Opened 8 months ago

Closed 8 months ago

#17176 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 (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.3.2-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

Thread 0x0000000328c8f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000327c83000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000326c77000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000325c6b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000324c5f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000323c53000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000322c47000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321c3b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315563000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000314557000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031354b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000002084d8840 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 67)


{"app_name":"ChimeraX","timestamp":"2025-03-21 18:21:59.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.2 (24D81)","roots_installed":0,"name":"ChimeraX","incident_id":"3BA56CF7-EBB8-4B7A-8077-A15083E24A31"}
{
  "uptime" : 200000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 4012,
  "osVersion" : {
    "train" : "macOS 15.3.2",
    "build" : "24D81",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-21 17:09:15.8768 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "3BA56CF7-EBB8-4B7A-8077-A15083E24A31",
  "pid" : 39327,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-17 10:48:46.0071 -0500",
  "procStartAbsTime" : 1597522658020,
  "procExitAbsTime" : 5000327943981,
  "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":"039446C8-56F1-54A1-9531-85BD2E8F600D","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3C03AB57-DF91-6538-731F-87145E7E925C",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "A7275150-C5A5-48E1-A7F7-1369D27D4EB2",
  "wakeTime" : 10391,
  "sleepWakeUUID" : "BE3D1F6A-78A0-4CC4-A517-28C1A78F7F5F",
  "sip" : "enabled",
  "vmRegionInfo" : "0x2157c0c42478 is not in any region.  Bytes after previous region: 36179743614073  Bytes before following region: 68892336315272\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, 0x0000a157c0c42478","rawCodes":[1,177398268306552],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a157c0c42478 -> 0x00002157c0c42478 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":39327},
  "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" : "0x2157c0c42478 is not in any region.  Bytes after previous region: 36179743614073  Bytes before following region: 68892336315272\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  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100567192},{"value":99},{"value":95},{"value":3458870066972047008},{"value":0},{"value":13392203380844384888},{"value":13392203389304986168},{"value":14757395258967641293},{"value":4294967286},{"value":5100567122},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8870011584},{"value":0},{"value":11},{"value":259},{"value":8729233696,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4324836912,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8692224000,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8692224000,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6957727600},"cpsr":{"value":1073745920},"fp":{"value":5100567264},"sp":{"value":5100567232},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/kompa012/Desktop/NiP N protein article/7nt5_J377_intactmodel-
> coot-0_real_space_refined_030.pdb"

Chain information for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb
#1  
---  
Chain | Description  
D E F G H I J K L M N O P Q | No description available  
Z | No description available  
  

> open "/Users/kompa012/Desktop/NiP N protein article/pdb_extract_3032647.cif"

Summary of feedback from opening /Users/kompa012/Desktop/NiP N protein
article/pdb_extract_3032647.cif  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for pdb_extract_3032647.cif #2  
---  
Chain | Description  
D E F G H I J K L M N O P Q | No description available  
Z | No description available  
  

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> open 7nt5 fromDatabase pdb format mmcif

Summary of feedback from opening 7nt5 fetched from pdb  
---  
note | Fetching compressed mmCIF 7nt5 from http://files.rcsb.org/download/7nt5.cif  
  
7nt5 title:  
CryoEM structure of the Nipah virus nucleocapsid single helical turn assembly
[more info...]  
  
Chain information for 7nt5 #3  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M | Nucleoprotein | NCAP_NIPAV 1-532  
N | RNA (78-MER) |   
  

> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J377_009_volume_map.mrc"

Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.0369, step 4, values float32  

> volume #4 step 1

> hide #!3 models

> ui tool show "Hide Dust"

> surface dust #4 size 5.31

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> style sel stick

Changed 44996 atom styles  

> hide #2 models

> select add #4

44996 atoms, 45905 bonds, 5656 residues, 3 models selected  

> select subtract #1

2 models selected  

> transparency #4.1 70

> volume #4 level 0.03

> volume #4 level 0.02

> volume #4 level 0.015

> volume #4 level 0.05

> ui mousemode right select

> select clear

> volume #4 level 0.06

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> show sel surfaces

> select subtract #1

15 models selected  

> select add #1.15

1680 atoms, 84 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select clear

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> color zone #4 near sel & #1 distance 5.31

> select clear

> hide #!1 models

> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J379_map_sharp.mrc"

Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.000704, step 4, values float32  

