, 123 bonds, 16 residues, 1 model selected  

> select up

651 atoms, 664 bonds, 83 residues, 1 model selected  

> delete sel

> mmaker #8/B:100-110 to #6/Aa:300-310

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
(#6) with 1emv, chain B (#8), sequence alignment score = 35.4  
RMSD between 9 pruned atom pairs is 0.264 angstroms; (across all 9 pairs:
0.264)  
  

> view

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #8 models

> show #8 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select #8/B:127

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> hide #!6 models

> show #!6 models

> select #8/B:100

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #8 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!2 models

> show #!6 models

> select #6/Aa:303

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/E:704

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/Aa:306

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/E:706

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/Ba:128

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!4 models

> lighting simple

> lighting soft

> lighting simple

> hide #!4 models

> hide #!2 models

> hide #!6 models

> show #8 models

> set chain

Expected a keyword  

> set chain #8/B A

Expected a keyword  

> set chain #8/B to A

Expected a keyword  

> set chain A #8/B

Expected a keyword  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_refined2.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> color #9/L light gray

> color #9/K dim gray

> color #9/J dark red

> color #9/I rebecca purple

> color #9/B forest green

> color #9/C,D,E,F,G,H khaki

> color #9/A steel blue

> color #9/A:232-350 dark turquoise

> style stick

Changed 106889 atom styles  

> hide #9 atoms

> show #9 cartoons

> hide #!9 models

> show #!3 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> show #9/M atoms

> show #9/N atoms

> hide #!9 models

> show #!9 models

> hide #8 models

> show #8 models

> hide #8 models

> hide #!9 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"

Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #10 atoms

> show #10 cartoons

> cartoon style nucleic xsection oval width 1.6 thickness 1.6

> color #10/L light gray

> color #10/K dim gray

> color #10/J dark red

> color #10/I rebecca purple

> color #10/B forest green

> color #10/C,D,E,F,G,H khaki

> color #10/A steel blue

> color #10/A:232-350 dark turquoise

> show #10/K atoms

> style stick

Changed 131055 atom styles  

> show #10 & nucleic atoms

> select #10

24166 atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected  

> nucleotides sel ladder

> select clear

> show #!4 models

> volume #4 level 0.06

> show #10/M,N,O atoms

> select clear

> select #10/K:4

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #10/K:3

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select add #10/K:2

45 atoms, 47 bonds, 3 residues, 1 model selected  

> select add #10/K:1

54 atoms, 56 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 54 atom styles  

> select clear

> color zone #4 near #10 distance 10

> transparency 50

> volume #4 level 0.05

> cartoon style nucleic xsection oval width 1 thickness 1

> color #10/L light gray

> color #10/K dim gray

> color #10/J dark red

> color #10/I rebecca purple

> color #10/B forest green

> color #10/C,D,E,F,G,H khaki

> color #10/A steel blue

> color #10/A:232-350 dark turquoise

> color zone #4 near #10 distance 10

> hide #!10 models

> hide #!4 models

> show #!10 models

> select #10/M:1@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> select #10/O:1@O

1 atom, 1 residue, 1 model selected  

> color sel blue

> select clear

> color zone #4 near #10 distance 10

> show #!4 models

> hide #!10 models

> color zone #4 near #10 distance 5

> volume #4 level 0.09

> lighting soft

> lighting full

> lighting soft

> color zone #4 near #10 distance 4

> color zone #4 near #10 distance 3

> volume #4 level 0.07

> surface zone #4 nearAtoms #10 distance 2.5

> surface zone #4 nearAtoms #10 distance 3

> select add #4

2 models selected  

> ui tool show "Color Actions"

> color sel navajo white

> set bgColor white

> lighting simple

> transparency sel 50

> show #!10 models

> volume #4 level 0.05

> volume #4 level 0.09

> volume #4 level 0.08

> color #10 byhetero

> select clear

> select #10/K:1@N9

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 9 bonds, 1 residue, 1 model selected  

