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Opened 98 minutes ago
#19941 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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 0x000070002a52a000 (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 0x0000700029527000 (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 0x0000700028524000 (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 0x0000700027521000 (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 0x000070002651e000 (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 0x000070002551b000 (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 0x0000700024518000 (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 0x0000700023515000 (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 0x0000700022512000 (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 0x000070002150f000 (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 0x000070002050c000 (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 0x000070001f509000 (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 0x000070001e506000 (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 0x000070001d503000 (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 0x000070001c500000 (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 0x00007ff85b3d5680 (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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, pyKVFinder._pyKVFinder, lxml._elementpath, lxml.etree, lxml.builder (total: 57)
{"app_name":"ChimeraX","timestamp":"2026-03-05 16:37:06.00 -0500","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":"A5DDED0B-FE03-49D1-B6C3-6A6AF103E8BA"}
{
"uptime" : 1200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 9277,
"osVersion" : {
"train" : "macOS 15.0",
"build" : "24A335",
"releaseType" : "User"
},
"captureTime" : "2026-03-05 16:36:57.9593 -0500",
"codeSigningMonitor" : 0,
"incident" : "A5DDED0B-FE03-49D1-B6C3-6A6AF103E8BA",
"pid" : 29694,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-20 15:13:04.2570 -0500",
"procStartAbsTime" : 102038320211822,
"procExitAbsTime" : 1230233251302684,
"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" : "5F911262-7D79-4290-B72C-DD722B42B4BC",
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4404514808
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 106879000-10687b000 [ 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":29694},
"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: 4404514808
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 106879000-10687b000 [ 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":141},
{"imageOffset":284828,"symbol": "raise" ,"symbolLocation":24,"imageIndex":142},
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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":532035,"symbol": "QWindowContainer::parentWasChanged(QWidget*)" ,"symbolLocation":435,"imageIndex":49},
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{"imageOffset":315618,"symbol": "QWidget::setParent(QWidget*, QFlags)" ,"symbolLocation":2322,"imageIndex":49},
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
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/Desktop/MOE Files/88309 and 88310
> Docking/MeV_L_Homology_NiV_L_RNA_2.pdb" format pdb
MeV_L_Homology_NiV_L_RNA_2.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MeV L RNA Bound [more
info...]
Chain information for MeV_L_Homology_NiV_L_RNA_2.pdb #1
---
Chain | Description
F | No description available
Computing secondary structure
> open "/Users/michael/Desktop/MOE Files/88309 and 88310
> Docking/9GJT_NiV_PL_Apo.moe"
Unrecognized file suffix '.moe'
> open /Users/michael/Downloads/9GJT.pdb
9GJT.pdb title:
Structure of nipah virus RNA polymerase complex - apo state [more info...]
Chain information for 9GJT.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
Non-standard residues in 9GJT.pdb #2
---
ZN — zinc ion
> close #1
> open /Users/michael/Downloads/9GJU.pdb
9GJU.pdb title:
Structure of replicating nipah virus RNA polymerase complex - RNA- bound state
[more info...]
Chain information for 9GJU.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
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.pdb #1
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
ZN — zinc ion
> show cartoons
> style stick
Changed 34952 atom styles
> hide atoms
> hide cartoons
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select
> #2/A:6-11,22-34,43-57,60-77,87-96,104-137,140-163,166-193,231-280,282-300,309-326,330-346,349-360,369-382,389-411,425-434,439-451,479-492,504-512,516-526,557-579,726-747,753-760,802-822,847-874,904-910,922-940,943-965,972-997,1014-1029,1033-1041,1049-1056,1067-1081,1096-1108,1115-1125,1156-1178,1191-1209,1238-1242,1291-1307,1310-1322,1328-1336,1366-1370,1391-1407
5807 atoms, 5883 bonds, 715 residues, 1 model selected
> select clear
> select #2/A:5-983
6844 atoms, 6990 bonds, 2 pseudobonds, 845 residues, 2 models selected
> color (#!2 & sel) forest green
> select clear
> select #1/A:6-983
7062 atoms, 7212 bonds, 1 pseudobond, 873 residues, 2 models selected
> color (#!1 & sel) forest green
> select #1/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:984-1452
3390 atoms, 3454 bonds, 3 pseudobonds, 426 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select #2/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:984-1451
3115 atoms, 3174 bonds, 4 pseudobonds, 388 residues, 2 models selected
> color (#!2 & sel) cornflower blue
> select clear
> select #1/A:1453
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1453-1743
2289 atoms, 2343 bonds, 1 pseudobond, 278 residues, 2 models selected
> color (#!1 & sel) yellow
> select clear
> select #1/A:1769-2096
2456 atoms, 2506 bonds, 2 pseudobonds, 310 residues, 2 models selected
> color (#!1 & sel) orange
> select #1/A:2097
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:2097-2244
1109 atoms, 1125 bonds, 1 pseudobond, 133 residues, 2 models selected
> color (#!1 & sel) red
> select clear
> color red
> undo
> select clear
> select #1/A:2010-2011
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/A:1685-2011
2293 atoms, 2339 bonds, 2 pseudobonds, 288 residues, 2 models selected
> select #1/A:1680-1681
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/A:1680-1682
26 atoms, 27 bonds, 3 residues, 1 model selected
> ui mousemode right select
> select clear
> select
> #2/A:6-11,22-34,43-57,60-77,87-96,104-137,140-163,166-193,231-280,282-300,309-326,330-346,349-360,369-382,389-411,425-434,439-451,479-492,504-512,516-526,557-579,726-747,753-760,802-822,847-874,904-910,922-940,943-965,972-997,1014-1029,1033-1041,1049-1056,1067-1081,1096-1108,1115-1125,1156-1178,1191-1209,1238-1242,1291-1307,1310-1322,1328-1336,1366-1370,1391-1407
5807 atoms, 5883 bonds, 715 residues, 1 model selected
> select
> #1/A:22-33,43-56,60-77,79-83,87-96,104-137,140-163,166-193,231-255,260-273,275-280,282-300,309-325,330-346,349-360,369-382,389-411,425-434,439-451,479-487,504-510,516-526,560-579,582-603,731-747,753-760,780-784,802-821,847-874,904-910,922-940,943-965,972-997,1004-1008,1014-1029,1033-1042,1049-1056,1067-1080,1096-1110,1115-1136,1161-1178,1191-1209,1220-1224,1238-1242,1291-1309,1311-1323,1329-1336,1391-1407,1482-1511,1515-1519,1530-1560,1565-1579,1581-1604,1614-1641,1653-1676,1689-1712,1727-1743,1780-1786,1804-1810,1818-1833,1847-1857,1883-1891,1895-1900,1910-1914,1918-1929,1948-1966,1984-1995,2028-2038,2044-2071,2083-2092,2097-2107,2113-2133,2151-2172,2177-2189,2198-2217,2227-2242
9652 atoms, 9763 bonds, 1185 residues, 1 model selected
> select #1/A:752
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:752
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:732
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:732
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> hide sel atoms
> color sel forest green
> select #2/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #1/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #1/A:419-438
157 atoms, 160 bonds, 20 residues, 1 model selected
> select #1/A:419-458
321 atoms, 329 bonds, 40 residues, 1 model selected
> select #1/A:438
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:435-438
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/A:799
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:803-883
653 atoms, 665 bonds, 81 residues, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:799
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:803-804
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/A:799
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:803
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:806
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:806
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:810
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:810
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:814
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:814
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:836
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:836
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:866
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:866
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:870
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:870
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:877
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:877
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:723
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:723
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #1/A:726
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:726
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> ui mousemode right clip
> select #1/A:799
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:799
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel cyan
> show sel atoms
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> style #!2 sphere
Changed 14017 atom styles
> style #!2 sphere
Changed 14017 atom styles
> style #!2 ball
Changed 14017 atom styles
> style #!2 stick
Changed 14017 atom styles
> style #!2 sphere
Changed 14017 atom styles
> style #!2 stick
Changed 14017 atom styles
> hide #!2 cartoons
> show #!2 cartoons
> select add #1
20935 atoms, 21379 bonds, 24 pseudobonds, 2565 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
20935 atoms, 21379 bonds, 24 pseudobonds, 2565 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #2
14017 atoms, 14280 bonds, 16 pseudobonds, 1743 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
14017 atoms, 14280 bonds, 16 pseudobonds, 1743 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
14017 atoms, 14280 bonds, 16 pseudobonds, 1743 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!1 models
> select #2/A:831
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:831-834
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel gray
> select #1/A:831
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:831-834
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel gray
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> surface sel
> select clear
> select #1/A:6-1076
7780 atoms, 7946 bonds, 1 pseudobond, 966 residues, 2 models selected
> select #1/A:6-1076
7780 atoms, 7946 bonds, 1 pseudobond, 966 residues, 2 models selected
> select #1/A:6-1076
7780 atoms, 7946 bonds, 1 pseudobond, 966 residues, 2 models selected
> ui mousemode right select
> ui mousemode right clip
> ui mousemode right select
> select clear
> surface #1
> ui tool show "Color Actions"
> color bychain
> undo
> surface hidePatches (#!1 & sel)
> select clear
> surface hidePatches #1
> select clear
> select #1/A:2223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:6-18
104 atoms, 106 bonds, 13 residues, 1 model selected
> select #1/A:6-18
104 atoms, 106 bonds, 13 residues, 1 model selected
> select clear
> surface #1
> select #1/D:589@CE
1 atom, 1 residue, 1 model selected
> select #1/A:1316@CD2
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right clip
> transparency #1 30
> transparency #1 60
> transparency #1 20
> select #1/A:803-883
653 atoms, 665 bonds, 81 residues, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:803-883
653 atoms, 665 bonds, 81 residues, 1 model selected
> select #1/A:799-800
13 atoms, 12 bonds, 2 residues, 1 model selected
> select
> #1/A:84-85,199-202,206-210,215-221,224-230,385-388,418-419,454-455,537-541,552-556,713-721,763-766,790-792,824-830,833-842,883-885,888-891,894-897,900-901,1225-1230,1246-1251,1371-1373,1379-1381,1384-1386,1418-1424,1647-1650,1721-1724,1775-1779,1838-1842,1862-1864,1934-1939,1967-1977,1996-2004,2014-2021,2191-2195,2221-2225
1511 atoms, 1516 bonds, 182 residues, 1 model selected
> select
> #1/A:22-33,43-56,60-77,79-83,87-96,104-137,140-163,166-193,231-255,260-273,275-280,282-300,309-325,330-346,349-360,369-382,389-411,425-434,439-451,479-487,504-510,516-526,560-579,582-603,731-747,753-760,780-784,802-821,847-874,904-910,922-940,943-965,972-997,1004-1008,1014-1029,1033-1042,1049-1056,1067-1080,1096-1110,1115-1136,1161-1178,1191-1209,1220-1224,1238-1242,1291-1309,1311-1323,1329-1336,1391-1407,1482-1511,1515-1519,1530-1560,1565-1579,1581-1604,1614-1641,1653-1676,1689-1712,1727-1743,1780-1786,1804-1810,1818-1833,1847-1857,1883-1891,1895-1900,1910-1914,1918-1929,1948-1966,1984-1995,2028-2038,2044-2071,2083-2092,2097-2107,2113-2133,2151-2172,2177-2189,2198-2217,2227-2242
9652 atoms, 9763 bonds, 1185 residues, 1 model selected
> select clear
> show #!2 models
> hide #!1 models
> surface #2
> surface hidePatches #2