> volume #5 step 1

> volume #5 level 0.02408

> surface dust #5 size 5.31

> volume #5 level 0.06

> volume #4 level 0.025

> show #!5 models

> hide #!4 models

> show #!1 models

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> hide sel surfaces

> show sel atoms

> select clear

> select add #5

2 models selected  

> transparency #5.1 80

> select clear

> volume #5 level 0.04

> transparency #1,5 60

> hide #!5 models

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> select subtract #1.10

41902 atoms, 42758 bonds, 5258 residues, 16 models selected  

> select subtract #1.11

38808 atoms, 39611 bonds, 4860 residues, 15 models selected  

> select subtract #1.15

37128 atoms, 37764 bonds, 4776 residues, 14 models selected  

> hide sel atoms

> select subtract #1.9

34034 atoms, 34617 bonds, 4378 residues, 13 models selected  

> select add #1.9

37128 atoms, 34617 bonds, 4776 residues, 12 models selected  

> select add #1

44996 atoms, 45905 bonds, 5656 residues, 13 models selected  

> select subtract #1

15 models selected  

> select add #1.9

3094 atoms, 398 residues, 1 model selected  

> show sel atoms

> select clear

Cell requested for row 3 is out of bounds for table with 20 rows! Resizing
table model.  

> ui tool show Contacts

> select add #1.15

1680 atoms, 84 residues, 1 model selected  

> select add #1.10

4774 atoms, 482 residues, 2 models selected  

> select add #1.11

7868 atoms, 880 residues, 3 models selected  

> select add #1.9

10962 atoms, 1278 residues, 4 models selected  

> contacts sel restrict both ignoreHiddenModels true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    5727 contacts
                                     atom1                                                                     atom2                                    overlap  distance
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1   0.708    3.052
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1   0.578    3.182
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 269 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 265 O     0.504    2.796
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2   0.444    3.076
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CG2   0.435    3.325
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 192 NH1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 66 P        0.403    3.337
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 269 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 265 O     0.401    2.899
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 192 NH1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 60 P        0.397    3.343
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 269 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 265 O     0.363    2.937
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG     0.325    3.195
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG    0.323    3.437
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 36 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 124 CD    0.280    3.240
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB    0.265    3.495
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 36 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 124 CD    0.261    3.259
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 137 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 133 O     0.255    3.045
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 137 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 133 O     0.238    3.062
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 137 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 133 O     0.236    3.064
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 36 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 124 CD    0.234    3.286
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 284 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 288 NE2   0.232    2.428
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 288 NE2   0.228    2.432
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 349 ND2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 51 N3       0.228    3.052
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 OE1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH    0.222    2.258
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 CD    0.220    3.120
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 50 OE1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 154 NH1   0.217    2.443
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 280 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 374 CG2   0.216    3.544
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 169 O     0.216    2.964
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 34 CA    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 98 O      0.214    3.086
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 192 NH1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 54 P        0.213    3.527
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 169 O     0.211    2.969
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 376 NE2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 278 CG    0.210    3.310
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 349 ND2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 63 N3       0.208    3.072
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 103 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 41 CB     0.205    3.555
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 290 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 287 O     0.204    3.096
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 101 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 89 NH1    0.201    3.319
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG     0.198    3.142
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 101 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 89 NH1    0.197    3.323
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 169 O     0.191    2.989
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 50 OE1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 154 NH1   0.191    2.469
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 ND2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 279 CD1   0.191    3.209
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 328 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 331 CB    0.189    3.111
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 157 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 160 OG1   0.187    3.153
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 280 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CD1   0.187    3.573
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 268 CE1   0.186    3.214
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 3 N      7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 381 CD    0.185    3.335
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 332 OG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 329 O     0.179    2.301
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 268 CE1   0.178    3.222
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 276 OE1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 292 ND2   0.177    2.483
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 233 OE1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 O     0.176    2.664
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1    0.176    3.344
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 318 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 20 NH2    0.176    3.344
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 12 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2    0.174    3.106
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 315 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 250 CD    0.174    3.126
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 101 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 89 NH1    0.174    3.346
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 144 CD    0.173    3.347
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 50 OE1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 154 NH1   0.173    2.487
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 227 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CG    0.172    3.128
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 329 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 332 OG    0.171    2.309
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 344 OG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 342 CG    0.170    3.170
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 373 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 388 CG    0.170    3.130
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 157 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 160 OG1   0.169    3.171
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 11 CE2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 15 NE2    0.166    3.234
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 227 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CG    0.165    3.135
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 11 CE2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2    0.165    3.235
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 227 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CG    0.162    3.138
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 11 CE2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2    0.160    3.240
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 344 OG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 342 CG    0.160    3.180
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2   0.159    3.361
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 31 CD1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 48 NH1    0.159    3.361
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 314 CD2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 229 CG    0.159    3.601
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 233 OE2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 307 NH2   0.158    2.502
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 OD2   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH    0.158    2.322
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 144 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH1    0.155    3.365
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 290 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 287 O     0.155    3.145
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 376 NE2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 278 CG    0.155    3.365
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 52 CG2    0.153    3.607
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 103 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 41 CB     0.153    3.607
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 314 CD2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 229 CG    0.153    3.607
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 368 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 364 O     0.152    3.148
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 368 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 364 O     0.150    3.150
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 332 OG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 329 O     0.150    2.330
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD2    0.149    3.371
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 315 OE2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 228 NH1   0.149    2.511
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 290 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 287 O     0.149    3.151
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 38 C5'     7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 37 C2'      0.149    3.611
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 CD1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 52 CG2    0.148    3.612
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 328 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 331 CB    0.147    3.153
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 283 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 O     0.147    3.153
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CD   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 94 CG     0.143    3.617
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 314 CD2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CG    0.143    3.617
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 368 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 364 O     0.143    3.157
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 114 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 CA    0.141    3.619
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 392 CD2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 CD2   0.141    3.619
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 44 C5'     7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 43 C2'      0.141    3.619
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 128 O    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CG2   0.140    3.160
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 72 C5'     7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 71 C2'      0.139    3.621
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 139 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1    0.138    3.382
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 144 CD    0.137    3.383
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 131 CG1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 127 O     0.133    3.167
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 139 CB   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1    0.133    3.387
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 157 CG   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 160 OG1   0.133    3.207
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CG1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 O     0.132    3.168
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 151 OH   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 57 CG     0.131    3.209
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 151 OH   7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 57 CG     0.129    3.211
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 172 CG1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 O     0.129    3.171
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 96 CG    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 246 CA    0.128    3.632
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 302 NH2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 14 CB     0.127    3.393
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 C2'     7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 50 C5'      0.127    3.633
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CD1   0.126    3.274
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CG1  7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 168 O     0.125    3.175
    7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 61 C2'     7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 62 C5'      0.125    3.635
[deleted to fit within ticket limits]


