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Opened 6 days ago
Closed 5 days ago
#20278 closed defect (duplicate)
Crash in QDockWidget::event() in Qt 6.9.2
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.0-x86_64-i386-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070002781e000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070002681b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000700025818000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000700024815000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000700023812000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070002280f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070002180c000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000700020809000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001f806000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001e803000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001d800000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001c7fd000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001b7fa000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000070001a7f7000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00007000197f4000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00007ff85aa52680 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 48)
{"app_name":"ChimeraX","timestamp":"2026-05-06 17:06:27.00 -0400","app_version":"1.11.1","slice_uuid":"5cbc32a0-c22e-3696-af85-4071e4699df0","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.0 (24A335)","roots_installed":0,"name":"ChimeraX","incident_id":"EE61AE45-B8E9-40A4-B847-532E0332FCD7"}
{
"uptime" : 510000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 28158,
"osVersion" : {
"train" : "macOS 15.0",
"build" : "24A335",
"releaseType" : "User"
},
"captureTime" : "2026-05-06 17:06:23.6931 -0400",
"codeSigningMonitor" : 0,
"incident" : "EE61AE45-B8E9-40A4-B847-532E0332FCD7",
"pid" : 46400,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-05-04 15:15:45.5887 -0400",
"procStartAbsTime" : 338655643194828,
"procExitAbsTime" : 518087454037856,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8A6AA598-6AAA-5F3D-859B-9DD4909E9083","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B6C49923-DB55-FA95-3A93-BDC7AF179334",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "449E809F-BB49-4876-A6A4-06B37DA50B83",
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4382351352
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 105356000-105358000 [ 8K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":46400},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
",
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4382351352
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 105356000-105358000 [ 8K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[0,72,133,192,117,218,232,197,143,63,0,235,37,77,133,228,116,32,76,137,231,232,6,129,1,0,76,139,0,72,137,199,68,137,254,49,210,76,137,225,65,255,144,224,0,0,0,65,137,198,68,137,51,72,131,196,8,91,65,92,65,93,65,94,65,95,93,195,102,102,102,46,15,31,132,0,0,0,0,0,85,72,137,229,83,80,72,137,248,72,141,29,24,58,75,0,72,139,64,8,72,139,112,16,246,128,140,0,0,0,1,117,25,72,133,246,116,18,72,137,223,232,156,31,64,0,72,133,192,117,221,232,168,143,63,0,49,246,72,137,240,72,131,196,8,91,93,195,102,102,102,46,15,31,132,0,0,0,0,0,85,72,137,229,65,86,83,72,137,243,72,139,5,223,251,78,0,72,133,192,116,13,72,137,222,255,208,73,137,198,72,133],"offset":96}},"frames":[
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{"imageOffset":24453,"symbol": "pthread_kill" ,"symbolLocation":262,"imageIndex":129},
{"imageOffset":284828,"symbol": "raise" ,"symbolLocation":24,"imageIndex":130},
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{"imageOffset":0,"imageIndex":132},
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{"imageOffset":1580817,"symbol": "QDockWidget::event(QEvent*)" ,"symbolLocation":369,"imageIndex":49},
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{"imageOffset":987725,"symbol": "QWindowPrivate::emitScreenChangedRecursion(QScreen*)" ,"symbolLocation":77,"imageIndex":50},
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{"imageOffset":312430,"symbol": "QWidget::create(unsigned long long, bool, bool)" ,"symbolLocation":382,"imageIndex":49},
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{"imageOffset":993267,"symbol": "QWindowPrivate::create(bool)" ,"symbolLocation":1043,"imageIndex":50},
{"imageOffset":982310,"symbol": "QWindow::setParent(QWindow*)" ,"symbolLocation":566,"imageIndex":50},
{"imageOffset":531923,"symbol": "QWindowContainer::parentWasChanged(QWidget*)" ,"symbolLocation":323,"imageIndex":49},
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{"imageOffset":532035,"symbol": "QWindowContainer::parentWasChanged(QWidget*)" ,"symbolLocation":435,"imageIndex":49},
{"imageOffset":315618,"symbol": "QWidget::setParent(QWidget*, QFlags)" ,"symbolLocation":2322,"imageIndex":49},
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/michael/Documents/Protein Structures PDB/9GJT NiV L Apo.pdb"
> "/Users/michael/Documents/Protein Structures PDB/9GJU NiV L RNA Bound.pdb"
9GJT NiV L Apo.pdb title:
Structure of nipah virus RNA polymerase complex - apo state [more info...]
Chain information for 9GJT NiV L Apo.pdb #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | L_NIPAV 2-2244
B C D E | protein P | PHOSP_NIPAV 1-709
Non-standard residues in 9GJT NiV L Apo.pdb #1
---
ZN — zinc ion
9GJU NiV L RNA Bound.pdb title:
Structure of replicating nipah virus RNA polymerase complex - RNA- bound state
[more info...]
Chain information for 9GJU NiV L RNA Bound.pdb #2
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | L_NIPAV 2-2244
B C D E | protein P | PHOSP_NIPAV 1-709
F | RNA (5'-R(P*ap*CP*CP*ap*ap*ap*CP*ap*A)-3') |
G | RNA (5'-R(P*CP*CP*CP*up*up*GP*up*up*up*GP*GP*U)-3') |
Non-standard residues in 9GJU NiV L RNA Bound.pdb #2
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
ZN — zinc ion
> ui mousemode right select
Drag select of 29843 atoms, 37 pseudobonds, 249 bonds
Drag select of 34952 atoms, 40 pseudobonds, 249 bonds
> style sel stick
Changed 34952 atom styles
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> select #2/A:2167
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 11592 atoms, 2374 residues, 24 pseudobonds, 9773 bonds
> hide sel atoms
Drag select of 2392 atoms, 659 residues, 2002 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 1624 atoms, 474 residues, 1361 bonds, 1 pseudobonds
Drag select of 1193 atoms, 427 residues, 3 pseudobonds, 1014 bonds
> hide sel atoms
Drag select of 882 atoms, 349 residues, 737 bonds
> ui mousemode right translate
> ui mousemode right select
> hide sel atoms
Drag select of 674 atoms, 1315 residues, 12 pseudobonds, 542 bonds
> hide sel atoms
Drag select of 289 atoms, 80 residues, 249 bonds
Drag select of 968 atoms, 419 residues, 4 pseudobonds, 830 bonds