> ui mousemode right select
> cartoon #2
> surface style #2 mesh
> surface #2
> color #2 red
> undo
> ui tool show "Color Actions"
Drag select of 9GJT.pdb_A SES surface, 10984 of 1024702 triangles, 31 residues
> select #2/A:378@CD
1 atom, 1 residue, 1 model selected
> select #2/B:704@O
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:319-984
4290 atoms, 4389 bonds, 2 pseudobonds, 532 residues, 2 models selected
> select #2/A:984-1004
161 atoms, 166 bonds, 21 residues, 1 model selected
> select #2/A:963-984
169 atoms, 170 bonds, 22 residues, 1 model selected
> select #2/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:5-984
6852 atoms, 6998 bonds, 2 pseudobonds, 846 residues, 2 models selected
> select clear
> select #2/A:5-984
6852 atoms, 6998 bonds, 2 pseudobonds, 846 residues, 2 models selected
> color (#!2 & sel) forest green
> select clear
> surface style #2 solid
> select #2/A:985
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:985-1431
2995 atoms, 3052 bonds, 3 pseudobonds, 373 residues, 2 models selected
> color (#!2 & sel) cornflower blue
> select clear
> select #2/A:1155-1156
16 atoms, 16 bonds, 2 residues, 1 model selected
> select clear
Drag select of 9GJT.pdb_A SES surface, 159707 of 1024702 triangles, 181
residues, 3 pseudobonds
Drag select of 9GJT.pdb_A SES surface, 21192 of 1024702 triangles, 36
residues, 1 pseudobonds
Drag select of 9GJT.pdb_A SES surface, 14576 of 1024702 triangles, 9GJT.pdb_B
SES surface, 708 of 256840 triangles, 26 residues
Drag select of 9GJT.pdb_A SES surface, 220107 of 1024702 triangles, 9GJT.pdb_B
SES surface, 16831 of 256840 triangles, 5 atoms, 327 residues, 2 pseudobonds,
4 bonds
> select #2/A:1382@O
1 atom, 1 residue, 1 model selected
Drag select of 9GJT.pdb_A SES surface, 3502 of 1024702 triangles, 9GJT.pdb_B
SES surface, 53 of 256840 triangles, 10 residues
Drag select of 9GJT.pdb_A SES surface, 38351 of 1024702 triangles, 9GJT.pdb_B
SES surface, 13651 of 256840 triangles, 11 atoms, 84 residues, 9 bonds
> select #2/A:1310@ND2
1 atom, 1 residue, 1 model selected
Drag select of 9GJT.pdb_A SES surface, 17107 of 1024702 triangles, 27 residues
> color (#!2 & sel) cornflower blue
Drag select of 9GJT.pdb_A SES surface, 93837 of 1024702 triangles, 9GJT.pdb_B
SES surface, 35560 of 256840 triangles, 13 atoms, 174 residues, 11 bonds
> select clear
Drag select of 9GJT.pdb_A SES surface, 145961 of 1024702 triangles, 154
residues, 1 pseudobonds
> color (#!2 & sel) cornflower blue
Drag select of 9GJT.pdb_A SES surface, 36160 of 1024702 triangles, 111
residues
> color (#!2 & sel) forest green
> select
> #2/A:6-11,22-34,43-57,60-77,87-96,104-137,140-163,166-193,231-280,282-300,309-326,330-346,349-360,369-382,389-411,425-434,439-451,479-492,504-512,516-526,557-579,726-747,753-760,802-822,847-874,904-910,922-940,943-965,972-997,1014-1029,1033-1041,1049-1056,1067-1081,1096-1108,1115-1125,1156-1178,1191-1209,1238-1242,1291-1307,1310-1322,1328-1336,1366-1370,1391-1407
5807 atoms, 5883 bonds, 715 residues, 1 model selected
> select #2/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) magenta
> select #2/A:831-833
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #2/A:831-834
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color (#!2 & sel) gray
> select #2/A:144@CG
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right clip
> select #2/A:919
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:919
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cyan
> select #2/A:1001
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:1001
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cyan
> select #2/A:1165
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:1165
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cyan
> select #2/A:1169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:1169
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cyan
> save /Users/michael/Desktop/image9.png supersample 3
> save /Users/michael/Desktop/image10.png supersample 3
> save /Users/michael/Desktop/image11.png supersample 3
> set bgColor white
> select #2/A:831
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:831-834
29 atoms, 28 bonds, 4 residues, 1 model selected
> color (#!2 & sel) purple
> color (#!2 & sel) hot pink
> color (#!2 & sel) forest green
> color (#!2 & sel) lime
> color (#!2 & sel) magenta
> ui mousemode right select
> select clear
> ui mousemode right clip
> save /Users/michael/Desktop/image12.png supersample 3
> open /Users/michael/Downloads/9DUS.pdb
9DUS.pdb title:
Cryo-em structure of the measles virus polymerase (L) protein In complex with
the tetrameric phosphoprotein (P) [more info...]
Chain information for 9DUS.pdb #3
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | Q83626_9MONO 1-2183
B C D E | protein P | PHOSP_MEASF 1-507
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> style #!3 stick
Changed 12691 atom styles
> show #!3 cartoons
> hide #!3 atoms
> surface #3
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select clear
> select #3/A:7-852
6215 atoms, 6372 bonds, 2 pseudobonds, 764 residues, 2 models selected
> color (#!3 & sel) forest green
> select #3/A:853
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:853-1411
3854 atoms, 3920 bonds, 4 pseudobonds, 489 residues, 2 models selected
> color (#!3 & sel) cornflower blue
> ui mousemode right select
> select clear
> select #3/A:772-773
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:772-775
29 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color (#!3 & sel) magenta
> select
> #3/A:21-32,43-56,59-77,90-95,103-135,143-158,161-183,224-248,251-273,275-293,302-319,323-339,346-353,362-375,382-404,418-428,432-444,476-485,497-505,509-519,550-573,666-688,694-701,721-725,743-763,788-815,846-852,863-882,884-906,913-938,955-970,975-983,990-997,1008-1024,1027-1031,1037-1050,1056-1079,1081-1093,1096-1120,1132-1150,1161-1165,1176-1183,1232-1249,1252-1264,1270-1278,1304-1309,1330-1348
5958 atoms, 6031 bonds, 737 residues, 1 model selected
> select #3/A:1106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:1106
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) cyan
> select #3/A:1110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:1110
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) cyan
> select #3/A:942-943
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:942-943
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:943-963
160 atoms, 161 bonds, 21 residues, 1 model selected
> select #3/A:943-963
160 atoms, 161 bonds, 21 residues, 1 model selected
> select #3/A:942-943
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:942-943
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:942
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:942
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) cyan
> select #3/A:869
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:869
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) cyan
> select #3/A:500@OD1
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right clip
> save /Users/michael/Desktop/image13.png supersample 3
> transparency #3 30
> transparency #3 40
> transparency #3 70
> transparency #3 40
> transparency #3 0
> open /Users/michael/Downloads/4XJN.pdb /Users/michael/Downloads/5WKN.pdb
> /Users/michael/Downloads/7EXA.pdb /Users/michael/Downloads/model_01.pdb
4XJN.pdb title:
Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight
INTO paramyxovirus polymerase activity [more info...]
Chain information for 4XJN.pdb #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M | nucleocapsid protein | W5QKM4_9PARA 1-509
N | RNA (78-mer) |
Non-standard residues in 4XJN.pdb #4
---
PB — lead (II) ion
5WKN.pdb title:
Crystal structure of the parainfluenza virus 5 nucleoprotein- phosphoprotein
complex [more info...]
Chain information for 5WKN.pdb #5
---
Chain | Description | UniProt
A B | nucleoprotein | NCAP_PIV5 32-372
C D | protein P | PHOSP_PIV5 2-50
7EXA.pdb title:
Structure of mumps virus nucleoprotein without C-arm [more info...]
Chain information for 7EXA.pdb #6
---
Chain | Description | UniProt
A | nucleoprotein | NCAP_MUMPJ 1-549
B | RNA (5'-R(P*up*up*up*up*up*U)-3') |
model_01.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MenV N [more info...]
Chain information for model_01.pdb #7
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!3 models
> show #6-7#!4-5 atoms
> hide #6-7#!4-5 atoms
> show #6-7#!4-5 cartoons
> ui tool show "Similar Structures"
> ui tool show Matchmaker
> matchmaker #6-7#!5 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4XJN.pdb, chain I (#4) with 7EXA.pdb, chain A (#6), sequence
alignment score = 1484.3
RMSD between 334 pruned atom pairs is 0.947 angstroms; (across all 368 pairs:
1.552)
Matchmaker 4XJN.pdb, chain M (#4) with model_01.pdb, chain A (#7), sequence
alignment score = 1246.6
RMSD between 330 pruned atom pairs is 0.909 angstroms; (across all 368 pairs:
1.532)
Matchmaker 4XJN.pdb, chain A (#4) with 5WKN.pdb, chain A (#5), sequence
alignment score = 1616.6
RMSD between 190 pruned atom pairs is 0.781 angstroms; (across all 323 pairs:
4.760)
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #7/A
Alignment identifier is 7/A
> select
> #5/A:44-61,65-79,81-89,123-135,141-145,159-177,194-202,206-210,212-241,248-262,266-276,281-313,320-348,358-371
1835 atoms, 1861 bonds, 225 residues, 1 model selected
> select #5/A:63
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:63-64
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #5/A:63
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:63
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #7/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show sel atoms
> color sel blue
> ui tool show Matchmaker
> matchmaker #6 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01.pdb, chain A (#7) with 7EXA.pdb, chain A (#6), sequence
alignment score = 1435.1
RMSD between 374 pruned atom pairs is 0.112 angstroms; (across all 374 pairs:
0.112)
> matchmaker #6 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01.pdb, chain A (#7) with 7EXA.pdb, chain A (#6), sequence
alignment score = 1435.1
RMSD between 374 pruned atom pairs is 0.112 angstroms; (across all 374 pairs:
0.112)
> ui tool show Matchmaker
> matchmaker #!5 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01.pdb, chain A (#7) with 5WKN.pdb, chain B (#5), sequence
alignment score = 1101.2
RMSD between 187 pruned atom pairs is 0.901 angstroms; (across all 328 pairs:
4.931)
> hide #!5 models
> hide #6 models
> select #7/A:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> color sel orange
> color sel black
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L
> #4/M
Alignment identifier is 1
> select
> #4/A-M:3-18,44-61,65-79,83-94,123-134,151-155,159-177,189-202,206-210,212-242,248-262,266-323,325-350,358-372,377-384,387-401
29809 atoms, 30147 bonds, 3692 residues, 1 model selected
> select #4/A-M:3-19
1859 atoms, 1872 bonds, 221 residues, 1 model selected
> select #4/A-B,D,G-I,K,M:3-401/C,E-F,J,L
40755 atoms, 41535 bonds, 13 pseudobonds, 5135 residues, 2 models selected
> color (#!4 & sel) cornflower blue
> color (#!4 & sel) white
> color (#!4 & sel) light gray
> ui mousemode right select
> select clear
> select #7/A:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel purple
> color sel magenta
> select #7/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A
2973 atoms, 3032 bonds, 374 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #7/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel magenta
> select #7/A:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select clear
Drag select of 5 residues
> save /Users/michael/Desktop/image14.png supersample 3
> hide #!4 models
> show #!5 models
Drag select of 18 residues
> select clear
> select #5/A:33-373
2588 atoms, 2640 bonds, 2 pseudobonds, 323 residues, 2 models selected
> color (#!5 & sel) light gray
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B
Alignment identifier is 2
> select clear
> select #5/A:33-373/B:33-372
5212 atoms, 5318 bonds, 3 pseudobonds, 651 residues, 2 models selected
> color (#!5 & sel) light gray
> color (#!5 & sel) dark gray
> hide #7 models
Drag select of 689 residues, 3 pseudobonds
> color (#!5 & sel) dark gray
> show #7 models
> select clear
Drag select of 126 residues
> select clear
Drag select of 8 residues
> select clear
> save /Users/michael/Desktop/image15.png supersample 3
> hide #!5 models
> show #6 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide target m
> show target m
> hide #!5 models
> hide target m
> show #!5 models
> show #7 models
> hide #7 models
> show #!4 models
> hide #!4 models
> show #6 models
> hide #6 models
> show #7 models
> select clear
> select #5/A:33-373
2588 atoms, 2640 bonds, 2 pseudobonds, 323 residues, 2 models selected
> color (#!5 & sel) black
> color (#!5 & sel) forest green
> select clear
Drag select of 9 residues
> select clear
> save /Users/michael/Desktop/image16.png supersample 3
> save /Users/michael/Desktop/image17.png supersample 3
> show #6 models
> hide #!5 models
> hide #6 models
> show #!5 models
> select #5/A:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:68
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> hide #!5 models
> hide #7 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> select clear
> show target m
> hide #!4 models
> hide #!5 models
> hide #6 models
> hide #7 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!1-3 cartoons
> ui mousemode right clip
> hide #!2 models
> hide #!1 models
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.4.2 which is incompatible.
scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.2 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder #3
129 cavities found for 9DUS.pdb #3
9DUS.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.7.76 | | 1006.78 | 697.02 | 4661 | 5.09 | 1.32
3.7.10 | | 570.67 | 577.56 | 2642 | 11.01 | 3.69
3.7.122 | | 501.98 | 518.26 | 2324 | 8.61 | 3.56
3.7.43 | | 464.83 | 383.94 | 2152 | 5.13 | 1.41
3.7.35 | | 427.25 | 335.45 | 1978 | 8.36 | 2.53
3.7.14 | | 354.24 | 357.18 | 1640 | 13.7 | 6.53
3.7.86 | | 319.68 | 328.83 | 1480 | 0 | 0
3.7.87 | | 278.64 | 347.73 | 1290 | 11.08 | 4.52
3.7.72 | | 277.99 | 292.53 | 1287 | 9.56 | 3.73
3.7.107 | | 267.84 | 195.85 | 1240 | 4.28 | 1.17
3.7.1 | | 258.55 | 293.45 | 1197 | 4.98 | 1.21
3.7.68 | | 231.77 | 232.09 | 1073 | 5.79 | 2.86
3.7.25 | | 202.18 | 205.84 | 936 | 8.38 | 2.18
3.7.103 | | 182.95 | 156.22 | 847 | 3.29 | 0.9
3.7.114 | | 140.18 | 148.11 | 649 | 2.16 | 0.61
3.7.58 | | 136.73 | 152.97 | 633 | 4.84 | 1.91
3.7.91 | | 136.08 | 186.13 | 630 | 0 | 0
3.7.85 | | 128.3 | 133.38 | 594 | 3.5 | 1.14
3.7.93 | | 125.06 | 126.19 | 579 | 4.49 | 1.35
3.7.105 | | 118.37 | 127.55 | 548 | 2.55 | 0.74
3.7.42 | | 117.72 | 154.53 | 545 | 0 | 0
3.7.27 | | 95.04 | 129.04 | 440 | 3.06 | 0.75
3.7.20 | | 94.82 | 116.49 | 439 | 8.53 | 3.04
3.7.8 | | 94.18 | 130.88 | 436 | 3.79 | 0.79
3.7.23 | | 83.81 | 98.66 | 388 | 0 | 0
3.7.65 | | 82.73 | 125.82 | 383 | 0 | 0
3.7.61 | | 77.98 | 95.32 | 361 | 0 | 0
3.7.116 | | 71.71 | 70.94 | 332 | 3.06 | 0.99
3.7.73 | | 69.77 | 97.11 | 323 | 0 | 0
3.7.50 | | 60.48 | 65.34 | 280 | 1.8 | 0.43
3.7.31 | | 58.32 | 78.03 | 270 | 5.4 | 2.88
3.7.40 | | 57.24 | 74.99 | 265 | 0 | 0
3.7.121 | | 57.02 | 81.41 | 264 | 4.87 | 2.22
3.7.2 | | 56.38 | 82.91 | 261 | 0 | 0
3.7.22 | | 54 | 74.91 | 250 | 1.9 | 0.61
3.7.90 | | 53.35 | 73.41 | 247 | 3.84 | 2.02
3.7.80 | | 52.27 | 72.15 | 242 | 0 | 0
3.7.118 | | 49.46 | 73.94 | 229 | 0 | 0
3.7.123 | | 48.17 | 83.83 | 223 | 6.41 | 2.36
3.7.69 | | 45.79 | 72.38 | 212 | 0 | 0
3.7.125 | | 44.93 | 61.59 | 208 | 2.55 | 0.62
3.7.34 | | 43.85 | 70.58 | 203 | 0 | 0
3.7.100 | | 42.34 | 78.14 | 196 | 0 | 0
3.7.11 | | 42.12 | 48.16 | 195 | 1.8 | 0.52
3.7.16 | | 41.47 | 63.02 | 192 | 0 | 0
3.7.78 | | 40.82 | 48.74 | 189 | 2.55 | 0.75
3.7.115 | | 40.39 | 52.41 | 187 | 3.39 | 1.29
3.7.75 | | 40.18 | 58.16 | 186 | 0 | 0
3.7.9 | | 39.74 | 70.8 | 184 | 3 | 0.71
3.7.26 | | 38.45 | 75.75 | 178 | 0 | 0
3.7.57 | | 38.45 | 65.62 | 178 | 0 | 0
3.7.19 | | 38.23 | 44.1 | 177 | 1.8 | 0.58
3.7.45 | | 36.94 | 45.56 | 171 | 2.16 | 0.94
3.7.89 | | 36.94 | 64.14 | 171 | 0 | 0
3.7.111 | | 36.72 | 52.72 | 170 | 1.34 | 0.44
3.7.37 | | 36.29 | 45.53 | 168 | 2.08 | 0.62
3.7.119 | | 36.07 | 52.49 | 167 | 3.45 | 1.52
3.7.77 | | 35.64 | 56.28 | 165 | 0 | 0
3.7.101 | | 35.21 | 50.94 | 163 | 1.8 | 0.57
3.7.38 | | 33.7 | 43.76 | 156 | 2.47 | 0.93
3.7.36 | | 32.18 | 41.93 | 149 | 1.34 | 0.33
3.7.59 | | 30.24 | 33.66 | 140 | 1.9 | 0.48
3.7.106 | | 30.24 | 52.87 | 140 | 0 | 0
3.7.104 | | 27.65 | 33.32 | 128 | 1.8 | 0.51
3.7.67 | | 27 | 45.49 | 125 | 1.8 | 0.54
3.7.117 | | 26.35 | 47.4 | 122 | 0 | 0
3.7.120 | | 25.49 | 39.57 | 118 | 3.06 | 1.26
3.7.98 | | 25.06 | 41.43 | 116 | 2.75 | 1.33
3.7.97 | | 24.41 | 41.34 | 113 | 0 | 0
3.7.79 | | 24.19 | 43.26 | 112 | 0 | 0
3.7.110 | | 23.98 | 42.69 | 111 | 2.62 | 1.5
3.7.46 | | 23.76 | 34.62 | 110 | 1.8 | 0.53
3.7.54 | | 22.46 | 35.7 | 104 | 0 | 0
3.7.70 | | 21.82 | 40.63 | 101 | 0 | 0
3.7.81 | | 21.82 | 40.63 | 101 | 0 | 0
3.7.64 | | 21.38 | 32.57 | 99 | 1.47 | 0.43
3.7.82 | | 21.38 | 37.45 | 99 | 0 | 0
3.7.4 | | 20.95 | 35.63 | 97 | 2.55 | 1.02
3.7.94 | | 20.3 | 34.95 | 94 | 1.2 | 0.32
3.7.102 | | 20.09 | 28.09 | 93 | 1.8 | 0.6
3.7.30 | | 19.87 | 36.19 | 92 | 0 | 0
3.7.92 | | 19.87 | 36.19 | 92 | 0 | 0
3.7.112 | | 19.87 | 36.19 | 92 | 0 | 0
3.7.113 | | 19.44 | 29.46 | 90 | 2.16 | 0.86
3.7.47 | | 19.01 | 33.37 | 88 | 2.62 | 1.31
3.7.56 | | 19.01 | 38.34 | 88 | 0 | 0
3.7.32 | | 17.28 | 26.42 | 80 | 2.16 | 0.81
3.7.21 | | 16.85 | 32.3 | 78 | 0 | 0
3.7.66 | | 16.85 | 32.3 | 78 | 0 | 0
3.7.124 | | 16.85 | 32.3 | 78 | 0 | 0
3.7.126 | | 16.85 | 32.3 | 78 | 0 | 0
3.7.109 | | 16.42 | 29.05 | 76 | 2.08 | 0.78
3.7.60 | | 15.98 | 28.28 | 74 | 1.2 | 0.31
3.7.55 | | 15.77 | 28.31 | 73 | 1.2 | 0.32
3.7.84 | | 15.77 | 27.97 | 73 | 0.85 | 0.16
3.7.13 | | 14.9 | 23.01 | 69 | 1.8 | 0.59
3.7.129 | | 14.47 | 22.2 | 67 | 1.2 | 0.4
3.7.24 | | 14.26 | 23.87 | 66 | 1.34 | 0.48
3.7.12 | | 12.96 | 21.1 | 60 | 1.7 | 0.61
3.7.39 | | 12.53 | 21.05 | 58 | 1.34 | 0.5
3.7.6 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.15 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.17 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.18 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.41 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.44 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.49 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.53 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.63 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.71 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.95 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.96 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.99 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.108 | | 12.31 | 29.54 | 57 | 0 | 0
3.7.88 | | 9.72 | 17.71 | 45 | 1.2 | 0.28
3.7.127 | | 9.07 | 19.54 | 42 | 1.34 | 0.51
3.7.29 | | 8.21 | 17 | 38 | 0.85 | 0.18
3.7.74 | | 7.99 | 19.18 | 37 | 1.34 | 0.47
3.7.83 | | 7.13 | 12.85 | 33 | 0.6 | 0.15
3.7.48 | | 6.91 | 14.87 | 32 | 0.6 | 0.17
3.7.51 | | 6.7 | 13.21 | 31 | 0.6 | 0.12
3.7.7 | | 6.48 | 16.63 | 30 | 0.85 | 0.26
3.7.33 | | 6.48 | 12.95 | 30 | 0.6 | 0.16
3.7.3 | | 6.26 | 13.96 | 29 | 0.6 | 0.21
3.7.128 | | 5.62 | 13.76 | 26 | 0.6 | 0.05
3.7.28 | | 5.4 | 12.01 | 25 | 0.85 | 0.28
3.7.5 | | 5.18 | 15.55 | 24 | 0.6 | 0.18
3.7.52 | | 5.18 | 9.64 | 24 | 0.6 | 0.08
3.7.62 | | 5.18 | 12.01 | 24 | 0.6 | 0.12
Populating font family aliases took 217 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> select #!3/A:869
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #!3/A:869
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #!3/A:942
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #!3/A:942
12 atoms, 12 bonds, 1 residue, 1 model selected
> surface (#!3 & sel)
> ui mousemode right select
> select clear
> surface #3
Drag select of 9DUS.pdb_A SES surface, 1867 of 1069594 triangles, 9DUS.pdb_B
SES surface, 698 of 103470 triangles, 9DUS.pdb_C SES surface, 360 of 171324
triangles, 9DUS.pdb_E SES surface, 329 of 102692 triangles, 11 residues, 103
atoms
> select clear
> ui mousemode right clip
> transparency #3 40
> view #3.7.10 @ zoom 0.75
moved plane near -47.43048456112391 [ 0.05243786 -0.99027195 0.12888612]
moved plane far -47.43048456112391 [ 0.05243786 -0.99027195 0.12888612]
> surface #3.7.1-129 transparency 50
> ~surface #3.7
> surface #3.7.10
> show
> #!3/A:125,128-129,132,137,140-142,144-145,148-149,247-250,879-880,882-887,948-951,1302-1304,1338-1339,1341-1342,1345-1351
> view #!3.7.25 @ zoom 0.75
moved plane near -36.20430785226863 [ 0.05243786 -0.99027195 0.12888612]
moved plane far -36.20430785226863 [ 0.05243786 -0.99027195 0.12888612]
> ~surface #3.7
> surface #!3.7.25
> show #!3/A:284-285,288,304,659-665,773-774,822-826,829-831
> hide #!3#!3.7.1-129 atoms
> show #!3#!3.7.1-129 atoms
> hide #!3#!3.7.1-129 atoms
> show #!3#!3.7.1-129 atoms
> hide #!3#!3.7.1-129 atoms
> show #!3#!3.7.1-129 atoms
> view #!3.7.72 @ zoom 0.75
moved plane near -33.97728730761829 [-0.57936343 -0.37612158 -0.72309781]
moved plane far -33.97728730761829 [-0.57936343 -0.37612158 -0.72309781]
> ~surface #3.7
> surface #!3.7.72
> show
> #!3/A:865,930,933,938-940,980,983-985,1003-1006,1110-1111,1113-1114,1116-1118,1120-1122
> transparency #3 70
> view #!3.7.107 @ zoom 0.75
moved plane near -31.238523181737182 [ 0.2726029 -0.26201744 0.92576153]
moved plane far -31.238523181737182 [ 0.2726029 -0.26201744 0.92576153]
> ~surface #3.7
> surface #!3.7.107
> show
> #!3/A:458-461,1065-1067,1070-1071,1074-1075,1078,1232-1234,1236,1266,1396-1400
> view #!3.7.76 @ zoom 0.75
moved plane near -52.17645122739856 [ 0.2726029 -0.26201744 0.92576153]
moved plane far -52.17645122739856 [ 0.2726029 -0.26201744 0.92576153]
> ~surface #3.7
> surface #!3.7.76
> show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> hide #!3#!3.7.1-129 atoms