> show #!5 models

> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J377_009_volume_map.mrc"

Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.0369, step 4, values float32  

> hide #!4 models

> show #!4 models

> volume #4 step 1

> ui tool show "Hide Dust"

> surface dust #4 size 5.31

> select add #4

2 models selected  

> color #4.1 gray

> transparency #4.1 80

> volume #4 level 0.0199

> volume #4 level 0.02843

> select clear

> select add #5

2 models selected  

> transparency #5.1 50

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 4 models selected  

> select subtract #5

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 17 models selected  

> show sel atoms

> hide sel cartoons

> select clear

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> style sel ball

Changed 44999 atom styles  

> select clear

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> volume #4 level 0.02843

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #4 level 0.02112

> volume #4 level 0.03573

> volume #4 level 0.01869

> volume #4 level 0.02477

> volume #4 level 0.03

> volume #4 level 0.027

> volume #4 level 0.026

> ui tool show "Color Actions"

> set bgColor white

> set bgColor #ffffff00

> select clear

> volume #4 level 0.0265

> volume #4 level 0.027

> ui tool show "Hide Dust"

> surface dust #5 size 6

> surface dust #4 size 5.31

> surface dust #4 size 6

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/4turns
> unsharpned_fit.png" width 3000 height 2729 supersample 3
> transparentBackground true

> hide #!4 models

> show #!4 models

> hide #!4 models

> select add #5

2 models selected  

> transparency #5.1 70

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/1turn
> sharpned_fit.png" width 3000 height 2729 supersample 3 transparentBackground
> true

> hide #!5 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> show sel surfaces

> transparency (#!1 & sel) 90

> transparency (#!1 & sel) 70

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Protein
> _surf_second.png" width 3000 height 2729 supersample 3 transparentBackground
> true

> select clear

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> hide sel surfaces

> select subtract #1

15 models selected  

> select add #1.9

3094 atoms, 398 residues, 1 model selected  

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected  

> select subtract #1.9

41905 atoms, 42762 bonds, 5258 residues, 16 models selected  

> hide sel cartoons

> select clear

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> show sel cartoons

> select clear

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!1 models

> volume #5 level 0.06

> volume #5 level 0.07

> show #!1 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> select add #5

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 19 models selected  

> color zone #5 near sel & #1 distance 5.31

> select clear

> hide #!1 models

> select clear

> volume #5 style mesh

> show #!1 models

> hide #!1 models

> select add #5

2 models selected  

> transparency #5.1 0

> select clear

> select add #5

2 models selected  

> select clear

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!3 models

> select add #3

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!3 to #1

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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain L
(#1) with 7nt5, chain G (#3), sequence alignment score = 1967.3  
RMSD between 359 pruned atom pairs is 0.815 angstroms; (across all 395 pairs:
1.674)  
  