> hide sel atoms
Drag select of 337 atoms, 159 residues, 286 bonds, 1 pseudobonds
> hide sel atoms
Drag select of 621 atoms, 580 residues, 524 bonds
Drag select of 481 atoms, 512 residues, 405 bonds
Drag select of 349 atoms, 420 residues, 300 bonds
> hide sel atoms
Drag select of 10 residues, 3 atoms
Drag select of 444 atoms, 441 residues, 365 bonds, 1 pseudobonds
> hide sel atoms
> select #2/G:9
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/G:10
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 14 residues, 8 bonds, 8 atoms
> hide #!2 models
Drag select of 544 atoms, 1707 residues, 8 pseudobonds, 445 bonds
> hide sel atoms
> select clear
> show #!2 models
> hide #!1 models
> ui mousemode right translate
> show #!1 models
> ui mousemode right select
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> sequence chain #1/B #1/C #1/D #1/E #2/B #2/C #2/D #2/E
Alignment identifier is 2
> sequence chain #2/F
Alignment identifier is 2/F
> sequence chain #2/G
Alignment identifier is 2/G
> select clear
> select #1/B-E #2/B-E
8209 atoms, 8327 bonds, 4 pseudobonds, 1028 residues, 4 models selected
Protein P [ID: 2] region 8 chains [1-709] RMSD: 6.897
> hide sel atoms
> color (#!1-2 & sel) gray
> color (#!1-2 & sel) light gray
> color (#!1-2 & sel) dim gray
> color (#!1-2 & sel) light gray
> select clear
> select #1/A:5-934 #2/A:6-934
13156 atoms, 13446 bonds, 3 pseudobonds, 1620 residues, 4 models selected
RNA-directed RNA Polymerase L [ID: 1] region 2 chains [1-936] RMSD: 7.443
> select clear
> select #1/A:5-983 #2/A:6-983
13906 atoms, 14202 bonds, 3 pseudobonds, 1718 residues, 4 models selected
RNA-directed RNA Polymerase L [ID: 1] region 2 chains [1-985] RMSD: 7.371
> color (#!1-2 & sel) cornflower blue
> select #1/A:984 #2/A:984
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:984-1451 #2/A:984-1452
6505 atoms, 6628 bonds, 7 pseudobonds, 814 residues, 4 models selected
RNA-directed RNA Polymerase L [ID: 1] region 2 chains [986-1454] RMSD: 8.314
> color (#!1-2 & sel) forest green
> color (#!1-2 & sel) lime
> color (#!1-2 & sel) forest green
> select #2/A:1453
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1453-1463
91 atoms, 94 bonds, 11 residues, 1 model selected
> color sel gray
> select clear
> select #2/A:1477-1743
2198 atoms, 2249 bonds, 267 residues, 1 model selected
> color sel yellow
> select clear
> select #2/A:1769-2098
2468 atoms, 2518 bonds, 2 pseudobonds, 312 residues, 2 models selected
> color (#!2 & sel) orange
> select #2/A:2099-2100
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:2099-2244
1097 atoms, 1113 bonds, 1 pseudobond, 131 residues, 2 models selected
> color (#!2 & sel) red
> select clear
> select #2/A:2098
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:2097
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 18 residues
> select #2/A:2098
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel red
> select #2/A:2097
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> hide #!2 models
> save "/Users/michael/Documents/Protein Structures PDB/[Name].pdb"
> save "/Users/michael/Documents/Protein Structures PDB/[Name] with colored
> domains.pdb"
> save "/Users/michael/Documents/Protein Structures PDB/[NAME].pdb"
> show #!2 models
Drag select of 126 residues, 1 pseudobonds
> select clear
> ui mousemode right translate
> hide #!2 models
> hide #!1 models
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses
> MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309 and
> 88310 Docking/88310 25poses MeV L Apo 909_942_1106_1110.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Chain information for 88309 25poses MeV L Apo 909_942_1106_1110.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses MeV L Apo 909_942_1106_1110.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> style #!3-4 stick
Changed 52946 atom styles
> show #!3-4 cartoons
Computing secondary structure
> hide #!3-4 atoms
> show #!3-4 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #4/A
Alignment identifier is 3
> sequence chain #3/B #4/B
Alignment identifier is 4
> sequence chain #3/C #4/C
Alignment identifier is 5
> sequence chain #3/D #4/D
Alignment identifier is 6
> sequence chain #3/E #4/E
Alignment identifier is 7
> select #3/B:325-326 #4/B:325-326
76 atoms, 76 bonds, 4 residues, 2 models selected
> select #3/B #4/B
2394 atoms, 2402 bonds, 2 pseudobonds, 148 residues, 4 models selected
4 [ID: 4] region 2 chains [1-74] RMSD: 0.000
> select clear
> select #3/C:429-507 #4/C:429-507
2610 atoms, 2624 bonds, 158 residues, 2 models selected
5 [ID: 5] region 2 chains [1-132] RMSD: 0.000
> hide sel atoms
> select #3/E:324 #4/E:324
48 atoms, 46 bonds, 2 residues, 2 models selected
> select #3/E #4/E
2358 atoms, 2370 bonds, 148 residues, 2 models selected
7 [ID: 7] region 2 chains [1-74] RMSD: 0.000
> hide sel atoms
> select #3/B:325-326 #4/B:325-326
76 atoms, 76 bonds, 4 residues, 2 models selected
> select #3/B #4/B
2394 atoms, 2402 bonds, 2 pseudobonds, 148 residues, 4 models selected
4 [ID: 4] region 2 chains [1-74] RMSD: 0.000
> hide sel atoms
> select #3/D:324-325 #4/D:324-325
86 atoms, 84 bonds, 4 residues, 2 models selected
> select #3/D #4/D
1850 atoms, 1854 bonds, 114 residues, 2 models selected
6 [ID: 6] region 2 chains [1-57] RMSD: 0.000
> hide sel atoms
> select clear
> select #3/C:429-507 #4/C:429-507
2610 atoms, 2624 bonds, 158 residues, 2 models selected
5 [ID: 5] region 2 chains [1-132] RMSD: 0.000
> select #3/C:507 #4/C:507
46 atoms, 44 bonds, 2 residues, 2 models selected
> select #3/C:507 #4/C:507
46 atoms, 44 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [132] RMSD: 0.000
> select #3/C:455-507 #4/C:455-507
1770 atoms, 1776 bonds, 106 residues, 2 models selected
> select #3/C:455-507 #4/C:455-507
1770 atoms, 1776 bonds, 106 residues, 2 models selected
5 [ID: 5] region 2 chains [80-132] RMSD: 0.000
> select #3/C:507 #4/C:507
46 atoms, 44 bonds, 2 residues, 2 models selected
> select #3/C:507 #4/C:507
46 atoms, 44 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [132] RMSD: 0.000
> select #3/A:7 #4/A:7
32 atoms, 30 bonds, 2 residues, 2 models selected
> select #3/A #4/A
40348 atoms, 40796 bonds, 12 pseudobonds, 2506 residues, 4 models selected
3 [ID: 3] region 2 chains [1-1253] RMSD: 0.000
> hide sel atoms
> select clear
> select #3/C:429-507 #4/C:429-507
2610 atoms, 2624 bonds, 158 residues, 2 models selected
5 [ID: 5] region 2 chains [1-132] RMSD: 0.000
> hide sel atoms
> ui mousemode right select
> select #3/C:357
14 atoms, 13 bonds, 1 residue, 1 model selected
Drag select of 1196 atoms, 1238 residues, 1100 bonds
> hide sel atoms
> select clear
> ui mousemode right translate
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses
> pose 1 MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE
> Files/88309 and 88310 Docking/88309 25poses pose 5 MeV L Apo
> 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309 and 88310