> view #!3.7.10 @ zoom 0.75
moved plane near -45.884873567237356 [ 0.13608676 -0.53920168 0.8311088 ]
moved plane far -45.884873567237356 [ 0.13608676 -0.53920168 0.8311088 ]
> ~surface #3.7
> surface #!3.7.10
> show
> #!3/A:125,128-129,132,137,140-142,144-145,148-149,247-250,879-880,882-887,948-951,1302-1304,1338-1339,1341-1342,1345-1351
> view #!3.7.76 @ zoom 0.75
moved plane near -49.979712529252 [ 0.13608676 -0.53920168 0.8311088 ]
moved plane far -49.979712529252 [ 0.13608676 -0.53920168 0.8311088 ]
> ~surface #3.7
> surface #!3.7.76
> show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> hide #!3#!3.7.1-129 atoms
> hide
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> hide #!3/A:987-988,999,1004,1008,1070,1077,1079-1080
> show #!3/A:987-988,999,1004,1008,1070,1077,1079-1080
> hide #!3/A:987-988,999,1004,1008,1070,1077,1079-1080
> show #!3/A:987-988,999,1004,1008,1070,1077,1079-1080
> select #!3.7.76
4661 atoms, 1 residue, 1 model selected
> ~select #!3.7.76
1 model selected
> select #!3 & (#!3.7.76 @ view #!3.7.10 @ zoom 0.75
moved plane near -51.62247161817882 [-0.88325281 -0.42696826 0.19381033]
moved plane far -51.62247161817882 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.10
> select #!3 & (#!3.7.10 @ show
> #!3/A:125,128-129,132,137,140-142,144-145,148-149,247-250,879-880,882-887,948-951,1302-1304,1338-1339,1341-1342,1345-1351
> view #!3.7.122 @ zoom 0.75
moved plane near -42.39954196207912 [-0.88325281 -0.42696826 0.19381033]
moved plane far -42.39954196207912 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.122
> select #!3 & (#!3.7.122 @ show
> #!3/A:1032-1033,1035,1040-1042,1044-1045,1047-1048,1067-1069,1072,1241,1261-1262,1264-1266,1384-1389,1391-1395,1398-1399
> view #!3.7.43 @ zoom 0.75
moved plane near -38.84930311579339 [-0.88325281 -0.42696826 0.19381033]
moved plane far -38.84930311579339 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.43
> select #!3 & (#!3.7.43 @ show
> #!3/A:373,376-381,662-667,669-670,672,809,812-819,822-823/B:374,395/C:434,437-439/D:371
> view #!3.7.35 @ zoom 0.75
moved plane near -35.728150129298534 [-0.88325281 -0.42696826 0.19381033]
moved plane far -35.728150129298534 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.35
> select #!3 & (#!3.7.35 @ show
> #!3/A:15-16,229-231,233-234,237-238,241,262,350-355,357-358,537,847-848,851-852,854
> view #!3.7.14 @ zoom 0.75
moved plane near -40.85434782024642 [-0.88325281 -0.42696826 0.19381033]
moved plane far -40.85434782024642 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.14
> select #!3 & (#!3.7.14 @ show
> #!3/A:250,344,348,834-835,841-846,848,877,880-882,1302-1307,1345,1348-1349
> view #!3.7.86 @ zoom 0.75
moved plane near -33.53184466066174 [-0.88325281 -0.42696826 0.19381033]
moved plane far -33.53184466066174 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.86
> select #!3 & (#!3.7.86 @ show
> #!3/B,E:339,342,346,349/C:339-340,342-343,346,349,353/D:339,342-343,346,349,353
> view #!3.7.87 @ zoom 0.75
moved plane near -43.53431079028464 [-0.88325281 -0.42696826 0.19381033]
moved plane far -43.53431079028464 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.87
> select #!3 & (#!3.7.87 @ show #!3/A:7-12,179-180,183,856,861-864,903,907-912,1009,1103-1108,1110
> view #!3.7.72 @ zoom 0.75
moved plane near -39.02140035584839 [-0.88325281 -0.42696826 0.19381033]
moved plane far -39.02140035584839 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.72
> select #!3 & (#!3.7.72 @ show
> #!3/A:865,930,933,938-940,980,983-985,1003-1006,1110-1111,1113-1114,1116-1118,1120-1122
> view #!3.7.107 @ zoom 0.75
moved plane near -33.85307340545291 [-0.88325281 -0.42696826 0.19381033]
moved plane far -33.85307340545291 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.107
> select #!3 & (#!3.7.107 @ show
> #!3/A:458-461,1065-1067,1070-1071,1074-1075,1078,1232-1234,1236,1266,1396-1400
> view #!3.7.1 @ zoom 0.75
moved plane near -42.02107543234164 [-0.88325281 -0.42696826 0.19381033]
moved plane far -42.02107543234164 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.1
> select #!3 & (#!3.7.1 @ show
> #!3/A:290-291,293-296,301,338-343,346,828,838-839,841,1197-1201,1352/C:469-472,505
> view #!3.7.68 @ zoom 0.75
moved plane near -34.842410491298615 [-0.88325281 -0.42696826 0.19381033]
moved plane far -34.842410491298615 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.68
> select #!3 & (#!3.7.68 @ show #!3/A:366,369-370,374,532,535,542-547,665-666,669,738-740,742
> view #!3.7.25 @ zoom 0.75
moved plane near -38.796713166446516 [-0.88325281 -0.42696826 0.19381033]
moved plane far -38.796713166446516 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.25
> select #!3 & (#!3.7.25 @ show #!3/A:284-285,288,304,659-665,773-774,822-826,829-831
> view #!3.7.103 @ zoom 0.75
moved plane near -31.379016548603776 [-0.88325281 -0.42696826 0.19381033]
moved plane far -31.379016548603776 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.103
> select #!3 & (#!3.7.103 @ show #!3/A:61,63-65,67-68,178,182,190-193,206-208
> view #!3.7.114 @ zoom 0.75
moved plane near -30.602661959589224 [-0.88325281 -0.42696826 0.19381033]
moved plane far -30.602661959589224 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.114
> select #!3 & (#!3.7.114 @ show #!3/A:469-472,475,478-479,492-496,501,531,548,550-551,706,708
> view #!3.7.58 @ zoom 0.75
moved plane near -29.334560084997218 [-0.88325281 -0.42696826 0.19381033]
moved plane far -29.334560084997218 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.58
> select #!3 & (#!3.7.58 @ show #!3/A:664-668,671,740-741,744,747-748,751-752,770,775
> view #!3.7.91 @ zoom 0.75
moved plane near -29.449843623056235 [-0.88325281 -0.42696826 0.19381033]
moved plane far -29.449843623056235 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.91
> select #!3 & (#!3.7.91 @ show #!3/A:557,560-561,564,676,693-697,742-747
> view #!3.7.85 @ zoom 0.75
moved plane near -35.714340154145575 [-0.88325281 -0.42696826 0.19381033]
moved plane far -35.714340154145575 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.85
> select #!3 & (#!3.7.85 @ show #!3/A:11-15,176,857-862,1010,1014,1082-1083,1086
> view #!3.7.93 @ zoom 0.75
moved plane near -31.365429070914004 [-0.88325281 -0.42696826 0.19381033]
moved plane far -31.365429070914004 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.93
> select #!3 & (#!3.7.93 @ show #!3/A:444-447,678,681-682,684-685/E:368-369,372,384-388
> view #!3.7.105 @ zoom 0.75
moved plane near -35.13960235467432 [-0.88325281 -0.42696826 0.19381033]
moved plane far -35.13960235467432 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.105
> select #!3 & (#!3.7.105 @ show #!3/A:517-518,520,522-523,673,690-691,694,698/E:371-378,383-386
> view #!3.7.42 @ zoom 0.75
moved plane near -27.497155377537485 [-0.88325281 -0.42696826 0.19381033]
moved plane far -27.497155377537485 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.42
> select #!3 & (#!3.7.42 @ show #!3/A:953-955,958-959,1159-1162,1165-1166,1331-1332,1335
> view #!3.7.27 @ zoom 0.75
moved plane near -33.433270398994125 [-0.88325281 -0.42696826 0.19381033]
moved plane far -33.433270398994125 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.27
> select #!3 & (#!3.7.27 @ show #!3/A:126-127,130-131,134-135,962,965-966,969-970,1130,1163-1164
> view #!3.7.20 @ zoom 0.75
moved plane near -29.336971875423405 [-0.88325281 -0.42696826 0.19381033]
moved plane far -29.336971875423405 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.20
> select #!3 & (#!3.7.20 @ show #!3/A:292,303-304,306-307,820-825/C:447-449
> view #!3.7.8 @ zoom 0.75
moved plane near -37.88152844356925 [-0.88325281 -0.42696826 0.19381033]
moved plane far -37.88152844356925 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.8
> select #!3 & (#!3.7.8 @ show #!3/A:313,316-317,321-324,326-328,331-332,335/C:458,461-462,465,469
> view #!3.7.23 @ zoom 0.75
moved plane near -25.608401902874178 [-0.88325281 -0.42696826 0.19381033]
moved plane far -25.608401902874178 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.23
> select #!3 & (#!3.7.23 @ show #!3/A:1166,1187-1188,1190,1318,1332-1333,1336-1337,1363-1365
> view #!3.7.65 @ zoom 0.75
moved plane near -28.732161869775613 [-0.88325281 -0.42696826 0.19381033]
moved plane far -28.732161869775613 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.65