> select add #10/K:2@OP2

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select up

29 atoms, 31 bonds, 2 residues, 1 model selected  

> select down

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select add #10/K:2@OP1

11 atoms, 12 bonds, 2 residues, 1 model selected  

> select add #10/K:2@O2

12 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #10/K:2@O4

13 atoms, 20 bonds, 2 residues, 1 model selected  

> select add #10/K:2@C5

14 atoms, 21 bonds, 2 residues, 1 model selected  

> select add #10/K:2@C7

15 atoms, 24 bonds, 2 residues, 1 model selected  

> select add #10/K:3@N6

16 atoms, 25 bonds, 3 residues, 1 model selected  

> select up

28 atoms, 27 bonds, 3 residues, 1 model selected  

> select up

50 atoms, 55 bonds, 3 residues, 1 model selected  

> hide #!4 models

> select subtract #10/K:3@OP1

49 atoms, 53 bonds, 3 residues, 1 model selected  

> select subtract #10/K:3@P

48 atoms, 51 bonds, 3 residues, 1 model selected  

> select subtract #10/K:3@OP2

47 atoms, 51 bonds, 3 residues, 1 model selected  

> select add #10/K:4@P

48 atoms, 51 bonds, 4 residues, 1 model selected  

> select add #10/K:4@OP1

49 atoms, 52 bonds, 4 residues, 1 model selected  

> select add #10/K:4@OP2

50 atoms, 54 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@O3'

49 atoms, 53 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@C4'

48 atoms, 50 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@O4'

47 atoms, 48 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@C3'

46 atoms, 48 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@C2'

45 atoms, 47 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@C1'

44 atoms, 46 bonds, 4 residues, 1 model selected  

> select subtract #10/K:2@C5'

43 atoms, 46 bonds, 4 residues, 1 model selected  

> hide sel atoms

> show #10/K:3 atoms

> hide sel atoms

> select #10/K:3@C5'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #10/K:3@C4'

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@O3'

2 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C2'

3 atoms, 1 residue, 1 model selected  

> select add #10/K:3@O4'

4 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select #10/K:3@C3'

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@C1'

2 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C8

3 atoms, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select down

3 atoms, 1 residue, 1 model selected  

> select add #10/K:3@N3

4 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C4

5 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C5

6 atoms, 1 residue, 1 model selected  

> select add #10/K:3@N7

7 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C6

8 atoms, 1 residue, 1 model selected  

> select add #10/K:3@N6

9 atoms, 1 residue, 1 model selected  

> select add #10/K:3@N1

10 atoms, 1 residue, 1 model selected  

> select add #10/K:3@C2

11 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select #10/K:3@N9

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show #!4 models

> select #10/K:2@C5'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> volume #4 level 0.07

> show #10/A:305,304,280,328

> volume #4 level 0.09

> select #10/K:4@O5'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> color #10/M red

> color #10/O blue

> color #10/O dark blue

> color #10/O blue

> volume #4 level 0.07

> show #10/K:2 atoms

> volume #4 level 0.06

> show #10/K:1-2 atoms

> show #!5 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> hide #!10 models

> show #!10 models

> select #10/K:1@O5'

1 atom, 1 residue, 1 model selected  

> select add #10/K:1@C5'

2 atoms, 1 residue, 1 model selected  

> select add #10/K:1@C4'

3 atoms, 1 residue, 1 model selected  

> select add #10/K:1@O4'

4 atoms, 1 residue, 1 model selected  

> select add #10/K:1@C1'

5 atoms, 1 residue, 1 model selected  

> select add #10/K:1@N9

6 atoms, 1 residue, 1 model selected  

> select add #10/K:1@C2'

7 atoms, 1 residue, 1 model selected  

> select add #10/K:1@C3'

8 atoms, 1 residue, 1 model selected  

> select add #10/K:1@O3'

9 atoms, 1 residue, 1 model selected  

> select add #10/K:2@P

10 atoms, 2 residues, 1 model selected  

> select add #10/K:2@OP2

11 atoms, 2 residues, 1 model selected  

> select add #10/K:2@OP1

12 atoms, 2 residues, 1 model selected  

> select add #10/K:2@O5'

13 atoms, 2 residues, 1 model selected  

> select add #10/K:2@C5'

14 atoms, 2 residues, 1 model selected  

> hide sel atoms

> show #!4 models

> hide #!4 models

> ui tool show Distances

> select #10/O:1@O

1 atom, 1 residue, 1 model selected  

> select #10/K:3@OP2

1 atom, 1 residue, 1 model selected  

> select add #10/O:1@O

2 atoms, 2 residues, 1 model selected  

> distance #10/K:3@OP2 #10/O:1@O

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2
and /O HOH 1 O: 2.479Å  

> select #10/A:304@ND1

1 atom, 1 residue, 1 model selected  

> select add #10/M:1@MG

2 atoms, 2 residues, 1 model selected  

> distance #10/A:304@ND1 #10/M:1@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1
and /M MG 1 MG: 2.377Å  