> Docking/88309 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 15 MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309
> and 88310 Docking/88309 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 25 MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309
> and 88310 Docking/88310 25poses pose 1 MeV L Apo 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 5 MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309
> and 88310 Docking/88310 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 15 MeV L Apo 909_942_1106_1110.pdb" "/Users/michael/Desktop/MOE Files/88309
> and 88310 Docking/88310 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 25 MeV L Apo 909_942_1106_1110.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 1 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 5 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 15 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 25 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 1 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 5 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 15 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 25 MeV L Apo 909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 130
HELIX 1 1 THR A 22 TYR A 31 1 Generated by MOE 10
Ignored bad PDB record found on line 131
HELIX 2 2 THR A 44 ASN A 55 1 Generated by MOE 12
Ignored bad PDB record found on line 132
HELIX 3 3 GLN A 60 LEU A 76 1 Generated by MOE 17
Ignored bad PDB record found on line 133
HELIX 4 4 ASN A 91 LEU A 94 1 Generated by MOE 4
Ignored bad PDB record found on line 134
HELIX 5 5 ARG A 104 ARG A 134 1 Generated by MOE 31
96 messages similar to the above omitted
Chain information for 88309 25poses pose 1 MeV L Apo 909_942_1106_1110.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88309 25poses pose 5 MeV L Apo 909_942_1106_1110.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88309 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88309 25poses pose 15 MeV L Apo 909_942_1106_1110.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88309 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88309 25poses pose 25 MeV L Apo 909_942_1106_1110.pdb
#10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 1 MeV L Apo 909_942_1106_1110.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 5 MeV L Apo 909_942_1106_1110.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 10 MeV L Apo 909_942_1106_1110.pdb
#13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 15 MeV L Apo 909_942_1106_1110.pdb
#14
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 20 MeV L Apo 909_942_1106_1110.pdb
#15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for 88310 25poses pose 25 MeV L Apo 909_942_1106_1110.pdb
#16
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!4 models
> hide #!3 models
> view clip false
> style #!5-16 stick
Changed 308172 atom styles
> show #!5-16 cartoons
Computing secondary structure
> show #!5-16 cartoons
> ui mousemode right select
Drag select of 130788 atoms, 12084 residues, 36 pseudobonds, 121704 bonds
> hide sel atoms
Drag select of 696 atoms, 1032 residues, 648 bonds
> hide sel atoms
Drag select of 36320 atoms, 5400 residues, 33541 bonds
> hide sel atoms
Drag select of 18816 atoms, 2532 residues, 24 pseudobonds, 17466 bonds
> hide sel atoms
Drag select of 8811 atoms, 2808 residues, 12 pseudobonds, 8038 bonds
> select clear
Drag select of 7620 atoms, 2700 residues, 7044 bonds
> hide sel atoms
Drag select of 2772 atoms, 2604 residues, 2544 bonds
> hide sel atoms
> select clear
> color #5 #0433ffff
> color #6 #00fa92ff
> color #7 #ff2600ff
> color #5 #ff2600ff
> color #6 #ff9300ff
> color #7 #fffb00ff
> color #8 #8efa00ff
> color #9 #00f900ff
> color #10 #00fa92ff
> color #11 #00fdffff
> color #12 #0096ffff
> color #13 #0433ffff
> color #14 #9437ffff
> color #15 #ff40ffff
> color #16 #ff2f92ff
> view clip false
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A #13/A
> #14/A #15/A #16/A
Alignment identifier is 8
> sequence chain #3/B #4/B #5/B #6/B #7/B #8/B #9/B #10/B #11/B #12/B #13/B
> #14/B #15/B #16/B
Alignment identifier is 9
> sequence chain #3/C #4/C #5/C #6/C #7/C #8/C #9/C #10/C #11/C #12/C #13/C
> #14/C #15/C #16/C
Alignment identifier is 10
> sequence chain #3/D #4/D #5/D #6/D #7/D #8/D #9/D #10/D #11/D #12/D #13/D
> #14/D #15/D #16/D
Alignment identifier is 11
> sequence chain #3/E #4/E #5/E #6/E #7/E #8/E #9/E #10/E #11/E #12/E #13/E
> #14/E #15/E #16/E
Alignment identifier is 12
> select #3/B:325 #4/B:325 #5/B:325 #6/B:325 #7/B:325 #8/B:325 #9/B:325
> #10/B:325 #11/B:325 #12/B:325 #13/B:325 #14/B:325 #15/B:325 #16/B:325
294 atoms, 280 bonds, 14 residues, 14 models selected
> select #3/B #4/B #5/B #6/B #7/B #8/B #9/B #10/B #11/B #12/B #13/B #14/B
> #15/B #16/B
16758 atoms, 16814 bonds, 14 pseudobonds, 1036 residues, 28 models selected
9 [ID: 9] region 14 chains [1-74] RMSD: 0.000
> hide sel & #!5-16 atoms
> select clear
> select #3/C:429-507 #4/C:429-507 #5/C:429-507 #6/C:429-507 #7/C:429-507
> #8/C:429-507 #9/C:429-507 #10/C:429-507 #11/C:429-507 #12/C:429-507
> #13/C:429-507 #14/C:429-507 #15/C:429-507 #16/C:429-507
18270 atoms, 18368 bonds, 1106 residues, 14 models selected
10 [ID: 10] region 14 chains [1-132] RMSD: 0.000
> hide sel & #!5-16 atoms
> select #3/D:324-325 #4/D:324-325 #5/D:324-325 #6/D:324-325 #7/D:324-325
> #8/D:324-325 #9/D:324-325 #10/D:324-325 #11/D:324-325 #12/D:324-325
> #13/D:324-325 #14/D:324-325 #15/D:324-325 #16/D:324-325
602 atoms, 588 bonds, 28 residues, 14 models selected
> select #3/D #4/D #5/D #6/D #7/D #8/D #9/D #10/D #11/D #12/D #13/D #14/D
> #15/D #16/D
12950 atoms, 12978 bonds, 798 residues, 14 models selected
11 [ID: 11] region 14 chains [1-57] RMSD: 0.000
> hide sel & #!5-16 atoms
> select #3/E:324-341 #4/E:324-341 #5/E:324-341 #6/E:324-341 #7/E:324-341
> #8/E:324-341 #9/E:324-341 #10/E:324-341 #11/E:324-341 #12/E:324-341
> #13/E:324-341 #14/E:324-341 #15/E:324-341 #16/E:324-341
4382 atoms, 4382 bonds, 252 residues, 14 models selected
> select #3/E #4/E #5/E #6/E #7/E #8/E #9/E #10/E #11/E #12/E #13/E #14/E
> #15/E #16/E
16506 atoms, 16590 bonds, 1036 residues, 14 models selected
12 [ID: 12] region 14 chains [1-74] RMSD: 0.000
> hide sel & #!5-16 atoms
> select #3/A:7 #4/A:7 #5/A:7 #6/A:7 #7/A:7 #8/A:7 #9/A:7 #10/A:7 #11/A:7
> #12/A:7 #13/A:7 #14/A:7 #15/A:7 #16/A:7
224 atoms, 210 bonds, 14 residues, 14 models selected
> select #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A #13/A #14/A
> #15/A #16/A
282436 atoms, 285572 bonds, 84 pseudobonds, 17542 residues, 28 models selected
8 [ID: 8] region 14 chains [1-1253] RMSD: 0.000
> hide sel & #!5-16 atoms
> ui mousemode right select
> select clear
> ui mousemode right translate
> select #3/A:991 #4/A:991 #5/A:991 #6/A:991 #7/A:991 #8/A:991 #9/A:991
> #10/A:991 #11/A:991 #12/A:991 #13/A:991 #14/A:991 #15/A:991 #16/A:991
280 atoms, 280 bonds, 14 residues, 14 models selected
> select #3/A:991 #4/A:991 #5/A:991 #6/A:991 #7/A:991 #8/A:991 #9/A:991