> select clear

> select add #3

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #3/J to #1/K pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 7nt5, chain J (#3), sequence alignment score = 1930.1  
RMSD between 357 pruned atom pairs is 0.744 angstroms; (across all 395 pairs:
1.541)  
  

> show #!1 models

> matchmaker #3/A to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 7nt5, chain A (#3), sequence alignment score = 1937.3  
RMSD between 371 pruned atom pairs is 0.854 angstroms; (across all 394 pairs:
1.236)  
  

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select add #1.14

3094 atoms, 398 residues, 1 model selected  

> hide sel cartoons

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected  

> select subtract #1

15 models selected  

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> select subtract #1.1

41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected  

> hide sel cartoons

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected  

> select add #3

85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 19 models selected  

> select subtract #1

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 17 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #3.2

37226 atoms, 37991 bonds, 2 pseudobonds, 4802 residues, 16 models selected  

> hide sel cartoons

> select add #3

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 15 models selected  

> select subtract #3

14 models selected  

> select add #3.15

1556 atoms, 78 residues, 1 model selected  

> show sel cartoons

Cell requested for row 0 is out of bounds for table with 21 rows! Resizing
table model.  

> select add #3

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 3 models selected  

> select add #1

85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 18 models selected  

> show sel cartoons

> open 7nt6 fromDatabase pdb format mmcif

Summary of feedback from opening 7nt6 fetched from pdb  
---  
note | Fetching compressed mmCIF 7nt6 from http://files.rcsb.org/download/7nt6.cif  
  
7nt6 title:  
CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
[more info...]  
  
Chain information for 7nt6 #7  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N O | Nucleoprotein | NCAP_NIPAV 1-532  
X | RNA (48-MER) |   
Z | RNA (42-MER) |   
  

> select subtract #3

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 31 models selected  

> select subtract #1

15 models selected  

> select add #7

24128 atoms, 24281 bonds, 10 pseudobonds, 5672 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> select clear

> select add #7.2

1320 atoms, 330 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #7/A to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 7nt6, chain A (#7), sequence alignment score = 1846.7  
RMSD between 301 pruned atom pairs is 1.187 angstroms; (across all 330 pairs:
1.360)  
  

> hide #!3 models

> select clear

> ui tool show Matchmaker

> matchmaker #7/O to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 7nt6, chain O (#7), sequence alignment score = 1909.1  
RMSD between 308 pruned atom pairs is 1.139 angstroms; (across all 364 pairs:
1.853)  
  

> matchmaker #7/H to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 7nt6, chain H (#7), sequence alignment score = 1919.9  
RMSD between 343 pruned atom pairs is 1.041 angstroms; (across all 381 pairs:
1.530)  
  

Cell requested for row 0 is out of bounds for table with 25 rows! Resizing
table model.  

> open 6M7D fromDatabase pdb format mmcif

Summary of feedback from opening 6M7D fetched from pdb  
---  
note | Fetching compressed mmCIF 6m7d from http://files.rcsb.org/download/6m7d.cif  
  
6m7d title:  
Structure of ncleoprotein of sendai virus [more info...]  
  
Chain information for 6m7d #8  
---  
Chain | Description | UniProt  
A | Nucleoprotein | NCAP_SENDO 1-524  
B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') |   
  

> hide #!7 models

> hide #!1 models

> open 6C54 fromDatabase pdb format mmcif

Summary of feedback from opening 6C54 fetched from pdb  
---  
note | Fetching compressed mmCIF 6c54 from http://files.rcsb.org/download/6c54.cif  
  
6c54 title:  
Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit [more
info...]  
  
Chain information for 6c54 #9  
---  
Chain | Description | UniProt  
A B | Nucleoprotein | A0A1L7B8E4_9MONO 25-457  
  
6c54 mmCIF Assemblies  
---  
1| representative helical assembly  
2| helical asymmetric unit  
3| helical asymmetric unit, std helical frame  
  

> open 4uft fromDatabase pdb format mmcif

Summary of feedback from opening 4uft fetched from pdb  
---  
note | Fetching compressed mmCIF 4uft from http://files.rcsb.org/download/4uft.cif  
  
4uft title:  
Structure of the helical Measles virus nucleocapsid [more info...]  
  