> select #!3 & (#!3.7.65 @ show #!3/A:16,18-20,358-359,361,534-539,543-544
> view #!3.7.61 @ zoom 0.75
moved plane near -24.612427650326435 [-0.88325281 -0.42696826 0.19381033]
moved plane far -24.612427650326435 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.61
> select #!3 & (#!3.7.61 @ show #!3/A:38,84-87,90,94,221-223,227,231
> view #!3.7.116 @ zoom 0.75
moved plane near -24.182196034885532 [-0.88325281 -0.42696826 0.19381033]
moved plane far -24.182196034885532 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.116
> select #!3 & (#!3.7.116 @ show #!3/A:466,497,499-500,1080-1082,1084-1085,1088
> view #!3.7.73 @ zoom 0.75
moved plane near -25.3899086566253 [-0.88325281 -0.42696826 0.19381033]
moved plane far -25.3899086566253 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.73
> select #!3 & (#!3.7.73 @ show #!3/A:14,169,172-173,176,856,862,902,906-908
> view #!3.7.76 @ zoom 0.75
moved plane near -55.858724141153225 [-0.88325281 -0.42696826 0.19381033]
moved plane far -55.858724141153225 [-0.88325281 -0.42696826 0.19381033]
> ~surface #3.7
> surface #!3.7.76
> select #!3 & (#!3.7.76 @ show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> hide sel atoms
> ui mousemode right select
> select clear
> hide #!3#!3.7.1-129 atoms
> view #!3.7.10 @ zoom 0.75
moved plane near -45.78858069822143 [-0.84836261 0.49115877 0.19759502]
moved plane far -45.78858069822143 [-0.84836261 0.49115877 0.19759502]
> ~surface #3.7
> surface #!3.7.10
> select #!3 & (#!3.7.10 @ show
> #!3/A:125,128-129,132,137,140-142,144-145,148-149,247-250,879-880,882-887,948-951,1302-1304,1338-1339,1341-1342,1345-1351
> view #!3.7.76 @ zoom 0.75
moved plane near -48.21059853012333 [-0.84836261 0.49115877 0.19759502]
moved plane far -48.21059853012333 [-0.84836261 0.49115877 0.19759502]
> ~surface #3.7
> surface #!3.7.76
> select #!3 & (#!3.7.76 @ show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> select clear
> hide #!3#!3.7.1-129 atoms
> ui mousemode right clip
> ui mousemode right select
> view #3
> view #!3.7.76 @ zoom 0.75
moved plane near -48.61714161740499 [0.29750189 0.86401957 0.40615592]
moved plane far -48.61714161740499 [0.29750189 0.86401957 0.40615592]
> ~surface #3.7
> surface #!3.7.76
> ~select #!3 & (#!3.7.76 @ select #!3 & (#!3.7.76 @ hide
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> show
> #!3/A:865,935-936,957,987-989,992-997,999-1009,1011-1012,1014-1016,1018-1019,1034,1039,1042,1061,1064-1065,1069-1070,1072-1073,1076-1077,1079-1081,1102-1103,1106,1110,1145
> open "/Users/michael/Downloads/XYZ77823.1 and 456 other sequences.aln"
Failed opening file /Users/michael/Downloads/XYZ77823.1 and 456 other
sequences.aln:
Cannot open files: Syntax error in ALN file 'XYZ77823.1 and 456 other
sequences.aln': First non-blank line does not start with 'CLUSTAL'
> hide #!3 models
> open "/Users/michael/Downloads/model_01 (1).pdb"
model_01 (1).pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MenV L [more info...]
Chain information for model_01 (1).pdb #8
---
Chain | Description
A | No description available
Non-standard residues in model_01 (1).pdb #8
---
ZN — (ZN)
Computing secondary structure
Drag select of 61 residues
> select clear
> ui mousemode right clip
> ui tool show Matchmaker
> matchmaker #8#!1-2 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9DUS.pdb, chain A (#3) with model_01 (1).pdb, chain A (#8),
sequence alignment score = 3011.6
RMSD between 699 pruned atom pairs is 1.277 angstroms; (across all 1235 pairs:
4.230)
Matchmaker 9DUS.pdb, chain A (#3) with 9GJU.pdb, chain A (#1), sequence
alignment score = 5108.8
RMSD between 637 pruned atom pairs is 1.176 angstroms; (across all 1217 pairs:
3.171)
Matchmaker 9DUS.pdb, chain A (#3) with 9GJT.pdb, chain A (#2), sequence
alignment score = 5129.6
RMSD between 896 pruned atom pairs is 1.096 angstroms; (across all 1189 pairs:
2.456)
> show #!3 models
> show #!2 models
> show #!1 models
> ui mousemode right select
> select clear
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> surface hidePatches #3,8
Drag select of 13 atoms, 70 residues, 16 bonds
> select clear
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select
> #8/A:20-29,50-54,59-69,98-101,112-128,130-143,151-153,169-174,182-204,243-264,266-268,273-290,292-309,318-337,343-354,361-371,381-389,400-422,436-444,451-454,493-497,508-510,522-527,534-542,559-565,575-594,606-618,677-682,685-687,690-698,707-714,736-738,757-772,801-826,859-864,876-892,897-916,927-934,936-942,947-949,958-961,968-982,989-995,1003-1008,1021-1035,1041-1045,1048-1060,1069-1078,1080-1089,1095-1103,1109-1116,1118-1129,1138-1143,1151-1162,1164-1167,1180-1183,1252-1263,1271-1284,1346-1365,1453-1466,1499-1517,1526-1536,1540-1549,1555-1562,1581-1597,1623-1637,1651-1665,1671-1674,1677-1682,1684-1686,1693-1704,1710-1713,1784-1789,1800-1812,1830-1837,1851-1853,1857-1859,1865-1874,1901-1903,1905-1914,1937-1947,1967-1977,2006-2008,2017-2026,2038-2058,2068-2071,2096-2117,2141-2160,2164-2174,2185-2190,2201-2204,2209-2213,2218-2221,2223-2236
7804 atoms, 7845 bonds, 963 residues, 1 model selected
> select #8/A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:5-984
7853 atoms, 8010 bonds, 980 residues, 1 model selected
> color sel forest green
> select #8/A:985
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:985-1464
3798 atoms, 3877 bonds, 480 residues, 1 model selected
> color sel cornflower blue
> select clear
Drag select of 197 residues
> select #8/A:1425-1426
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/A:1425-1484
460 atoms, 463 bonds, 60 residues, 1 model selected
> select #8/A:1425-1426
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/A:1425-1724
2382 atoms, 2428 bonds, 300 residues, 1 model selected
> color sel yellow
> select #8/A:1725
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:1725-2004
2227 atoms, 2287 bonds, 280 residues, 1 model selected
> color sel orange
> select
> #8/A:20-29,50-54,59-69,98-101,112-128,130-143,151-153,169-174,182-204,243-264,266-268,273-290,292-309,318-337,343-354,361-371,381-389,400-422,436-444,451-454,493-497,508-510,522-527,534-542,559-565,575-594,606-618,677-682,685-687,690-698,707-714,736-738,757-772,801-826,859-864,876-892,897-916,927-934,936-942,947-949,958-961,968-982,989-995,1003-1008,1021-1035,1041-1045,1048-1060,1069-1078,1080-1089,1095-1103,1109-1116,1118-1129,1138-1143,1151-1162,1164-1167,1180-1183,1252-1263,1271-1284,1346-1365,1453-1466,1499-1517,1526-1536,1540-1549,1555-1562,1581-1597,1623-1637,1651-1665,1671-1674,1677-1682,1684-1686,1693-1704,1710-1713,1784-1789,1800-1812,1830-1837,1851-1853,1857-1859,1865-1874,1901-1903,1905-1914,1937-1947,1967-1977,2006-2008,2017-2026,2038-2058,2068-2071,2096-2117,2141-2160,2164-2174,2185-2190,2201-2204,2209-2213,2218-2221,2223-2236
7804 atoms, 7845 bonds, 963 residues, 1 model selected
> select #8/A:2005
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:2005-2030
201 atoms, 203 bonds, 26 residues, 1 model selected
> select #8/A:2005-2006
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:2005-2237
1885 atoms, 1915 bonds, 233 residues, 1 model selected
> color sel red
> select clear
> select #8/A:2005-2007
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #8/A:2005-2044
312 atoms, 315 bonds, 40 residues, 1 model selected
> select #8/A:2005-2006
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:2005-2038
259 atoms, 261 bonds, 34 residues, 1 model selected
> color sel orange
> select #8/A:2037-2038
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:2037-2041
43 atoms, 43 bonds, 5 residues, 1 model selected
> color sel red
> select clear
> select #8/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> select #8/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> select #8/A:1679-1680
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:1679-1680
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:1680
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:1679-1680
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:1678-1679
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:1678-1679
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> select #8/A:618
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save /Users/michael/Desktop/image1.png supersample 3
> open /Users/michael/Downloads/4UC6.pdb
4UC6.pdb title:
N-terminal globular domain of the RSV nucleoprotein [more info...]