> #10/A:991 #11/A:991 #12/A:991 #13/A:991 #14/A:991 #15/A:991 #16/A:991
280 atoms, 280 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [903] RMSD: 0.000
> show sel & #!5-16 atoms
> select #3/A:1024 #4/A:1024 #5/A:1024 #6/A:1024 #7/A:1024 #8/A:1024 #9/A:1024
> #10/A:1024 #11/A:1024 #12/A:1024 #13/A:1024 #14/A:1024 #15/A:1024 #16/A:1024
238 atoms, 238 bonds, 14 residues, 14 models selected
> select #3/A:1024 #4/A:1024 #5/A:1024 #6/A:1024 #7/A:1024 #8/A:1024 #9/A:1024
> #10/A:1024 #11/A:1024 #12/A:1024 #13/A:1024 #14/A:1024 #15/A:1024 #16/A:1024
238 atoms, 238 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [936] RMSD: 0.000
> show sel & #!5-16 atoms
> select
> #3/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #4/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #5/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #6/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #7/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #8/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #9/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #10/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #11/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #12/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #13/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #14/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #15/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
> #16/A:22-31,44-55,60-76,91-94,104-134,144-150,152-157,162-182,225-247,249-272,274-294,303-318,324-338,347-352,363-374,382-403,419-427,433-438,477-479,482-484,498-504,510-518,551-571,667-670,673-687,695-702,722-724,744-762,789-814,847-851,864-881,885-905,914-922,924-932,935-937,956-969,976-983,991-996,1009-1023,1038-1050,1057-1066,1068-1078,1082-1092,1097-1103,1106-1119,1133-1144,1146-1149,1162-1165,1177-1182,1233-1248,1253-1265,1271-1277,1303-1306,1330-1347
147770 atoms, 148330 bonds, 8932 residues, 14 models selected
> select #3/A:7 #4/A:7 #5/A:7 #6/A:7 #7/A:7 #8/A:7 #9/A:7 #10/A:7 #11/A:7
> #12/A:7 #13/A:7 #14/A:7 #15/A:7 #16/A:7
224 atoms, 210 bonds, 14 residues, 14 models selected
> select #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A #13/A #14/A
> #15/A #16/A
282436 atoms, 285572 bonds, 84 pseudobonds, 17542 residues, 28 models selected
8 [ID: 8] region 14 chains [1-1253] RMSD: 0.000
> hide sel & #!5-16 atoms
> ui mousemode right select
> select clear
> ui mousemode right translate
> select #3/A:7 #4/A:7 #5/A:7 #6/A:7 #7/A:7 #8/A:7 #9/A:7 #10/A:7 #11/A:7
> #12/A:7 #13/A:7 #14/A:7 #15/A:7 #16/A:7
224 atoms, 210 bonds, 14 residues, 14 models selected
> select #3/A:7 #4/A:7 #5/A:7 #6/A:7 #7/A:7 #8/A:7 #9/A:7 #10/A:7 #11/A:7
> #12/A:7 #13/A:7 #14/A:7 #15/A:7 #16/A:7
224 atoms, 210 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [1] RMSD: 0.000
> select #3/A:909 #4/A:909 #5/A:909 #6/A:909 #7/A:909 #8/A:909 #9/A:909
> #10/A:909 #11/A:909 #12/A:909 #13/A:909 #14/A:909 #15/A:909 #16/A:909
196 atoms, 182 bonds, 14 residues, 14 models selected
> select #3/A:909 #4/A:909 #5/A:909 #6/A:909 #7/A:909 #8/A:909 #9/A:909
> #10/A:909 #11/A:909 #12/A:909 #13/A:909 #14/A:909 #15/A:909 #16/A:909
196 atoms, 182 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [821] RMSD: 0.000
> show sel & #!5-16 atoms
> select #3/A:942-943 #4/A:942-943 #5/A:942-943 #6/A:942-943 #7/A:942-943
> #8/A:942-943 #9/A:942-943 #10/A:942-943 #11/A:942-943 #12/A:942-943
> #13/A:942-943 #14/A:942-943 #15/A:942-943 #16/A:942-943
560 atoms, 560 bonds, 28 residues, 14 models selected
> select #3/A:942 #4/A:942 #5/A:942 #6/A:942 #7/A:942 #8/A:942 #9/A:942
> #10/A:942 #11/A:942 #12/A:942 #13/A:942 #14/A:942 #15/A:942 #16/A:942
294 atoms, 294 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [854] RMSD: 0.000
> select #3/A:942 #4/A:942 #5/A:942 #6/A:942 #7/A:942 #8/A:942 #9/A:942
> #10/A:942 #11/A:942 #12/A:942 #13/A:942 #14/A:942 #15/A:942 #16/A:942
294 atoms, 294 bonds, 14 residues, 14 models selected
> select #3/A:942 #4/A:942 #5/A:942 #6/A:942 #7/A:942 #8/A:942 #9/A:942
> #10/A:942 #11/A:942 #12/A:942 #13/A:942 #14/A:942 #15/A:942 #16/A:942
294 atoms, 294 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [854] RMSD: 0.000
> show sel & #!5-16 atoms
> select #3/A:1106 #4/A:1106 #5/A:1106 #6/A:1106 #7/A:1106 #8/A:1106 #9/A:1106
> #10/A:1106 #11/A:1106 #12/A:1106 #13/A:1106 #14/A:1106 #15/A:1106 #16/A:1106
294 atoms, 294 bonds, 14 residues, 14 models selected
> select #3/A:1106 #4/A:1106 #5/A:1106 #6/A:1106 #7/A:1106 #8/A:1106 #9/A:1106
> #10/A:1106 #11/A:1106 #12/A:1106 #13/A:1106 #14/A:1106 #15/A:1106 #16/A:1106
294 atoms, 294 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [1018] RMSD: 0.000
> show sel & #!5-16 atoms
> select #3/A:1110 #4/A:1110 #5/A:1110 #6/A:1110 #7/A:1110 #8/A:1110 #9/A:1110
> #10/A:1110 #11/A:1110 #12/A:1110 #13/A:1110 #14/A:1110 #15/A:1110 #16/A:1110
238 atoms, 224 bonds, 14 residues, 14 models selected
> select #3/A:1110 #4/A:1110 #5/A:1110 #6/A:1110 #7/A:1110 #8/A:1110 #9/A:1110
> #10/A:1110 #11/A:1110 #12/A:1110 #13/A:1110 #14/A:1110 #15/A:1110 #16/A:1110
238 atoms, 224 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [1022] RMSD: 0.000
> show sel & #!5-16 atoms
> color (#!5-16 & sel) light gray
> select #3/A:1106 #4/A:1106 #5/A:1106 #6/A:1106 #7/A:1106 #8/A:1106 #9/A:1106
> #10/A:1106 #11/A:1106 #12/A:1106 #13/A:1106 #14/A:1106 #15/A:1106 #16/A:1106
294 atoms, 294 bonds, 14 residues, 14 models selected
> select #3/A:1106 #4/A:1106 #5/A:1106 #6/A:1106 #7/A:1106 #8/A:1106 #9/A:1106
> #10/A:1106 #11/A:1106 #12/A:1106 #13/A:1106 #14/A:1106 #15/A:1106 #16/A:1106
294 atoms, 294 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [1018] RMSD: 0.000
> color (#!5-16 & sel) light gray
> select #3/A:942 #4/A:942 #5/A:942 #6/A:942 #7/A:942 #8/A:942 #9/A:942
> #10/A:942 #11/A:942 #12/A:942 #13/A:942 #14/A:942 #15/A:942 #16/A:942
294 atoms, 294 bonds, 14 residues, 14 models selected
> select #3/A:942 #4/A:942 #5/A:942 #6/A:942 #7/A:942 #8/A:942 #9/A:942
> #10/A:942 #11/A:942 #12/A:942 #13/A:942 #14/A:942 #15/A:942 #16/A:942
294 atoms, 294 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [854] RMSD: 0.000
> color (#!5-16 & sel) light gray
> select #3/A:909 #4/A:909 #5/A:909 #6/A:909 #7/A:909 #8/A:909 #9/A:909
> #10/A:909 #11/A:909 #12/A:909 #13/A:909 #14/A:909 #15/A:909 #16/A:909
196 atoms, 182 bonds, 14 residues, 14 models selected
> select #3/A:909 #4/A:909 #5/A:909 #6/A:909 #7/A:909 #8/A:909 #9/A:909
> #10/A:909 #11/A:909 #12/A:909 #13/A:909 #14/A:909 #15/A:909 #16/A:909
196 atoms, 182 bonds, 14 residues, 14 models selected
8 [ID: 8] region 14 chains [821] RMSD: 0.000
> color (#!5-16 & sel) light gray
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right clip
> ui mousemode right translate
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> save /Users/michael/Desktop/image1.png supersample 3
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!16 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> save /Users/michael/Desktop/image2.png supersample 3