> select #10/A:328@NE2

1 atom, 1 residue, 1 model selected  

> select add #10/M:1@MG

2 atoms, 2 residues, 1 model selected  

> distance #10/A:328@NE2 #10/M:1@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2
and /M MG 1 MG: 2.352Å  

> select #10/M:1@MG

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@OP1

2 atoms, 2 residues, 1 model selected  

> distance #10/M:1@MG #10/K:3@OP1

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and
/K DA 3 OP1: 3.166Å  

> select #10/A:280@NH2

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #10/A:280@NH2 #10/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å  

> select #10/A:280@NH1

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@O5'

2 atoms, 2 residues, 1 model selected  

> distance #10/A:280@NH1 #10/K:3@O5'

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1
and /K DA 3 O5': 2.765Å  

> select #10/A:238

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #10/A:319

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #10/A:305@ND1

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #10/A:305@ND1 #10/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP2: 3.592Å  

> select #10/A:309

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> select #10/A:309@N

1 atom, 1 residue, 1 model selected  

> select add #10/O:1@O

2 atoms, 2 residues, 1 model selected  

> distance #10/A:309@N #10/O:1@O

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N
and /O HOH 1 O: 3.104Å  

> select #10/A:309@N

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> view

> select #10/A:305@ND1

1 atom, 1 residue, 1 model selected  

> select add #10/K:3@OP1

2 atoms, 2 residues, 1 model selected  

> distance #10/A:305@ND1 #10/K:3@OP1

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP1: 3.734Å  

> delete sel

> ~distance #10/A:305@ND1 #10/K:3@OP1

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"

Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> style stick

Changed 155221 atom styles  

> hide #12 atoms

> color #12/L light gray

> color #12/K dim gray

> color #12/J dark red

> color #12/I rebecca purple

> color #12/B forest green

> color #12/C,D,E,F,G,H khaki

> color #12/A steel blue

> color #12/A:232-350 dark turquoise

> hide #!11 models

> show #!11 models

> close #11

> show #12 cartoons

> cartoon style nucleic xsection oval width 1 thickness 1

> show #12/K:2-3 atoms

> hide #12/K:1-3 cartoons

> select clear

> select #12/K:2@OP1

1 atom, 1 residue, 1 model selected  

> select add #12/K:2@OP2

2 atoms, 1 residue, 1 model selected  

> select add #12/K:2@P

3 atoms, 1 residue, 1 model selected  

> select add #12/K:2@C5'

4 atoms, 1 residue, 1 model selected  

> select add #12/K:3@C5'

5 atoms, 2 residues, 1 model selected  

> select add #12/K:3@C4'

6 atoms, 2 residues, 1 model selected  

> select add #12/K:3@C3'

7 atoms, 2 residues, 1 model selected  

> select add #12/K:4

11 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@O4'

12 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C2'

13 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C1'

14 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@N9

15 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C8

16 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C4

17 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C5

18 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@N7

19 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C6

20 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@N6

21 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@N1

22 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@C2

23 atoms, 3 bonds, 3 residues, 1 model selected  

> select add #12/K:3@N3

24 atoms, 3 bonds, 3 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #12/K:3@O3'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> select #12/K:2@O5'

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show #12/M,O atoms

> select #12/O:1@O

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> select clear

> show #12/A:304-305,328,280

> select #12/A:319

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select ~sel & ##selected

24158 atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected  

> show #12/A:304-305,328,280,319

> color #12 byhetero

> select #12/O:1@O

1 atom, 1 residue, 1 model selected  

> select add #12/M:1@MG

2 atoms, 2 residues, 1 model selected  

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> select #12/O:1@O

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> select clear

> select #12/A:305@ND1

1 atom, 1 residue, 1 model selected  

> select add #12/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #12/A:305@ND1 #12/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1
and /K DA 3 OP2: 3.159Å  

> select #12/A:280@NH2

1 atom, 1 residue, 1 model selected  

> select add #12/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #12/A:280@NH2 #12/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å  

> select #12/A:280@NH1

1 atom, 1 residue, 1 model selected  

> select add #12/K:3@O5'

2 atoms, 2 residues, 1 model selected  

> distance #12/A:280@NH1 #12/K:3@O5'