Chain information for 4uft #10  
---  
Chain | Description | UniProt  
B | NUCLEOPROTEIN | NCAP_MEASH 1-391  
R | 5'-R(*CP*CP*CP*CP*CP*CP)-3' |   
  
4uft mmCIF Assemblies  
---  
1| representative helical assembly  
2| helical asymmetric unit  
3| helical asymmetric unit, std helical frame  
  

> ui tool show Matchmaker

> matchmaker #10/B to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 4uft, chain B (#10), sequence alignment score = 767.3  
RMSD between 260 pruned atom pairs is 1.191 angstroms; (across all 367 pairs:
3.339)  
  

> matchmaker #9/A to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 6c54, chain A (#9), sequence alignment score = 285.6  
RMSD between 64 pruned atom pairs is 1.098 angstroms; (across all 329 pairs:
7.821)  
  

> matchmaker #8/A to #1/D pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain D
(#1) with 6m7d, chain A (#8), sequence alignment score = 667.3  
RMSD between 235 pruned atom pairs is 1.101 angstroms; (across all 366 pairs:
8.432)  
  

> show #!7 models

> hide #!7 models

> show #!1 models

> hide #9 models

> hide #!10 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> show #9 models

> show #!10 models

> hide #8 models

> hide #9 models

> hide #!10 models

> show #9 models

> hide #9 models

> show #!4 models

> volume #4 level 0.03199

> volume #4 level 0.03448

> volume #4 level 0.03822

> volume #4 level 0.038

> volume #4 level 0.04

> volume #4 level 0.042

> volume #4 level 0.044

> hide #!4 models

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein..png"
> width 3000 height 2733 supersample 3 transparentBackground true

> show #!5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/1turn
> sharpned_fit.png" width 3000 height 2733 supersample 3 transparentBackground
> true

> select add #5

2 models selected  

> transparency #5.1 60

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/1turn
> sharpned_fit.png" width 3000 height 2733 supersample 3 transparentBackground
> true

> hide #!5 models

> show #!4 models

> hide #!1 models

> show #!1 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/4turns
> unsharpned_fit.png" width 3000 height 2733 supersample 3
> transparentBackground true

> hide #!4 models

> show #!5 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/1turn
> sharpned_fit.png" width 3000 height 2733 supersample 3 transparentBackground
> true

> hide #!5 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein..png"
> width 3000 height 2733 supersample 3 transparentBackground true

> select clear

> turn x #1 90

Expected a number or a keyword  

> turn x 90

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/protein90.png"
> width 3000 height 2733 supersample 3 transparentBackground true

> show #!5 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/1turn
> sharpned_fit 90.png" width 3000 height 2733 supersample 3
> transparentBackground true

> show #!10 models

> show #9 models

> show #8 models

> show #!7 models

> hide #!5 models

> ui tool show "Change Chain IDs"

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/figure 1
> overall.cxs"

> ui tool show "Change Chain IDs"

> changechains 1.1

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (1.1/3/)  

> changechains 1.1

Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (1.1/3/)  

> select add #1.1

3094 atoms, 398 residues, 1 model selected  

> open "/Users/kompa012/Desktop/NiP N protein article/7nt5_J377_intactmodel-
> coot-0_real_space_refined_030.pdb"

Chain information for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb
#11  
---  
Chain | Description  
D E F G H I J K L M N O P Q | No description available  
Z | No description available  
  

Cell requested for row 0 is out of bounds for table with 25 rows! Resizing
table model.  

> hide #9 models

> hide #!10 models

> hide #8 models

> hide #!7 models

> hide #!1 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected  

> select subtract #1

15 models selected  

> rename #11 "7nt5_J377_intactmodel-coot-Chain D.pdb"

> select add #11

44996 atoms, 45905 bonds, 5656 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select subtract #11.1

41902 atoms, 42758 bonds, 5258 residues, 16 models selected  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

> select add #11.1

3094 atoms, 398 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select clear

> select add #11

3094 atoms, 3147 bonds, 398 residues, 1 model selected  

> select subtract #11

1 model selected  

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NiV Nprote
> monomer.pdb" models #11 relModel #5

> show #!10 models

> show #9 models

> hide #9 models

> show #8 models

> show #!7 models

> hide #!7 models

> hide #!10 models

> hide #!11 models

> hide #8 models

> show #!11 models

> hide #11.1 models

> show #!1 models

> hide #!1 models

> show #!5 models

> ui tool show Matchmaker

> matchmaker #11/D to #1/K pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 7nt5_J377_intactmodel-coot-Chain D.pdb, chain D (#11), sequence
alignment score = 1993.7  
RMSD between 398 pruned atom pairs is 0.213 angstroms; (across all 398 pairs:
0.213)  
  

> select add #5

2 models selected  

> select subtract #5

Nothing selected  

> select add #5

2 models selected  

> select add #11

3094 atoms, 3147 bonds, 398 residues, 3 models selected  

> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J379_map_sharp.mrc"