> set bgColor white
> save /Users/michael/Desktop/image3.png supersample 3
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> save /Users/michael/Desktop/image4.png supersample 3
> ui mousemode right select
> select #5/A:942
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:1110
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5/A:1106@HE1
1 atom, 1 residue, 1 model selected
> select #5/A:909
14 atoms, 13 bonds, 1 residue, 1 model selected
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses
> pose 1 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 5 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 10 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 15 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 20 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88309 25poses pose
> 25 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 1 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 5 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 10 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 15 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 20 MeV L Elongation Homology 909_942_1106_1110.pdb"
> "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/88310 25poses pose
> 25 MeV L Elongation Homology 909_942_1106_1110.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 1 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 5 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 10 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 15 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 20 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88309 25poses pose 25 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 1 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 5 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 10 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 15 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 20 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/88310 25poses pose 25 MeV L Elongation Homology
909_942_1106_1110.pdb
---
warnings | Ignored bad PDB record found on line 173
HELIX 1 1 THR F 22 ALA F 32 1 Generated by MOE 11
Ignored bad PDB record found on line 174
HELIX 2 2 PRO F 43 LYS F 54 1 Generated by MOE 12
Ignored bad PDB record found on line 175
HELIX 3 3 GLN F 60 LYS F 75 1 Generated by MOE 16
Ignored bad PDB record found on line 176
HELIX 4 4 TYR F 79 ALA F 81 5 Generated by MOE 3
Ignored bad PDB record found on line 177
HELIX 5 5 TYR F 87 LEU F 94 1 Generated by MOE 8
143 messages similar to the above omitted
Chain information for 88309 25poses pose 1 MeV L Elongation Homology
909_942_1106_1110.pdb #17
---
Chain | Description
F | No description available
Chain information for 88309 25poses pose 5 MeV L Elongation Homology
909_942_1106_1110.pdb #18
---
Chain | Description
F | No description available
Chain information for 88309 25poses pose 10 MeV L Elongation Homology
909_942_1106_1110.pdb #19
---
Chain | Description
F | No description available
Chain information for 88309 25poses pose 15 MeV L Elongation Homology
909_942_1106_1110.pdb #20
---
Chain | Description
F | No description available
Chain information for 88309 25poses pose 20 MeV L Elongation Homology
909_942_1106_1110.pdb #21
---
Chain | Description
F | No description available
Chain information for 88309 25poses pose 25 MeV L Elongation Homology
909_942_1106_1110.pdb #22
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 1 MeV L Elongation Homology
909_942_1106_1110.pdb #23
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 5 MeV L Elongation Homology
909_942_1106_1110.pdb #24
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 10 MeV L Elongation Homology
909_942_1106_1110.pdb #25
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 15 MeV L Elongation Homology
909_942_1106_1110.pdb #26
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 20 MeV L Elongation Homology
909_942_1106_1110.pdb #27
---
Chain | Description
F | No description available
Chain information for 88310 25poses pose 25 MeV L Elongation Homology
909_942_1106_1110.pdb #28
---
Chain | Description
F | No description available
Computing secondary structure
> ui tool show "Similar Structures"
> align
Missing or invalid "atoms" argument: empty atom specifier
> select add #5
25679 atoms, 25926 bonds, 8 pseudobonds, 1591 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> color #17 #941100ff
> color #18 #945200ff
> color #19 #929000ff
> color #20 #4f8f00ff
> color #21 #008f00ff
> color #22 #009051ff
> color #23 #009193ff
> color #24 #005493ff
> color #25 #011993ff
> color #26 #531b93ff
> color #27 #942193ff
> color #28 #941751ff
> ui mousemode right translate
> hide #17 models
> show #17 models
> ui tool show "Show Sequence Viewer"
> sequence chain #17/F #18/F #19/F #20/F #21/F #22/F #23/F #24/F #25/F #26/F
> #27/F #28/F
Alignment identifier is 13
> select #17/F:909-910 #18/F:909-910 #19/F:909-910 #20/F:909-910 #21/F:909-910
> #22/F:909-910 #23/F:909-910 #24/F:909-910 #25/F:909-910 #26/F:909-910
> #27/F:909-910 #28/F:909-910
300 atoms, 288 bonds, 24 residues, 12 models selected
> select #17/F:909-910 #18/F:909-910 #19/F:909-910 #20/F:909-910 #21/F:909-910
> #22/F:909-910 #23/F:909-910 #24/F:909-910 #25/F:909-910 #26/F:909-910
> #27/F:909-910 #28/F:909-910
300 atoms, 288 bonds, 24 residues, 12 models selected
13 [ID: 13] region 12 chains [905-906] RMSD: 0.000
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [905] RMSD: 0.000
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [905] RMSD: 0.000
> show sel atoms
> color sel light gray
> select #17/F:942-943 #18/F:942-943 #19/F:942-943 #20/F:942-943 #21/F:942-943
> #22/F:942-943 #23/F:942-943 #24/F:942-943 #25/F:942-943 #26/F:942-943
> #27/F:942-943 #28/F:942-943
480 atoms, 480 bonds, 24 residues, 12 models selected
> select #17/F:942-943 #18/F:942-943 #19/F:942-943 #20/F:942-943 #21/F:942-943
> #22/F:942-943 #23/F:942-943 #24/F:942-943 #25/F:942-943 #26/F:942-943
> #27/F:942-943 #28/F:942-943
480 atoms, 480 bonds, 24 residues, 12 models selected
13 [ID: 13] region 12 chains [938-939] RMSD: 0.000
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [938] RMSD: 0.000
> show sel atoms
> color sel light gray
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1102] RMSD: 0.000
> show sel atoms
> color sel light gray
> select #17/F:1110-1111 #18/F:1110-1111 #19/F:1110-1111 #20/F:1110-1111
> #21/F:1110-1111 #22/F:1110-1111 #23/F:1110-1111 #24/F:1110-1111
> #25/F:1110-1111 #26/F:1110-1111 #27/F:1110-1111 #28/F:1110-1111
444 atoms, 444 bonds, 24 residues, 12 models selected
> select #17/F:1110-1111 #18/F:1110-1111 #19/F:1110-1111 #20/F:1110-1111
> #21/F:1110-1111 #22/F:1110-1111 #23/F:1110-1111 #24/F:1110-1111
> #25/F:1110-1111 #26/F:1110-1111 #27/F:1110-1111 #28/F:1110-1111
444 atoms, 444 bonds, 24 residues, 12 models selected