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1
and /K DA 3 O5': 2.765Å  

> view

> select #12/K:3@OP1

1 atom, 1 residue, 1 model selected  

> select add #12/M:1@MG

2 atoms, 2 residues, 1 model selected  

> distance #12/K:3@OP1 #12/M:1@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1
and /M MG 1 MG: 3.166Å  

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> select add #12/A:304@ND1

2 atoms, 2 residues, 1 model selected  

> distance #12/M:1@MG #12/A:304@ND1

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and
/A HIS 304 ND1: 2.377Å  

> select #12/A:328@NE2

1 atom, 1 residue, 1 model selected  

> select add #12/M:1@MG

2 atoms, 2 residues, 1 model selected  

> distance #12/A:328@NE2 #12/M:1@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2
and /M MG 1 MG: 2.352Å  

> select clear

> color sel maroon

> color sel teal

> color sel cornflower blue

> color sel dark salmon

> color sel dark khaki

> color sel peru

> select #12/O:1@O

1 atom, 1 residue, 1 model selected  

> select add #12/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> color sel indigo

> color sel red

> select #12/O:1@O

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #12/K:3@OP2

1 atom, 1 residue, 1 model selected  

> select add #12/O:1@O

2 atoms, 2 residues, 1 model selected  

> distance #12/K:3@OP2 #12/O:1@O

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2
and /O HOH 1 O: 2.479Å  

> color sel indigo

> select clear

> color sel dark blue

> select clear

> select #12/A:309

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #12/O:1@O

9 atoms, 7 bonds, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> select #12/A LEU 309 N

Expected a keyword  

> select #12/A:309

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> select #12/A:309@N

1 atom, 1 residue, 1 model selected  

> select add #12/O:1@O

2 atoms, 2 residues, 1 model selected  

> distance #12/A:309@N #12/O:1@O

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N
and /O HOH 1 O: 3.104Å  

> distance style decimalPlaces 2

> distance style decimalPlaces 1

> select subtract #12/O:1@O

1 atom, 1 residue, 1 model selected  

> select ~sel & ##selected

24165 atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected  

> hide #12/A:309 atoms

> show #12/A:309 cartoons

> select clear

> show #!4 models

> volume #4 level 0.07

> volume #4 level 0.08

> select #12/K:2@N3

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

886 atoms, 986 bonds, 45 residues, 1 model selected  

> select down

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> surface dust #4 size 7.25

> surface dust #4 1

Expected a keyword  

> surface dust #4 size 1

> show (sel-residues & sidechain) target ab

> hide sel atoms

> select clear

> select #12/K:3@O5'

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> show #12/K:2 atoms

> select #12/K:2@C2

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide #!4 models

> select subtract #12/K:2@O3'

19 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #!4 models

> volume #4 level 0.06

> volume #4 level 0.08

> volume #4 level 0.09

> volume #4 level 0.08

> view matrix models
> #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143

> show #!10 models

> hide #!10 models

> mmaker #12 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#10) with
halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment
score = 1753  
RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs:
0.001)  
  

> ui tool show "Side View"

> hide #11.1 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3 transparentBackground true

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> select #2/E:804@O1

1 atom, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #2/E:731@CG

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select up

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select up

17 atoms, 15 bonds, 3 residues, 1 model selected  

> select up

19 atoms, 16 bonds, 4 residues, 1 model selected  

> select add #12/A:319@OD1

20 atoms, 16 bonds, 5 residues, 2 models selected  

> select up

39 atoms, 35 bonds, 5 residues, 2 models selected  

> select add #2/E:31@O

40 atoms, 35 bonds, 6 residues, 2 models selected  

> select add #2/E:298@O

41 atoms, 35 bonds, 7 residues, 2 models selected  

> select subtract #2/E:298@O

40 atoms, 35 bonds, 6 residues, 2 models selected  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> select add #12

24198 atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected  

> select subtract #12

32 atoms, 28 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select #2/E:701@CB

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #12/A:319@OD1

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/E:298@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> color sel dark blue

> select clear

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!12 models

> hide #!4 models

> show #!2 models

> select #2/E:904@ZN

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> hide #!2 models

> show #!12 models

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> color sel silver

> color sel metallic

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel dark gray

> color sel dim gray

> select clear

> color sel red

> select #12/M:1@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> color sel dim gray