Opened cryosparc_P78_J379_map_sharp.mrc as #12, grid size 540,540,540, pixel
0.885, shown at level 0.000704, step 4, values float32  

> rename #12 cryosparc_P78_J379_map_sharp_one.mrc

> volume #12 step 1

> hide #!5 models

> select subtract #5

3094 atoms, 3147 bonds, 398 residues, 2 models selected  

> volume #12 level 0.01236

> volume #12 level 0.07

> show #!5 models

> hide #!12 models

> show #!12 models

> hide #!5 models

> volume zone #12 nearAtoms sel & #11 range 5.31

> ui tool show "Surface Zone"

> surface zone #12 nearAtoms #11 distance 5.31

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 1

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 3.5

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 3.3

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 3.2

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 3.1

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 4

> surface zone #12 nearAtoms #11 distance 5

> surface zone #12 nearAtoms #11 distance 6

> surface zone #12 nearAtoms #11 distance 7

> select subtract #11.1

1 model selected  

> select add #11

3094 atoms, 3147 bonds, 398 residues, 1 model selected  

> select subtract #11

1 model selected  

> select add #12

2 models selected  

> volume #12 style mesh

> transparency #12.1 70

> select clear

> surface zone #12 nearAtoms #11 distance 4

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 4

> surface zone #12 nearAtoms #11 distance 5

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.1

> hide #!12 models

> show #!12 models

> hide #!11 models

> show #!1 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> select subtract #1.9

41905 atoms, 42762 bonds, 5258 residues, 16 models selected  

> hide sel cartoons

> show sel cartoons

> select subtract #1.8

38811 atoms, 39615 bonds, 4860 residues, 15 models selected  

> select add #1.9

41905 atoms, 39615 bonds, 5258 residues, 14 models selected  

> hide sel cartoons

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected  

> select subtract #1

15 models selected  

> select add #1.15

1683 atoms, 84 residues, 1 model selected  

> show sel cartoons

> ui mousemode right select

> show sel atoms

> hide sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1683 atom styles  

> select clear

> select #1 /z :3-40

760 atoms, 835 bonds, 38 residues, 1 model selected  

> hide sel atoms

> select #1 /z :51-86

723 atoms, 795 bonds, 36 residues, 1 model selected  

> hide sel atoms

> show #!7 models

> show #!10 models

> show #8 models

> show #9 models

> hide #!7 models

> hide #!10 models

> show #!7 models

> hide #8 models

> hide #9 models

> hide #!12 models

> hide #!1 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 3 models selected  

> show #!1 models

> hide #!7 models

> show #!3 models

> select subtract #1

15 models selected  

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> show sel cartoons

> select subtract #1.14

41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected  

> select add #1.14

44999 atoms, 42762 bonds, 9 pseudobonds, 5656 residues, 16 models selected  

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 17 models selected  

> select subtract #1

15 models selected  

> select add #1.14

3094 atoms, 398 residues, 1 model selected  

> hide sel surfaces

> hide sel atoms

> hide sel cartoons

> ui mousemode right distance

> select add #1.15

4777 atoms, 482 residues, 2 models selected  

> show sel atoms

> select add #3.15

6333 atoms, 560 residues, 4 models selected  

> show sel atoms

> style sel ball

Changed 6333 atom styles  

> distance #3/N:65@N1 #1/Z:65@C5

Distance between 7nt5 #3/N U 65 N1 and 7nt5_J377_intactmodel-
coot-0_real_space_refined_030.pdb #1/Z U 65 C5: 4.363Å  

> ui mousemode right select

> select clear

Drag select of 37 residues  

> show sel atoms

> style sel ball

Changed 276 atom styles  

> select clear

> select add #3

40200 atoms, 41016 bonds, 2 pseudobonds, 5196 residues, 2 models selected  

> select add #1

85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 18 models selected  

> hide sel cartoons

> select clear

> ui mousemode right distance

> distance #1/P:126@CA #3/M:126@CA

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/P
GLU 126 CA and 7nt5 #3/M GLU 126 CA: 5.502Å  

> show #!6 models

Cell requested for row 5 is out of bounds for table with 14 rows! Resizing
table model.  