13 [ID: 13] region 12 chains [1106-1107] RMSD: 0.000
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1106] RMSD: 0.000
> show sel atoms
> color sel light gray
> ui mousemode right select
> select #17/F:858
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/F:858
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #17/F:858
15 atoms, 14 bonds, 1 residue, 1 model selected
Drag select of 96 residues, 6 atoms, 4 bonds
Drag select of 48 atoms, 480 residues, 43 bonds
Drag select of 432 residues, 2 atoms, 2 bonds
> hide sel atoms
> select #17/F:1101
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #17/F:1102
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #17/F:863
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/F:863
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #17/F:862
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/F:863
15 atoms, 14 bonds, 1 residue, 1 model selected
Drag select of 132 residues, 5 atoms, 6 bonds
Drag select of 180 residues, 15 atoms, 3 bonds
Drag select of 48 residues
Drag select of 372 residues, 40 atoms, 30 bonds
> select #17/F:5-88 #18/F:5-88 #19/F:5-88 #20/F:5-88 #21/F:5-88 #22/F:5-88
> #23/F:5-88 #24/F:5-88 #25/F:5-88 #26/F:5-88 #27/F:5-88 #28/F:5-88
16296 atoms, 16500 bonds, 1008 residues, 12 models selected
> select #17/F #18/F #19/F #20/F #21/F #22/F #23/F #24/F #25/F #26/F #27/F
> #28/F
418728 atoms, 423324 bonds, 26124 residues, 12 models selected
13 [ID: 13] region 12 chains [1-2177] RMSD: 0.000
> hide sel atoms
> select clear
> select #17/F:1110
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/F:1106
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/F:909
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/F:942
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right translate
> ui mousemode right clip
> ui mousemode right select
> ui mousemode right translate
> hide #17 models
> show #17 models
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [905] RMSD: 0.000
> show sel atoms
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [938] RMSD: 0.000
> show sel atoms
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1102] RMSD: 0.000
> show sel atoms
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1106] RMSD: 0.000
> show sel atoms
> ui mousemode right select
> select clear
> ui mousemode right translate
> color #28 #ff85ffff
> color #28 #941751ff
> hide #23 models
> hide #24 models
> hide #25 models
> hide #26 models
> hide #27 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> save /Users/michael/Desktop/image1.png supersample 3
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> show #23 models
> show #24 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
> select #17/F:1110 #18/F:1110 #19/F:1110 #20/F:1110 #21/F:1110 #22/F:1110
> #23/F:1110 #24/F:1110 #25/F:1110 #26/F:1110 #27/F:1110 #28/F:1110
204 atoms, 192 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1106] RMSD: 0.000
> color (#23-28 & sel) light gray
> select #17/F:1106-1107 #18/F:1106-1107 #19/F:1106-1107 #20/F:1106-1107
> #21/F:1106-1107 #22/F:1106-1107 #23/F:1106-1107 #24/F:1106-1107
> #25/F:1106-1107 #26/F:1106-1107 #27/F:1106-1107 #28/F:1106-1107
396 atoms, 396 bonds, 24 residues, 12 models selected
> select #17/F:1106-1107 #18/F:1106-1107 #19/F:1106-1107 #20/F:1106-1107
> #21/F:1106-1107 #22/F:1106-1107 #23/F:1106-1107 #24/F:1106-1107
> #25/F:1106-1107 #26/F:1106-1107 #27/F:1106-1107 #28/F:1106-1107
396 atoms, 396 bonds, 24 residues, 12 models selected
13 [ID: 13] region 12 chains [1102-1103] RMSD: 0.000
> select #17/F:1107 #18/F:1107 #19/F:1107 #20/F:1107 #21/F:1107 #22/F:1107
> #23/F:1107 #24/F:1107 #25/F:1107 #26/F:1107 #27/F:1107 #28/F:1107
144 atoms, 132 bonds, 12 residues, 12 models selected
> select #17/F:1106-1107 #18/F:1106-1107 #19/F:1106-1107 #20/F:1106-1107
> #21/F:1106-1107 #22/F:1106-1107 #23/F:1106-1107 #24/F:1106-1107
> #25/F:1106-1107 #26/F:1106-1107 #27/F:1106-1107 #28/F:1106-1107
396 atoms, 396 bonds, 24 residues, 12 models selected
13 [ID: 13] region 12 chains [1102-1103] RMSD: 0.000
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1102] RMSD: 0.000
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:1106 #18/F:1106 #19/F:1106 #20/F:1106 #21/F:1106 #22/F:1106
> #23/F:1106 #24/F:1106 #25/F:1106 #26/F:1106 #27/F:1106 #28/F:1106
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [1102] RMSD: 0.000
> color (#23-28 & sel) light gray
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
> select #17/F:942 #18/F:942 #19/F:942 #20/F:942 #21/F:942 #22/F:942 #23/F:942
> #24/F:942 #25/F:942 #26/F:942 #27/F:942 #28/F:942
252 atoms, 252 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [938] RMSD: 0.000
> color (#23-28 & sel) light gray
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
> select #17/F:909 #18/F:909 #19/F:909 #20/F:909 #21/F:909 #22/F:909 #23/F:909
> #24/F:909 #25/F:909 #26/F:909 #27/F:909 #28/F:909
168 atoms, 156 bonds, 12 residues, 12 models selected
13 [ID: 13] region 12 chains [905] RMSD: 0.000
> color (#23-28 & sel) light gray
> ui mousemode right select
> select clear
> ui mousemode right translate
> save /Users/michael/Desktop/image2.png supersample 3
> ui mousemode right clip
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "crop volume"
> ui mousemode right clip
> ui mousemode right translate
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/Sensitized
> NiV L /88309_Docked_NiV_L_APO_Sensitized.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/Sensitized NiV L /88309_Docked_NiV_L_APO_Sensitized.pdb
---
warnings | Ignored bad PDB record found on line 141
HELIX 1 1 PRO C 480 PHE C 484 1 Generated by MOE 5
Ignored bad PDB record found on line 142
HELIX 2 2 PRO C 490 LEU C 503 1 Generated by MOE 14
Ignored bad PDB record found on line 143
HELIX 3 3 LEU C 508 GLU C 537 1 Generated by MOE 30
Ignored bad PDB record found on line 144
HELIX 4 4 GLN C 539 LYS C 541 5 Generated by MOE 3
Ignored bad PDB record found on line 145
HELIX 5 5 ILE C 543 SER C 573 1 Generated by MOE 31
109 messages similar to the above omitted
Chain information for 88309_Docked_NiV_L_APO_Sensitized.pdb #29
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/Sensitized
> NiV L /88309_Docked_NiV_L_RNA_Sensitized.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/Sensitized NiV L /88309_Docked_NiV_L_RNA_Sensitized.pdb
---
warnings | Ignored bad PDB record found on line 204
HELIX 1 1 PRO C 480 ASP C 483 1 Generated by MOE 4
Ignored bad PDB record found on line 205
HELIX 2 2 PRO C 490 ASP C 501 1 Generated by MOE 12
Ignored bad PDB record found on line 206
HELIX 3 3 LEU C 508 VAL C 540 1 Generated by MOE 33
Ignored bad PDB record found on line 207
HELIX 4 4 ILE C 543 VAL C 572 1 Generated by MOE 30
Ignored bad PDB record found on line 208
HELIX 5 5 PRO D 480 ASP D 483 1 Generated by MOE 4
163 messages similar to the above omitted
Chain information for 88309_Docked_NiV_L_RNA_Sensitized.pdb #30
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/Sensitized