> select clear

> show #!2 models

> hide #!2 models

> show #!4 models

> color sel red

> color #12/M red

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> color sel tan

> color sel dim gray

> show #!4 models

> select clear

> hide #!2 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3

> hide #!4 models

> show #!2 models

> hide #!11 models

> color #2 yellow

> sle #2/E

Unknown command: sle #2/E  

> select #2/E

1109 atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected  

> select clear

> ui tool show "Show Sequence Viewer"

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!2 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"

Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #13 atoms

> show #13 cartoons

> cartoon style nucleic xsection oval width 1 thickness 1

> color #13/DA light gray

> color #13/EA dim gray

> color #13/FA dark red

> color #13/Ca rebecca purple

> color #13/Ba forest green

> color #13/Da,Db,Dc,Dd,De,Df khaki

> color #13/Aa steel blue

> color #13/Aa:232-350 dark turquoise

> hide #!12 models

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> color #13/L light gray

> color #13/K dim gray

> color #13/J dark red

> color #13/I rebecca purple

> color #13/B forest green

> color #13/C,D,E,F,G,H khaki

> color #13/A steel blue

> color #13/A:232-350 dark turquoise

> color #13 byhetero

> hide #!12 models

> color #13/M red

> show #13/K:2 atoms

> style stick

Changed 179387 atom styles  

> select #13/K:3

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #13/K:4

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select add #13/K:2

45 atoms, 47 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> show #13/K:3 atoms

> select subtract #13/K:3@O5'

44 atoms, 45 bonds, 3 residues, 1 model selected  

> select subtract #13/K:3@OP2

43 atoms, 44 bonds, 3 residues, 1 model selected  

> select subtract #13/K:3@OP1

42 atoms, 43 bonds, 3 residues, 1 model selected  

> select subtract #13/K:2@O3'

41 atoms, 42 bonds, 3 residues, 1 model selected  

> select subtract #13/K:2@C3'

40 atoms, 40 bonds, 3 residues, 1 model selected  

> select add #13/K:2@C3'

41 atoms, 40 bonds, 3 residues, 1 model selected  

> select subtract #13/K:2@C3'

40 atoms, 40 bonds, 3 residues, 1 model selected  

> select add #13/K:2@C3'

41 atoms, 40 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select #13/K:2@O3'

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

886 atoms, 986 bonds, 45 residues, 1 model selected  

> show sel atoms

> select #13/K:4@O5'

1 atom, 1 residue, 1 model selected  

> select add #13/K:4@OP1

2 atoms, 1 residue, 1 model selected  

> select add #13/K:3@O3'

3 atoms, 2 residues, 1 model selected  

> select up

25 atoms, 27 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@O5'

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@P

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@OP1

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@OP2

21 atoms, 23 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select up

23 atoms, 24 bonds, 3 residues, 1 model selected  

> select up

45 atoms, 49 bonds, 3 residues, 1 model selected  

> select down

23 atoms, 24 bonds, 3 residues, 1 model selected  

> select #13/K:2@N1

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select subtract #13/K:2@O3'

19 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #13/A:304-305,328,280

> show #13/M,O

> select #13/O:1@O

1 atom, 1 residue, 1 model selected  

> color sel blue

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!4 models

> show #!12 models

> hide #!12 models

> select #13/K:1

9 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #13/K:1@O5'

1 atom, 1 residue, 1 model selected  

> select add #13/K:1@C5'

2 atoms, 1 residue, 1 model selected  

> hide sel atoms

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select Mg

6 atoms, 6 residues, 6 models selected  

> select Zn

5 atoms, 5 residues, 2 models selected  

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> select add #2

4547 atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected  

> select subtract #2

1 atom, 1 residue, 1 model selected  

> hide #!4 models

> select add #5

6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select subtract #5

Nothing selected  

> select add #5

6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select Zn

5 atoms, 5 residues, 2 models selected  

> select add #5

10 atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected  

> select subtract #5

4 atoms, 4 residues, 1 model selected  

> show sel atoms

> show #!2 models

> select water

Expected an objects specifier or a keyword  

> ui tool show "Check Waters"

> hbonds #13/O interModel false reveal true restrict any name "water H-bonds"

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9  

2 hydrogen bonds found  

> show #4 models

> select #13/O

1 atom, 1 residue, 1 model selected  

> display #13/O : view #13/O @ select add #13/K:3@N7

2 atoms, 2 residues, 1 model selected  

> select up

22 atoms, 23 bonds, 2 residues, 1 model selected  

> hide #!2 models

> hide #!4 models

> select subtract #13/K:3@O5'