> hide #!6 models

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> show sel cartoons

> select add #3

85199 atoms, 86925 bonds, 11 pseudobonds, 10852 residues, 19 models selected  

> select add #6

85199 atoms, 86925 bonds, 13 pseudobonds, 10852 residues, 34 models selected  

> select subtract #6

85199 atoms, 86925 bonds, 2 pseudobonds, 10852 residues, 32 models selected  

> show #!6 models

> hide #!6 models

> show sel cartoons

> hide #!3 models

> select subtract #3

44999 atoms, 45909 bonds, 5656 residues, 30 models selected  

> ui mousemode right select

> select clear

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> select subtract #1.7

41905 atoms, 42762 bonds, 9 pseudobonds, 5258 residues, 17 models selected  

> hide sel cartoons

> select add #6

41905 atoms, 42762 bonds, 11 pseudobonds, 5258 residues, 17 models selected  

> select subtract #6

41905 atoms, 42762 bonds, 5258 residues, 15 models selected  

> show #!12 models

> hide #!12 models

> show #!12 models

> select add #1.7

44999 atoms, 42762 bonds, 5656 residues, 15 models selected  

> hide sel cartoons

> show sel cartoons

> select subtract #1.8

41905 atoms, 39615 bonds, 5258 residues, 16 models selected  

> hide sel cartoons

> hide sel atoms

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 16 models selected  

> select subtract #1

15 models selected  

> select add #1

44999 atoms, 45909 bonds, 9 pseudobonds, 5656 residues, 2 models selected  

> select subtract #1

15 models selected  

> select add #1.15

1683 atoms, 84 residues, 1 model selected  

> show sel atoms

> select #1 /z :51-86

723 atoms, 795 bonds, 36 residues, 1 model selected  

> hide sel atoms

> select #1 /z :3-40

760 atoms, 835 bonds, 38 residues, 1 model selected  

> hide sel atoms

> select subtract #1.15

1 model selected  

> select add #1.7

3094 atoms, 398 residues, 1 model selected  

> select subtract #1.7

1 model selected  

> select add #1.8

3094 atoms, 398 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 3094 atom styles  

> select clear

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.5

> surface zone #12 nearAtoms #11 distance 3

> select add #1.7

3094 atoms, 398 residues, 1 model selected  

> select subtract #1.7

1 model selected  

> select add #1.8

3094 atoms, 398 residues, 1 model selected  

> hide sel atoms

> select clear

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.5

Cell requested for row 5 is out of bounds for table with 28 rows! Resizing
table model.  

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!12 models

> surface zone #12 nearAtoms #11 distance 2.5

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 1

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 1

> surface zone #12 nearAtoms #11 distance 1.9

> hide #!12 models

> show #!12 models

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.5

> surface zone #12 nearAtoms #11 distance 4

> surface zone #12 nearAtoms #11 distance 3

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.5

> surface zone #12 nearAtoms #11 distance 2

> surface zone #12 nearAtoms #11 distance 2.5

> surface zone #12 nearAtoms #11 distance 2

> select #1 /k :178, 192,193,196,199,200,258,263, 265, 344, 349,352

104 atoms, 95 bonds, 12 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 104 atom styles  

> select clear

> hide #!12 models

> select #1 /k :178, 192,193,196,199,200,258,263, 265, 344, 349,352

104 atoms, 95 bonds, 12 residues, 1 model selected  

> color (#!1 & sel) byhetero

> select #1 /z :41-50

200 atoms, 219 bonds, 10 residues, 1 model selected  

> color (#!1 & sel) byhetero

> select clear

> ui mousemode right distance

> distance #1/Z:49@N1 #1/K:200@OE1

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 49 N1 and /K GLN 200 OE1: 3.740Å  

> show #!6 models

> distance #1/Z:49@O4' #1/K:196@NZ

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 49 O4' and /K LYS 196 NZ: 2.984Å  

> distance #1/K:199@NE2 #1/Z:50@O2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
GLN 199 NE2 and /Z U 50 O2: 3.210Å  

> distance #1/K:199@OE1 #1/Z:49@N3

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
GLN 199 OE1 and /Z U 49 N3: 3.255Å  

> distance #1/Z:49@OP2 #1/K:258@OH

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 49 OP2 and /K TYR 258 OH: 2.341Å  

> distance #1/K:193@NH2 #1/Z:48@OP2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 193 NH2 and /Z U 48 OP2: 3.185Å  

> distance #1/K:192@NH1 #1/Z:48@OP1

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 192 NH1 and /Z U 48 OP1: 3.556Å  

> distance #1/K:192@NH1 #1/Z:48@OP2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 192 NH1 and /Z U 48 OP2: 2.734Å  

> ~distance #1/K:192@NH1 #1/Z:48@OP1

> distance #1/K:178@NZ #1/Z:47@OP2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
LYS 178 NZ and /Z U 47 OP2: 2.955Å  

> distance #1/K:352@NH1 #1/Z:44@OP2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
ARG 352 NH1 and /Z U 44 OP2: 2.806Å  