> NiV L /88310_Docked_NiV_L_APO_Sensitized.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/Sensitized NiV L /88310_Docked_NiV_L_APO_Sensitized.pdb
---
warnings | Ignored bad PDB record found on line 141
HELIX 1 1 PRO C 480 PHE C 484 1 Generated by MOE 5
Ignored bad PDB record found on line 142
HELIX 2 2 PRO C 490 LEU C 503 1 Generated by MOE 14
Ignored bad PDB record found on line 143
HELIX 3 3 LEU C 508 GLU C 537 1 Generated by MOE 30
Ignored bad PDB record found on line 144
HELIX 4 4 GLN C 539 LYS C 541 5 Generated by MOE 3
Ignored bad PDB record found on line 145
HELIX 5 5 ILE C 543 SER C 573 1 Generated by MOE 31
109 messages similar to the above omitted
Chain information for 88310_Docked_NiV_L_APO_Sensitized.pdb #31
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/Sensitized
> NiV L /88310_Docked_NiV_L_RNA_Sensitized.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/Sensitized NiV L /88310_Docked_NiV_L_RNA_Sensitized.pdb
---
warnings | Ignored bad PDB record found on line 204
HELIX 1 1 PRO C 480 ASP C 483 1 Generated by MOE 4
Ignored bad PDB record found on line 205
HELIX 2 2 PRO C 490 ASP C 501 1 Generated by MOE 12
Ignored bad PDB record found on line 206
HELIX 3 3 LEU C 508 VAL C 540 1 Generated by MOE 33
Ignored bad PDB record found on line 207
HELIX 4 4 ILE C 543 VAL C 572 1 Generated by MOE 30
Ignored bad PDB record found on line 208
HELIX 5 5 PRO D 480 ASP D 483 1 Generated by MOE 4
163 messages similar to the above omitted
Chain information for 88310_Docked_NiV_L_RNA_Sensitized.pdb #32
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> color #29 #ff7e79ff
> color #30 #ffd479ff
> color #31 #fffc79ff
> color #32 #d4fb79ff
> ui mousemode right clip
> hide #28 models
> hide #27 models
> hide #26 models
> hide #25 models
> hide #24 models
> hide #23 models
> ui mousemode right translate
> style #!29-32 stick
Changed 139344 atom styles
> show #!29-32 cartoons
Computing secondary structure
> ui tool show "Show Sequence Viewer"
> sequence chain #30/E #32/E
Alignment identifier is 1
> sequence chain #30/B #32/B
Alignment identifier is 2
> sequence chain #30/C #32/C
Alignment identifier is 3
> sequence chain #30/D #32/D
Alignment identifier is 4
> select #30/C:479-496 #32/C:479-496
558 atoms, 568 bonds, 36 residues, 2 models selected
> select #30/C #32/C
3226 atoms, 3252 bonds, 202 residues, 2 models selected
3 [ID: 3] region 2 chains [1-101] RMSD: 0.000
> hide sel atoms
> select #30/D:480-483,490-502,508-577 #32/D:480-483,490-502,508-577
2780 atoms, 2792 bonds, 174 residues, 2 models selected
> select #30/D:478-479 #32/D:478-479
76 atoms, 74 bonds, 4 residues, 2 models selected
> select #30/D #32/D
3770 atoms, 3798 bonds, 236 residues, 2 models selected
4 [ID: 4] region 2 chains [1-118] RMSD: 0.000
> hide sel atoms
> select #30/E:478-495 #32/E:478-495
558 atoms, 568 bonds, 36 residues, 2 models selected
> select #30/E #32/E
3380 atoms, 3406 bonds, 212 residues, 2 models selected
1 [ID: 1] region 2 chains [1-106] RMSD: 0.000
> hide sel atoms
> select #30/B:477 #32/B:477
46 atoms, 46 bonds, 2 residues, 2 models selected
> select #30/B #32/B
6288 atoms, 6326 bonds, 4 pseudobonds, 390 residues, 4 models selected
2 [ID: 2] region 2 chains [1-195] RMSD: 0.000
> hide sel atoms
> select #30/B:709 #32/B:709
40 atoms, 38 bonds, 2 residues, 2 models selected
> select #30/B:709 #32/B:709
40 atoms, 38 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [195] RMSD: 0.000
> ui tool show "Show Sequence Viewer"
> sequence chain #29/A #31/A
Alignment identifier is 5
> sequence chain #29/B #31/B
Alignment identifier is 6
> sequence chain #29/C #31/C
Alignment identifier is 7
> sequence chain #29/D #31/D
Alignment identifier is 8
> sequence chain #29/E #31/E
Alignment identifier is 9
> sequence chain #30/A #32/A
Alignment identifier is 10
> sequence chain #30/B #32/B
Alignment identifier is 11
> sequence chain #30/C #32/C
Alignment identifier is 12
> sequence chain #30/D #32/D
Alignment identifier is 13
> sequence chain #30/E #32/E
Alignment identifier is 14
> select #30/E:480-485,490-505,508-572 #32/E:480-485,490-505,508-572
2756 atoms, 2770 bonds, 174 residues, 2 models selected
> select #30/D:480-483,490-502,508-577 #32/D:480-483,490-502,508-577
2780 atoms, 2792 bonds, 174 residues, 2 models selected
> select #30/C:480-483,490-502,508-573 #32/C:480-483,490-502,508-573
2640 atoms, 2652 bonds, 166 residues, 2 models selected
> select #30/B:480-483,490-501,508-574,603-608,658-671,675-687,691-705
> #32/B:480-483,490-501,508-574,603-608,658-671,675-687,691-705
4222 atoms, 4228 bonds, 262 residues, 2 models selected
> select #30/B:609 #32/B:609
42 atoms, 42 bonds, 2 residues, 2 models selected
> select #30/B:576-609 #32/B:576-609
620 atoms, 620 bonds, 2 pseudobonds, 36 residues, 4 models selected
11 [ID: 11] region 2 chains [100-117] RMSD: 0.000
> select #29/C:480-484,490-505,508-537,539-573
> #31/C:480-484,490-505,508-537,539-573
2726 atoms, 2738 bonds, 172 residues, 2 models selected
> select #29/D:480-485,490-505,508-577 #31/D:480-485,490-505,508-577
2918 atoms, 2932 bonds, 184 residues, 2 models selected
> select #29/E:480-483,490-503,508-573 #31/E:480-483,490-503,508-573
2678 atoms, 2690 bonds, 168 residues, 2 models selected
> select #29/B:480-487,490-503,508-526,529-571,658-671,675-687,691-705
> #31/B:480-487,490-503,508-526,529-571,658-671,675-687,691-705
4062 atoms, 4072 bonds, 252 residues, 2 models selected
> select #29/B:475 #31/B:475
28 atoms, 26 bonds, 2 residues, 2 models selected
> select #29/B #31/B
6286 atoms, 6324 bonds, 4 pseudobonds, 392 residues, 4 models selected
6 [ID: 6] region 2 chains [1-196] RMSD: 0.000
> hide sel atoms
> select #29/C:476 #31/C:476
48 atoms, 46 bonds, 2 residues, 2 models selected
> select #29/C #31/C
3364 atoms, 3392 bonds, 210 residues, 2 models selected
7 [ID: 7] region 2 chains [1-105] RMSD: 0.000
> hide sel atoms
> select #29/D:478 #31/D:478
42 atoms, 40 bonds, 2 residues, 2 models selected
> select #29/D #31/D
3278 atoms, 3304 bonds, 206 residues, 2 models selected
8 [ID: 8] region 2 chains [1-103] RMSD: 0.000
> hide sel atoms
> select #29/E:478-497 #31/E:478-497
624 atoms, 634 bonds, 40 residues, 2 models selected
> select #29/E #31/E
3322 atoms, 3348 bonds, 208 residues, 2 models selected
9 [ID: 9] region 2 chains [1-104] RMSD: 0.000
> hide sel atoms
> select
> #30/A:23-32,44-55,61-76,80-82,90-93,101-136,141-155,157-162,167-188,190-193,232-254,259-301,310-325,331-345,350-361,370-381,389-408,426-432,440-445,448-450,480-486,505-509,517-525,561-572,575-578,588-602,726-729,732-745,754-759,803-821,848-873,905-907,909-911,923-939,944-964,973-980,983-991,994-996,1004-1007,1015-1028,1034-1041,1050-1055,1068-1080,1096-1109,1116-1125,1127-1134,1165-1178,1192-1203,1205-1208,1221-1224,1239-1241,1292-1307,1312-1324,1330-1336,1392-1406,1483-1485,1488-1511,1516-1518,1531-1536,1539-1553,1555-1561,1565-1578,1582-1592,1595-1603,1620-1640,1654-1676,1690-1707,1728-1742,1780-1785,1805-1809,1819-1832,1848-1856,1884-1890,1896-1899,1911-1913,1919-1928,1949-1966,1985-1995,2029-2035,2044-2070,2084-2091,2098-2106,2114-2132,2151-2171,2178-2189,2199-2204,2207-2216,2228-2243