Chain information for 4UC6.pdb #9
---
Chain | Description | UniProt
A | nucleoprotein | NCAP_HRSVA 31-252
B | nucleoprotein | NCAP_HRSVA 31-252
Non-standard residues in 4UC6.pdb #9
---
SO4 — sulfate ion
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3467 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> select clear
> show #7 models
> show #6 models
> show #!5 models
> show #!4 models
> hide #8 models
> ui tool show Matchmaker
> matchmaker #9 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7EXA.pdb, chain A (#6) with 4UC6.pdb, chain A (#9), sequence
alignment score = 165.8
RMSD between 18 pruned atom pairs is 1.215 angstroms; (across all 202 pairs:
11.887)
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #7 models
> ui tool show Matchmaker
> matchmaker #9 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01.pdb, chain A (#7) with 4UC6.pdb, chain A (#9), sequence
alignment score = 147.4
RMSD between 21 pruned atom pairs is 1.289 angstroms; (across all 207 pairs:
11.187)
> show #7 models
> hide #7 models
> hide #9 atoms
> show #7 models
> hide #7 models
Drag select of 442 residues
> color sel dark gray
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:109-110
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/A:109-110
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:134
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:134
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #9/A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
Drag select of 218 residues
> select clear
Drag select of 223 residues
> select #9/A:173
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/A:174
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
Drag select of 129 residues
Drag select of 221 residues
Drag select of 220 residues
> hide sel cartoons
> show #7 models
> hide #7 models
> select add #9
3632 atoms, 3537 bonds, 595 residues, 1 model selected
> select subtract #9
Nothing selected
> save /Users/michael/Desktop/image2.png supersample 3
> show #7 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> ui tool show Matchmaker
> matchmaker #9 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01.pdb, chain A (#7) with 4UC6.pdb, chain A (#9), sequence
alignment score = 147.4
RMSD between 21 pruned atom pairs is 1.289 angstroms; (across all 207 pairs:
11.187)
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
Drag select of 32 residues
> select clear
> save /Users/michael/Desktop/image3.png supersample 3
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/MeV L
> Elongation Homology 88309 Alpha PMI Top 5.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/MeV L Elongation Homology 88309 Alpha PMI Top 5.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 MeV L Elongation Homology 88309 Alpha PMI Top 5.pdb #10
---
Chain | Description
F | No description available
Computing secondary structure
> hide #7 models
> open "/Users/michael/Desktop/MOE Files/88309 and 88310 Docking/MeV L
> Elongation Homology 88310 Alpha PMI Top 5.pdb"
Summary of feedback from opening /Users/michael/Desktop/MOE Files/88309 and
88310 Docking/MeV L Elongation Homology 88310 Alpha PMI Top 5.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 MeV L Elongation Homology 88310 Alpha PMI Top 5.pdb #11
---
Chain | Description
F | No description available
Computing secondary structure
> surface #10-11
> ui mousemode right clip
> show #8 models
> hide #!10 models
> hide #!11 models
> show #!3 models
> hide #!3 models
> surface #8
> transparency #8 40
> transparency #8 70
> show #7 models
> hide #7 models
> show #!3 models
> surface hidePatches #3,8
> hide #!3 models
> open "/Users/michael/Downloads/MenV L Homology NiV L Elongation.pdb"
MenV L Homology NiV L Elongation.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MenV L NIV Elongation [more
info...]
Chain information for MenV L Homology NiV L Elongation.pdb #12
---
Chain | Description
F | No description available
Non-standard residues in MenV L Homology NiV L Elongation.pdb #12
---
MG — (MG)
ZN — (ZN)
Computing secondary structure
> open "/Users/michael/Downloads/MenV L Homology RSV L promoter
> Elongation.pdb"
MenV L Homology RSV L promoter Elongation.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MenV L Elongation RSV [more
info...]
Chain information for MenV L Homology RSV L promoter Elongation.pdb #13
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #12-13 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model_01 (1).pdb, chain A (#8) with MenV L Homology NiV L
Elongation.pdb, chain F (#12), sequence alignment score = 10015.8
RMSD between 642 pruned atom pairs is 1.214 angstroms; (across all 2233 pairs:
23.657)
Matchmaker model_01 (1).pdb, chain A (#8) with MenV L Homology RSV L promoter
Elongation.pdb, chain A (#13), sequence alignment score = 5471.8
RMSD between 333 pruned atom pairs is 1.358 angstroms; (across all 1216 pairs:
7.375)
> ui tool show "Show Sequence Viewer"
> sequence chain #12/F
Alignment identifier is 12/F
> sequence chain #13/A
Alignment identifier is 13/A
> select #13/A:1356
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:904-1356
3597 atoms, 3669 bonds, 453 residues, 1 model selected
> select #13/A:1372-1394
178 atoms, 181 bonds, 23 residues, 1 model selected
> select #13/A:1372-1394
178 atoms, 181 bonds, 23 residues, 1 model selected
> select #13/A:1024,1372-1394
189 atoms, 192 bonds, 24 residues, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel magenta
> select #12/F:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/F:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/F:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #12/F:1024,1147,1679
28 atoms, 26 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel magenta
> select #8/A:865
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:865-867
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #8/A:1601
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:1009-1601
4699 atoms, 4796 bonds, 593 residues, 1 model selected
> select #8/A:1604
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1604
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1009-1601
4699 atoms, 4796 bonds, 593 residues, 1 model selected
> select #8/A:1604
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1613-1634
165 atoms, 164 bonds, 22 residues, 1 model selected
> select #8/A:1613-1677
491 atoms, 496 bonds, 65 residues, 1 model selected
> select #8/A:1613-1677
491 atoms, 496 bonds, 65 residues, 1 model selected
> select #8/A:1613-1721
870 atoms, 886 bonds, 109 residues, 1 model selected
> select #8/A:1107-1904
6299 atoms, 6442 bonds, 798 residues, 1 model selected
> select #8/A:1107-1904
6299 atoms, 6442 bonds, 798 residues, 1 model selected
> select #8/A:1107-1904
6299 atoms, 6442 bonds, 798 residues, 1 model selected
> select #8/A:1618
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1618-1638
166 atoms, 167 bonds, 21 residues, 1 model selected
> select #8/A:1618
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1618
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1644
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:1603-1644
324 atoms, 328 bonds, 42 residues, 1 model selected
> select #8/A:1604
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1603-1604
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/A:1009-1601
4699 atoms, 4796 bonds, 593 residues, 1 model selected
> select #8/A:1600-1601
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #8/A:1600-1601
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #8/A:1600-1601
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #8/A:1604
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1009-1601
4699 atoms, 4796 bonds, 593 residues, 1 model selected
> select #13/A:179
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> color sel forest green
> select #13/A:964-984
158 atoms, 159 bonds, 21 residues, 1 model selected
> select #13/A:984-1394
3255 atoms, 3322 bonds, 411 residues, 1 model selected
> color sel cornflower blue
> ui mousemode right select
> select clear
> select #13/A:276-296
173 atoms, 176 bonds, 21 residues, 1 model selected
> select #13/A:237-296
485 atoms, 495 bonds, 60 residues, 1 model selected
> select #13/A:279-298
163 atoms, 165 bonds, 20 residues, 1 model selected
> select #13/A:279-298
163 atoms, 165 bonds, 20 residues, 1 model selected
> select #8/A:2103
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:2104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #13/A:1162
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:1142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:5-108
846 atoms, 867 bonds, 104 residues, 1 model selected
> select #8/A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:5-982
7836 atoms, 7993 bonds, 978 residues, 1 model selected
> color (#!8 & sel) forest green
> select #8/A:983-1003
171 atoms, 176 bonds, 21 residues, 1 model selected
> select #8/A:983-1452
3720 atoms, 3797 bonds, 470 residues, 1 model selected
> hide #!8 models
> hide #13 models
> show #13 models
> hide #12 models
> show #12 models
> hide #13 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #12/F:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> color sel forest green
> select #12/F:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:984-1495
4040 atoms, 4122 bonds, 512 residues, 1 model selected
> color sel cornflower blue
> select #12/F:1483
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/F:1483-1525
368 atoms, 379 bonds, 43 residues, 1 model selected
> hide #!8 models
> select
> #12/F:20-29,43-52,58-81,95-102,112-143,164-170,172-178,182-203,243-265,267-312,321-337,342-356,361-372,381-392,400-421,437-444,451-456,491-497,500-502,504-509,522-528,534-540,545-547,577-595,600-602,605-619,680-682,685-699,707-714,734-736,756-773,801-825,832-834,859-864,876-893,897-917,926-933,936-944,947-949,957-960,968-981,987-994,1003-1008,1021-1033,1050-1062,1069-1078,1080-1087,1097-1100,1112-1114,1128-1130,1151-1162,1164-1167,1198-1200,1251-1267,1271-1283,1334-1336,1351-1365,1442-1444,1447-1471,1475-1477,1490-1495,1498-1519,1525-1536,1541-1551,1554-1562,1579-1599,1615-1635,1637-1639,1649-1666,1670-1672,1674-1676,1693-1706,1748-1750,1786-1790,1799-1812,1829-1837,1865-1868,1896-1898,1904-1914,1934-1951,1970-1978,2015-2022,2029-2041,2051-2062,2069-2077,2092-2094,2099-2117,2124-2126,2137-2158,2165-2176,2198-2207,2223-2234