> select #1 /k :265

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

> hide sel cartoons

> distance #1/Z:45@OP1 #1/K:265@N

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 45 OP1 and /K ALA 265 N: 3.167Å  

> ui mousemode right select

> select clear

> ui mousemode right distance

> distance #1/Z:45@O4 #1/K:349@ND2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z
U 45 O4 and /K ASN 349 ND2: 3.380Å  

> select #1 /k :263

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

> show sel atoms

> ui mousemode right select

> select clear

> ui mousemode right distance

> distance #1/K:344@OG #1/Z:46@O2

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
SER 344 OG and /Z U 46 O2: 3.110Å  

> hide #6.1 models

> ui tool show "Side View"

> show #!12 models

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/one subunit nad
> rna.png" width 3000 height 3072 supersample 3 transparentBackground true

> show #!10 models

> hide #!10 models

> ui tool show Matchmaker

> matchmaker #10/B to #1/K pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 4uft, chain B (#10), sequence alignment score = 768.7  
RMSD between 261 pruned atom pairs is 1.177 angstroms; (across all 371 pairs:
3.056)  
  

> show #!10 models

> show #9 models

> show #8 models

> show #!7 models

> hide #!7 models

> matchmaker #9/A to #1/K pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6c54, chain A (#9), sequence alignment score = 283.7  
RMSD between 61 pruned atom pairs is 1.090 angstroms; (across all 329 pairs:
8.097)  
  

> matchmaker #8/A to #1/K pairing ss

Parameters  
---  
Chain pairing | ss  
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 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain K
(#1) with 6m7d, chain A (#8), sequence alignment score = 692.5  
RMSD between 242 pruned atom pairs is 1.153 angstroms; (across all 366 pairs:
8.444)  
  

> hide #9 models

> hide #!10 models

> hide #8 models

> select #1 /z :41-50

200 atoms, 219 bonds, 10 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> nucleotides sel tube/slab shape box

> undo

> ui mousemode right select

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/one subunit nad
> rna.png" width 3000 height 3072 supersample 3 transparentBackground true

> hide #!12 models

> select add #1.9

3094 atoms, 398 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1 /z :43-54

240 atoms, 263 bonds, 12 residues, 1 model selected  

> show sel atoms

> select #1 /z :40-43

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

> hide sel atoms

> select #1 /z :44-54

220 atoms, 241 bonds, 11 residues, 1 model selected  

> color (#!1 & sel) byhetero

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> aup.cxs"

> select add #1.6

3094 atoms, 398 residues, 1 model selected  

> select subtract #1.6

1 model selected  

> select add #1.7

3094 atoms, 398 residues, 1 model selected  

> select subtract #1.7

1 model selected  

> select add #1.8

3094 atoms, 398 residues, 1 model selected  

> select add #1

44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 3 models selected  

> select subtract #1

15 models selected  

> select add #1

44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected  

> show sel cartoons

> select clear

> select add #1

44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected  

> show sel surfaces

> transparency (#!1 & sel) 0

> hide sel cartoons

> view sel

> hide #!6 models

> select add #6

44999 atoms, 45909 bonds, 23 pseudobonds, 5656 residues, 18 models selected  

> select subtract #6

44999 atoms, 45909 bonds, 5656 residues, 16 models selected  

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for
> measurement.png" width 3000 height 3072 supersample 3 transparentBackground
> true

> select add #1

44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 9 models selected  

> hide sel atoms

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for
> measurement.png" width 3000 height 3072 supersample 3 transparentBackground
> true

> turn y 90

> turn y -90

> turn x 90

> turn x -180

> turn x 90

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Top view for
> measurement.png" width 3000 height 3072 supersample 3 transparentBackground
> true

> turn x -90

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/side view for
> measurement.png" width 3000 height 3072 supersample 3 transparentBackground
> true

> turn x 90

> hide #!1 models

> show #!1 models

> select add #1

44999 atoms, 45909 bonds, 21 pseudobonds, 5656 residues, 2 models selected  

> hide sel surfaces

> show sel atoms

> select clear

> save "/Users/kompa012/Desktop/NiP N protein article/Figures/measurement
> spiral.cxs"

> ui mousemode right distance

> distance #1/H:380@OD1 #1/N:380@O

Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/H
ASN 380 OD1 and /N ASN 380 O: 64.756Å  

> show #!6 models


===== 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 - 89.3
OpenGL renderer: Apple M2
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: Mac14,7
      Model Number: Z16S0005DLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 10 days, 10 hours, 32 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 272P7VU:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 8 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 8 months ago

Resolution: → duplicate
Status: assigned → closed
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