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@OP2

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select subtract #13/K:3@OP1

19 atoms, 19 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select #13/K:3@O5'

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select subtract #13/K:3@P

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select subtract #13/K:3@OP1

19 atoms, 20 bonds, 1 residue, 1 model selected  

> select subtract #13/K:3@OP2

18 atoms, 20 bonds, 1 residue, 1 model selected  

> select subtract #13/K:3@O5'

17 atoms, 19 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select subtract #13/K:2@O3'

19 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

9 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #13/A:308@CD

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel cartoons

> select #13/A:309@N

1 atom, 1 residue, 1 model selected  

> show #13/O atoms

> show #!11 models

> hide #!11 models

> close #11

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide sel

> select #13/O:1@O

1 atom, 1 residue, 1 model selected  

> select add #13/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #13/O:1@O #13/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and
/K DA 3 OP2: 2.5Å  

> select #13/A:309

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show sel atoms

> select #13/A:309@N

1 atom, 1 residue, 1 model selected  

> select add #13/O:1@O

2 atoms, 2 residues, 1 model selected  

> distance #13/A:309@N #13/O:1@O

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N
and /O HOH 1 O: 3.1Å  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide #11.1 models

> select #13/M:2@MG

1 atom, 1 residue, 1 model selected  

> select add #13/K:2@O3'

2 atoms, 2 residues, 1 model selected  

> distance #13/M:2@MG #13/K:2@O3'

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and
/K DT 2 O3': 2.9Å  

> select #13/A:304@ND1

1 atom, 1 residue, 1 model selected  

> select add #13/M:2@MG

2 atoms, 2 residues, 1 model selected  

> distance #13/A:304@ND1 #13/M:2@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1
and /M MG 2 MG: 2.6Å  

> select #13/A:328@NE2

1 atom, 1 residue, 1 model selected  

> select add #13/M:2@MG

2 atoms, 2 residues, 1 model selected  

> distance #13/A:328@NE2 #13/M:2@MG

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2
and /M MG 2 MG: 2.0Å  

> select clear

> select #13/A:305@ND1

1 atom, 1 residue, 1 model selected  

> select add #13/K:3@OP2

2 atoms, 2 residues, 1 model selected  

> distance #13/A:305@ND1 #13/K:3@OP2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1
and /K DA 3 OP2: 3.2Å  

> select #13/K:3@O5'

1 atom, 1 residue, 1 model selected  

> select add #13/A:280@NH1

2 atoms, 2 residues, 1 model selected  

> distance #13/K:3@O5' #13/A:280@NH1

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5'
and /A ARG 280 NH1: 2.8Å  

> select #13/K:3@OP2

1 atom, 1 residue, 1 model selected  

> select add #13/A:280@NH2

2 atoms, 2 residues, 1 model selected  

> distance #13/K:3@OP2 #13/A:280@NH2

Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2
and /A ARG 280 NH2: 2.4Å  

> select add #11

8 pseudobonds, 2 models selected  

> color sel dim gray

> show #!2 models

> hide #!2 models

> show #!4 models

> unsel

Unknown command: unsel  

> select

179387 atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected  

> select clear

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3

> show #!2 models

> hide #!4 models

> hide #!11 models

> select #2/E:31@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3

> lighting soft

> show #!4 models

> hide #!2 models

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> show #!2 models

> hide #!4 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #4 level 0.09

> volume #4 level 0.1

> volume #4 level 0.95

> volume #4 level 0.095

> volume #4 level 0.09

> volume #4 level 0.08

> volume #4 level 0.09

> select #13/K:6

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show #13/L atoms

> select clear

> show #13/L,J atoms

> select clear

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"


===== Log before crash end =====

OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0)
      OS Loader Version: 582~3311

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 6 days, 20 hours, 9 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Odyssey G70B:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: H1AK500000  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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
    biopython: 1.84
    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
    DiffFit: 0.2
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    fsspec: 2024.6.1
    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
    joblib: 1.4.2
    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
    mpmath: 1.3.0
    mrcfile: 1.5.1
    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
    scikit-learn: 1.5.1
    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
    sympy: 1.13.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    threadpoolctl: 3.5.0
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    torch: 2.2.2
    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 Eric Pettersen, 7 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 Eric Pettersen, 7 months ago

Resolution: duplicate
Status: assignedclosed
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