8203 atoms, 8254 bonds, 1017 residues, 1 model selected
> select #12/F:1483
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/F:1483-1619
1095 atoms, 1119 bonds, 137 residues, 1 model selected
> select #12/F:1483
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/F:1483-1762
2232 atoms, 2282 bonds, 280 residues, 1 model selected
> show #!8 models
> select #12/F:1483-1503
170 atoms, 173 bonds, 21 residues, 1 model selected
> select #12/F:1483-1742
2074 atoms, 2119 bonds, 260 residues, 1 model selected
> color sel yellow
> select #12/F:1743-1744
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #12/F:1743-2062
2550 atoms, 2613 bonds, 320 residues, 1 model selected
> select #12/F:2042-2082
332 atoms, 334 bonds, 41 residues, 1 model selected
> select #12/F:2042-2082
332 atoms, 334 bonds, 41 residues, 1 model selected
> select #12/F:2094
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:1783-2094
2476 atoms, 2531 bonds, 312 residues, 1 model selected
> color sel orange
> select #12/F:2179
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/F:2179-2180
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #12/F:2091
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2091-2238
1213 atoms, 1236 bonds, 148 residues, 1 model selected
> color sel red
> select clear
> select #12/F:1743
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/F:1743-1745
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #12/F:1743-1762
158 atoms, 162 bonds, 20 residues, 1 model selected
> color sel orange
> select #12/F:1763
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1763-1782
162 atoms, 165 bonds, 20 residues, 1 model selected
> color sel orange
> select clear
> select #12/F:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/F:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/F:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #12/F:1024,1147,1679-1680
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #12/F:1024,1147,1679-1680
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #12/F:1024,1147,1679-1680
33 atoms, 31 bonds, 4 residues, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1147,1679
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #12/F:1024,1147,1679
28 atoms, 26 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel magenta
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> show #12#!8 atoms
> undo
> show #13 models
> select clear
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1024,1147
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1024,1372-1394
189 atoms, 192 bonds, 24 residues, 1 model selected
> select
> #13/A:219-223,228-232,237-241,554-558,569-572,666-675,717-719,777-783,786-795,835-838,842-844,847-850,853-855,1185-1188,1205-1208,1329-1332,1389-1392
684 atoms, 684 bonds, 84 residues, 1 model selected
> select
> #13/A:180-183,188-208,243-266,274-289,291-296,298-312,316-337,346-357,361-372,381-392,400-421,437-444,455-461,478-481,494-496,505-510,522-527,536-543,575-592,602-606,610-616,661-663,679-682,685-699,708-710,712-714,756-774,804-826,858-861,876-894,897-913,918-930,936-944,947-949,958-960,968-983,989-992,1002-1008,1022-1035,1040-1045,1047-1061,1069-1078,1081-1093,1100-1102,1109-1127,1152-1163,1167-1169,1180-1183,1198-1200,1210-1213,1251-1267,1276-1284,1289-1295,1304-1307,1323-1328,1336-1340,1351-1366
4618 atoms, 4640 bonds, 573 residues, 1 model selected
> select clear
> surface #8,12-13
> help help:user
> select #8/A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:5-983
7845 atoms, 8002 bonds, 979 residues, 1 model selected
> transparency (#!8 & sel) 80
> select #8/A:985
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:985-1452
3703 atoms, 3780 bonds, 468 residues, 1 model selected
> transparency (#!8 & sel) 80
> select clear
> transparency #8,12-13 80
> hide #!12 models
> hide #!8 models
> select #13/A:983@O
1 atom, 1 residue, 1 model selected
> select #13/A:963-983
161 atoms, 162 bonds, 21 residues, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:984-1276
2322 atoms, 2372 bonds, 293 residues, 1 model selected
> select #13/A:984-1394
3255 atoms, 3322 bonds, 411 residues, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
Position Coverage for "chain A [1-805]"
---
Alignment | 1-805
chain A | 179-983
MenV L Homology RSV L promoter Elongation.pdb #13/A | ASN 179-LYS 983
Position Coverage for "chain A [1-805]"
---
Alignment | 1-805
chain A | 179-983
MenV L Homology RSV L promoter Elongation.pdb #13/A | ASN 179-LYS 983
> select clear
> transparency #13 20
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> color (#!13 & sel) forest green
> select #13/A:984-1394
3255 atoms, 3322 bonds, 411 residues, 1 model selected
> color (#!13 & sel) cornflower blue
> select clear
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!13 & sel) magenta
> show sel atoms
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:179-983
6439 atoms, 6562 bonds, 805 residues, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:179-983,1147
6447 atoms, 6569 bonds, 806 residues, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!13 & sel) magenta
> show #!12 models
> hide #!13 models
> select
> #12/F:20-29,43-52,58-81,95-102,112-143,164-170,172-178,182-203,243-265,267-312,321-337,342-356,361-372,381-392,400-421,437-444,451-456,491-497,500-502,504-509,522-528,534-540,545-547,577-595,600-602,605-619,680-682,685-699,707-714,734-736,756-773,801-825,832-834,859-864,876-893,897-917,926-933,936-944,947-949,957-960,968-981,987-994,1003-1008,1021-1033,1050-1062,1069-1078,1080-1087,1097-1100,1112-1114,1128-1130,1151-1162,1164-1167,1198-1200,1251-1267,1271-1283,1334-1336,1351-1365,1442-1444,1447-1471,1475-1477,1490-1495,1498-1519,1525-1536,1541-1551,1554-1562,1579-1599,1615-1635,1637-1639,1649-1666,1670-1672,1674-1676,1693-1706,1748-1750,1786-1790,1799-1812,1829-1837,1865-1868,1896-1898,1904-1914,1934-1951,1970-1978,2015-2022,2029-2041,2051-2062,2069-2077,2092-2094,2099-2117,2124-2126,2137-2158,2165-2176,2198-2207,2223-2234
8203 atoms, 8254 bonds, 1017 residues, 1 model selected
> select clear
> select #12/F:468@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #12/F:983@CA
1 atom, 1 residue, 1 model selected
> select #12/F:983
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:83-983
7201 atoms, 7342 bonds, 901 residues, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> select #12/F:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> select #12/F:515@CG
1 atom, 1 residue, 1 model selected
> select #12/F:983
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> color (#!12 & sel) forest green
> select clear
> select #12/F:1706@CB
1 atom, 1 residue, 1 model selected
> select #12/F:1706
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:982-1706
5730 atoms, 5847 bonds, 725 residues, 1 model selected
> select #12/F:981
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:183-981
6389 atoms, 6511 bonds, 799 residues, 1 model selected
> select #12/F:981
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:3-981
7844 atoms, 8002 bonds, 979 residues, 1 model selected
> select #12/F:982-1706
5730 atoms, 5847 bonds, 725 residues, 1 model selected
> select clear
> select #12/F:983@C
1 atom, 1 residue, 1 model selected
> select #12/F:983
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> select #12/F:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:984-1706
5716 atoms, 5833 bonds, 723 residues, 1 model selected
> color (#!12 & sel) cornflower blue
> select #12/F:183-981
6389 atoms, 6511 bonds, 799 residues, 1 model selected
> select #12/F:982-1706
5730 atoms, 5847 bonds, 725 residues, 1 model selected
> select #12/F:3-983
7858 atoms, 8016 bonds, 981 residues, 1 model selected
> select clear
> select #12/F:1707@CA
1 atom, 1 residue, 1 model selected
> select #12/F:1742@O
1 atom, 1 residue, 1 model selected
> select #12/F:984-1706
5716 atoms, 5833 bonds, 723 residues, 1 model selected
> select #12/F:1440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:984-1462
3789 atoms, 3868 bonds, 479 residues, 1 model selected
> color (#!12 & sel) cornflower blue
> select #12/F:1440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1323-1363
329 atoms, 333 bonds, 41 residues, 1 model selected
> select #12/F:1243-1363
954 atoms, 970 bonds, 121 residues, 1 model selected
> select #12/F:1463
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1463
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1243-1363
954 atoms, 970 bonds, 121 residues, 1 model selected
> select #12/F:1463
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1463
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1239@NH2
1 atom, 1 residue, 1 model selected
> select #13/A:984-1394
3255 atoms, 3322 bonds, 411 residues, 1 model selected
> select #12/F:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:984-1382
3172 atoms, 3237 bonds, 399 residues, 1 model selected
> select #12/F:1463
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/F:1463-1746
2249 atoms, 2294 bonds, 284 residues, 1 model selected
> color (#!12 & sel) yellow
> select #12/F:1727-1747
154 atoms, 155 bonds, 21 residues, 1 model selected
> select #12/F:1747-2098
2808 atoms, 2874 bonds, 352 residues, 1 model selected
> select clear
> select #12/F:1787
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/F:1787-1809
181 atoms, 187 bonds, 23 residues, 1 model selected
> select #12/F:1747
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/F:1747-2101
2835 atoms, 2901 bonds, 355 residues, 1 model selected
> color (#!12 & sel) orange
> select #12/F:2102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:2102-2162
492 atoms, 498 bonds, 61 residues, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2102-2238
1119 atoms, 1140 bonds, 137 residues, 1 model selected
> color (#!12 & sel) orange red
> color (#!12 & sel) red
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:2102-2238
1119 atoms, 1140 bonds, 137 residues, 1 model selected
> select #12/F:2102-2238
1119 atoms, 1140 bonds, 137 residues, 1 model selected
> select #12/F:2180-2200