> #32/A:23-32,44-55,61-76,80-82,90-93,101-136,141-155,157-162,167-188,190-193,232-254,259-301,310-325,331-345,350-361,370-381,389-408,426-432,440-445,448-450,480-486,505-509,517-525,561-572,575-578,588-602,726-729,732-745,754-759,803-821,848-873,905-907,909-911,923-939,944-964,973-980,983-991,994-996,1004-1007,1015-1028,1034-1041,1050-1055,1068-1080,1096-1109,1116-1125,1127-1134,1165-1178,1192-1203,1205-1208,1221-1224,1239-1241,1292-1307,1312-1324,1330-1336,1392-1406,1483-1485,1488-1511,1516-1518,1531-1536,1539-1553,1555-1561,1565-1578,1582-1592,1595-1603,1620-1640,1654-1676,1690-1707,1728-1742,1780-1785,1805-1809,1819-1832,1848-1856,1884-1890,1896-1899,1911-1913,1919-1928,1949-1966,1985-1995,2029-2035,2044-2070,2084-2091,2098-2106,2114-2132,2151-2171,2178-2189,2199-2204,2207-2216,2228-2243
34312 atoms, 34446 bonds, 2052 residues, 2 models selected
> select #29/A:5 #31/A:5
42 atoms, 40 bonds, 2 residues, 2 models selected
> select #29/A:5-1451 #31/A:5-1451
39956 atoms, 40368 bonds, 12 pseudobonds, 2466 residues, 4 models selected
5 [ID: 5] region 2 chains [1-1233] RMSD: 0.000
> hide sel atoms
> select #30/A:6-130 #32/A:6-130
4122 atoms, 4154 bonds, 250 residues, 2 models selected
> select #30/A:6-2244 #32/A:6-2244
65574 atoms, 66248 bonds, 18 pseudobonds, 4040 residues, 4 models selected
10 [ID: 10] region 2 chains [1-2020] RMSD: 0.000
> hide sel atoms
> select #29/A:1451 #31/A:1451
34 atoms, 32 bonds, 2 residues, 2 models selected
> select #29/A:1419-1451 #31/A:1419-1451
872 atoms, 880 bonds, 2 pseudobonds, 54 residues, 4 models selected
5 [ID: 5] region 2 chains [1207-1233] RMSD: 0.000
> select #29/A:1451 #31/A:1451
34 atoms, 32 bonds, 2 residues, 2 models selected
> select #29/A:1451 #31/A:1451
34 atoms, 32 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [1233] RMSD: 0.000
> hide #!29 models
> hide #!31 models
> ui mousemode right select
> select #32/?:0@@serial_number=41526
1 atom, 1 residue, 1 model selected
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/NIV L
> Elongation 88309 Bound Triangle Matcher.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/NIV L Elongation 88309 Bound Triangle Matcher.pdb
---
warnings | Ignored bad PDB record found on line 204
HELIX 1 1 PRO C 480 PHE C 484 1 Generated by MOE 5
Ignored bad PDB record found on line 205
HELIX 2 2 PRO C 490 LEU C 503 1 Generated by MOE 14
Ignored bad PDB record found on line 206
HELIX 3 3 LEU C 508 VAL C 540 1 Generated by MOE 33
Ignored bad PDB record found on line 207
HELIX 4 4 ILE C 543 SER C 573 1 Generated by MOE 31
Ignored bad PDB record found on line 208
HELIX 5 5 PRO D 480 PHE D 484 1 Generated by MOE 5
169 messages similar to the above omitted
Chain information for NIV L Elongation 88309 Bound Triangle Matcher.pdb #33
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/NIV L
> Elongation 88310 Bound Triangle Matcher.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/NIV L Elongation 88310 Bound Triangle Matcher.pdb
---
warnings | Ignored bad PDB record found on line 204
HELIX 1 1 PRO C 480 PHE C 484 1 Generated by MOE 5
Ignored bad PDB record found on line 205
HELIX 2 2 PRO C 490 LEU C 503 1 Generated by MOE 14
Ignored bad PDB record found on line 206
HELIX 3 3 LEU C 508 VAL C 540 1 Generated by MOE 33
Ignored bad PDB record found on line 207
HELIX 4 4 ILE C 543 SER C 573 1 Generated by MOE 31
Ignored bad PDB record found on line 208
HELIX 5 5 PRO D 480 PHE D 484 1 Generated by MOE 5
169 messages similar to the above omitted
Chain information for NIV L Elongation 88310 Bound Triangle Matcher.pdb #34
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> style sel stick
Changed 0 atom styles
> show sel cartoons
> style sel stick
Changed 0 atom styles
> style sel stick
Changed 0 atom styles
> style sel stick
Changed 0 atom styles
> style sel stick
Changed 0 atom styles
Drag select of 83856 atoms, 5080 residues, 30 pseudobonds, 928 bonds
> style sel stick
Changed 166094 atom styles
> show sel cartoons
Computing secondary structure
> select clear
> color #33 #73fa79ff
> color #34 #73fcd6ff
> select clear
> select #33/A:2179@OE2
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 17702 atoms, 3380 residues, 8 pseudobonds, 16472 bonds
> select clear
> select #30/D:554
12 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #33/A #34/A
Alignment identifier is 11
> select #33/A:6 #34/A:6
24 atoms, 22 bonds, 2 residues, 2 models selected
> select #33/A:6-2244 #34/A:6-2244
65548 atoms, 66222 bonds, 18 pseudobonds, 4040 residues, 4 models selected
11 [ID: 11] region 2 chains [1-2020] RMSD: 0.000
> hide sel atoms
> select clear
> hide #!32 models
> hide #!30 models
> hide #!34 models
> show #!34 models
> hide #!33 models
> show #!33 models
> select #33/A:6-72 #34/A:6-72
2188 atoms, 2206 bonds, 134 residues, 2 models selected
> select #33/A:6-2244 #34/A:6-2244
65548 atoms, 66222 bonds, 18 pseudobonds, 4040 residues, 4 models selected
11 [ID: 11] region 2 chains [1-2020] RMSD: 0.000
> hide sel cartoons
Drag select of 1510 atoms, 140 residues, 1390 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 4866 atoms, 470 residues, 2 pseudobonds, 4514 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 3284 atoms, 332 residues, 3034 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 794 atoms, 68 residues, 736 bonds
> hide sel cartoons
> hide sel atoms
> show #!32 models
> hide #!33 models
> ui mousemode right translate
> surface (#!34 & sel)
> ui mousemode right select
> select clear
> surface #32,34
> hide #!32 models
> hide #!34 models
> show #!5 models
> ui mousemode right translate
> show #!5 surfaces
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> ui mousemode right select
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
OS Loader Version: 582~1023
Software:
System Software Overview:
System Version: macOS 15.0 (24A335)
Kernel Version: Darwin 24.0.0
Time since boot: 5 days, 23 hours, 55 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-011
Option ROM Version: 113-D322A1XL-011
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LEN D24f-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c1
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
ChimeraX-MutationScores: 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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.17.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 5 days ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in QDockWidget::event() in Qt 6.9.2 |
comment:2 by , 5 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Was deleting a QDockWidget. Maybe this happens when dragging a docked tool to be floating. Qt bug.
Note:
See TracTickets
for help on using tickets.
There was a QWindowContainer::parentWasChanged higher up in the stack.