169 atoms, 172 bonds, 21 residues, 1 model selected
> select #12/F:2102-2238
1119 atoms, 1140 bonds, 137 residues, 1 model selected
> select #12/F:2180-2200
169 atoms, 172 bonds, 21 residues, 1 model selected
> select #12/F:2102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:2102-2238
1119 atoms, 1140 bonds, 137 residues, 1 model selected
> select #12/F:2238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1679-1680
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/F:1679-1680
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/F:1147,1679
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #12/F:1024,1147,1679
28 atoms, 26 bonds, 3 residues, 1 model selected
> color (#!12 & sel) magenta
> show sel atoms
> select #12/F:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/F:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> transparency #12 20
> show #!13 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> hide #!12 models
> hide #!13 models
> show #!1 models
> show #!2 models
> hide #!1 models
Drag select of 238 residues
Drag select of 91 residues
> select clear
> hide #!2 models
> show #!8 models
> show #!12 models
> show #!13 models
> transparency #8,12-13 60
> hide #!13 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> select #8/A:985-1452
3703 atoms, 3780 bonds, 468 residues, 1 model selected
> select #8/A:5-983
7845 atoms, 8002 bonds, 979 residues, 1 model selected
> select #8/A:1059
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:1039-1059
166 atoms, 167 bonds, 21 residues, 1 model selected
> select #8/A:984
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:984-1330
2749 atoms, 2808 bonds, 347 residues, 1 model selected
> color (#!8 & sel) cornflower blue
> select #8/A:1424@C
1 atom, 1 residue, 1 model selected
> select #8/A:1331-1332
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:1331-1424
741 atoms, 756 bonds, 94 residues, 1 model selected
> color (#!8 & sel) cornflower blue
> select #8/A:1425@CA
1 atom, 1 residue, 1 model selected
> select #8/A:1725@N
1 atom, 1 residue, 1 model selected
> select #8/A:1425
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1425-1725
2391 atoms, 2437 bonds, 301 residues, 1 model selected
> color (#!8 & sel) yellow
> select #8/A:1679@CG
1 atom, 1 residue, 1 model selected
> color (#!8 & sel) magenta
> select clear
Drag select of model_01 (1).pdb_A SES surface, 16 of 2364674 triangles
> select #8/A:1679@CA
1 atom, 1 residue, 1 model selected
> select #8/A:1679@CB
1 atom, 1 residue, 1 model selected
> select #8/A:1678@O
1 atom, 1 residue, 1 model selected
> select #8/A:1735
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1735
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:1679
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!8 & sel) magenta
> select clear
> select #8/A:1728@OD1
1 atom, 1 residue, 1 model selected
> select #8/A:1725@CG
1 atom, 1 residue, 1 model selected
> select #8/A:1728@CG
1 atom, 1 residue, 1 model selected
> select #8/A:1726
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:1726-1728
28 atoms, 29 bonds, 3 residues, 1 model selected
> select #8/A:2037@CE
1 atom, 1 residue, 1 model selected
> select #8/A:1726-1747
164 atoms, 166 bonds, 22 residues, 1 model selected
> select #8/A:1726-2037
2470 atoms, 2533 bonds, 312 residues, 1 model selected
> color (#!8 & sel) orange
> select #8/A:2038
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:2038-2237
1633 atoms, 1660 bonds, 200 residues, 1 model selected
> color (#!8 & sel) red
> select clear
> select #8/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:1024
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!8 & sel) magenta
> select #8/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1147
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!8 & sel) magenta
> select #8/A:983@CE
1 atom, 1 residue, 1 model selected
> select #8/A:982-984
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #8/A:981-984
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #8/A:983
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:982-983
14 atoms, 13 bonds, 2 residues, 1 model selected
> color (#!8 & sel) forest green
> select clear
> show #!12 models
> show #!13 models
> transparency #8,12-13 0
> ui tool show "Find Cavities"
> kvfinder #8,12-13
206 cavities found for model_01 (1).pdb #8
model_01 (1).pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
8.2.8 | | 17448 | 14274.6 | 80778 | 13.76 | 4.49
8.2.79 | | 2165.62 | 1988.94 | 10026 | 14.06 | 2.9
8.2.6 | | 1563.62 | 1349.06 | 7239 | 14.5 | 4.17
8.2.15 | | 1018.87 | 842.45 | 4717 | 10.06 | 3.18
8.2.129 | | 896.62 | 906.85 | 4151 | 11.16 | 3.95
8.2.165 | | 814.75 | 634.99 | 3772 | 12.3 | 5.81
8.2.102 | | 651.46 | 609.58 | 3016 | 16.78 | 6.61
8.2.14 | | 492.91 | 464.05 | 2282 | 14.51 | 6.08
8.2.170 | | 485.57 | 532.78 | 2248 | 10.63 | 4.56
8.2.156 | | 464.83 | 384.33 | 2152 | 6.38 | 1.51
8.2.188 | | 420.55 | 425.1 | 1947 | 9.66 | 4.81
8.2.34 | | 402.62 | 263.1 | 1864 | 5.91 | 1.83
8.2.85 | | 398.09 | 310.08 | 1843 | 8.4 | 3.29
8.2.139 | | 378.86 | 368.32 | 1754 | 7.8 | 2.09
8.2.206 | | 353.59 | 385.15 | 1637 | 6.03 | 1.81
8.2.107 | | 350.57 | 432.61 | 1623 | 11.08 | 6.67
8.2.150 | | 330.26 | 418.42 | 1529 | 16.67 | 9.05
8.2.193 | | 320.98 | 302.17 | 1486 | 8.61 | 3.34
8.2.201 | | 290.74 | 219.79 | 1346 | 5.94 | 2.17
8.2.190 | | 284.26 | 323.27 | 1316 | 0 | 0
8.2.10 | | 268.92 | 232.6 | 1245 | 5.66 | 2.19
8.2.91 | | 250.78 | 265.73 | 1161 | 4.02 | 1.11
8.2.89 | | 246.89 | 271.02 | 1143 | 12.25 | 5.06
8.2.2 | | 232.63 | 271.17 | 1077 | 8 | 3.64
8.2.114 | | 231.55 | 239.36 | 1072 | 8.18 | 2.63
8.2.168 | | 217.08 | 270.12 | 1005 | 4.28 | 1.19
8.2.44 | | 209.52 | 210.38 | 970 | 9.97 | 4.43
8.2.141 | | 196.56 | 165.32 | 910 | 3.6 | 0.88
8.2.121 | | 181.44 | 195.88 | 840 | 0 | 0
8.2.92 | | 179.28 | 189.13 | 830 | 0 | 0
8.2.12 | | 178.85 | 178.37 | 828 | 6.41 | 2.81
8.2.11 | | 175.82 | 226.25 | 814 | 12.94 | 6.08
8.2.24 | | 175.39 | 199.83 | 812 | 0 | 0
8.2.106 | | 167.62 | 206.53 | 776 | 0 | 0
8.2.126 | | 155.09 | 158.12 | 718 | 4.24 | 1.29
8.2.192 | | 154.66 | 147.47 | 716 | 5.2 | 1.88
8.2.145 | | 148.82 | 155.06 | 689 | 0 | 0
8.2.152 | | 147.31 | 147.9 | 682 | 4.28 | 1.82
8.2.130 | | 144.5 | 152.71 | 669 | 0 | 0
8.2.35 | | 137.59 | 125.75 | 637 | 3.84 | 1.48
8.2.118 | | 131.76 | 113.34 | 610 | 2.75 | 0.95
8.2.174 | | 128.52 | 173.68 | 595 | 6.63 | 3.48
8.2.128 | | 127.44 | 140.35 | 590 | 3.45 | 0.85
8.2.45 | | 124.42 | 149.72 | 576 | 3.23 | 1.05
8.2.105 | | 122.47 | 156.79 | 567 | 0 | 0
8.2.176 | | 116.42 | 138.77 | 539 | 0 | 0
8.2.155 | | 113.18 | 135.14 | 524 | 3.5 | 0.74
8.2.122 | | 104.76 | 141.22 | 485 | 8.09 | 4.15
8.2.49 | | 101.95 | 121.95 | 472 | 6.38 | 2.8
8.2.86 | | 101.52 | 154.21 | 470 | 0 | 0
8.2.169 | | 101.09 | 139.71 | 468 | 0 | 0
8.2.1 | | 96.34 | 118.12 | 446 | 3.65 | 0.97
8.2.72 | | 91.8 | 113.92 | 425 | 4.57 | 2.31
8.2.41 | | 91.58 | 153.03 | 424 | 7.61 | 3.24
8.2.200 | | 89.64 | 96.6 | 415 | 3.6 | 0.99
8.2.204 | | 89.64 | 130.27 | 415 | 5.4 | 2.32
8.2.43 | | 88.99 | 120.98 | 412 | 7.68 | 3.26
8.2.124 | | 87.91 | 114.21 | 407 | 3.06 | 0.85
8.2.182 | | 85.1 | 127.41 | 394 | 5.37 | 1.21
8.2.162 | | 81.86 | 106.74 | 379 | 0 | 0
8.2.138 | | 81 | 90.77 | 375 | 3 | 0.78
8.2.93 | | 76.25 | 92.04 | 353 | 4.57 | 1.25
8.2.31 | | 75.38 | 101.4 | 349 | 0 | 0
8.2.55 | | 74.52 | 107.09 | 345 | 3.89 | 1.44
8.2.111 | | 73.87 | 83.06 | 342 | 2.75 | 1.21
8.2.136 | | 71.71 | 100.45 | 332 | 7.25 | 3.17
8.2.23 | | 70.85 | 100.09 | 328 | 2.47 | 0.57
8.2.95 | | 69.98 | 89.01 | 324 | 0 | 0
8.2.109 | | 69.34 | 87.37 | 321 | 4.41 | 1.35
8.2.74 | | 66.96 | 102 | 310 | 0 | 0
8.2.104 | | 66.31 | 96.86 | 307 | 0 | 0
8.2.100 | | 63.5 | 81.36 | 294 | 0 | 0
8.2.191 | | 62.21 | 93.97 | 288 | 0 | 0
8.2.144 | | 60.7 | 75.59 | 281 | 0 | 0
8.2.187 | | 60.26 | 75.41 | 279 | 1.7 | 0.48
8.2.3 | | 59.4 | 87.96 | 275 | 0 | 0
8.2.57 | | 59.4 | 77.23 | 275 | 0 | 0
8.2.157 | | 58.32 | 80.78 | 270 | 4.02 | 1.98
8.2.127 | | 56.59 | 88.22 | 262 | 0 | 0
8.2.20 | | 56.16 | 76.74 | 260 | 3.7 | 1.58
8.2.172 | | 55.51 | 85.74 | 257 | 5.97 | 2.4
8.2.58 | | 54.65 | 73.64 | 253 | 5.4 | 2.43
8.2.90 | | 54.43 | 77.64 | 252 | 5.66 | 2.55
8.2.17 | | 54.22 | 69.38 | 251 | 2.81 | 0.92
8.2.97 | | 49.68 | 88.84 | 230 | 0 | 0
8.2.63 | | 48.82 | 60.86 | 226 | 3.39 | 1.38
8.2.36 | | 47.74 | 60.43 | 221 | 2.16 | 0.57
8.2.195 | | 46.87 | 68.62 | 217 | 4.61 | 2.37
8.2.13 | | 46.66 | 54.98 | 216 | 2.81 | 1
8.2.137 | | 44.28 | 52.16 | 205 | 2.4 | 0.84
8.2.125 | | 42.77 | 75.98 | 198 | 0 | 0
8.2.140 | | 42.12 | 49.41 | 195 | 1.8 | 0.64
8.2.184 | | 40.61 | 78.3 | 188 | 0 | 0
8.2.78 | | 39.1 | 70.99 | 181 | 0 | 0
8.2.186 | | 38.23 | 59.09 | 177 | 0 | 0
8.2.53 | | 37.8 | 57.39 | 175 | 0 | 0
8.2.119 | | 37.58 | 67.55 | 174 | 0 | 0
8.2.26 | | 37.37 | 55.21 | 173 | 0 | 0
8.2.4 | | 37.15 | 55.26 | 172 | 0 | 0
8.2.65 | | 36.5 | 53.94 | 169 | 3.12 | 1.77
8.2.146 | | 35.64 | 58.27 | 165 | 4.28 | 2.18
8.2.198 | | 35.64 | 48.05 | 165 | 1.34 | 0.29
8.2.56 | | 35.21 | 49.07 | 163 | 1.7 | 0.43
8.2.117 | | 35.21 | 59.8 | 163 | 0 | 0
8.2.69 | | 34.34 | 52.52 | 159 | 2.55 | 0.86
8.2.175 | | 34.34 | 56.08 | 159 | 0 | 0
8.2.38 | | 33.7 | 48.61 | 156 | 0 | 0
8.2.40 | | 33.48 | 58.35 | 155 | 0 | 0
8.2.37 | | 32.4 | 57.41 | 150 | 0 | 0
8.2.143 | | 31.54 | 56.15 | 146 | 0 | 0
8.2.164 | | 30.89 | 44.75 | 143 | 1.34 | 0.35
8.2.52 | | 30.67 | 51.4 | 142 | 0 | 0
8.2.133 | | 28.94 | 39.13 | 134 | 1.2 | 0.38
8.2.199 | | 28.94 | 55.75 | 134 | 0 | 0
8.2.66 | | 28.73 | 47.27 | 133 | 2.68 | 1.17
8.2.77 | | 27.65 | 38.46 | 128 | 1.8 | 0.44
8.2.73 | | 27 | 48.36 | 125 | 0 | 0
8.2.71 | | 26.35 | 37.77 | 122 | 1.2 | 0.31
8.2.19 | | 26.14 | 32.63 | 121 | 1.8 | 0.47
8.2.178 | | 26.14 | 46.24 | 121 | 0 | 0
8.2.202 | | 24.84 | 44.52 | 115 | 0 | 0
8.2.96 | | 24.19 | 36.19 | 112 | 2.4 | 0.89
8.2.21 | | 23.98 | 46.07 | 111 | 0 | 0
8.2.181 | | 23.11 | 40.33 | 107 | 0 | 0
8.2.116 | | 22.9 | 41.28 | 106 | 0 | 0
8.2.158 | | 22.9 | 35.2 | 106 | 1.8 | 0.7
8.2.163 | | 22.9 | 40.08 | 106 | 0 | 0
8.2.183 | | 22.9 | 39.3 | 106 | 0 | 0
8.2.81 | | 22.46 | 35.7 | 104 | 0 | 0
8.2.80 | | 21.82 | 30.12 | 101 | 1.7 | 0.64
8.2.50 | | 21.17 | 39.07 | 98 | 0 | 0
8.2.113 | | 21.17 | 39.07 | 98 | 0 | 0
8.2.29 | | 20.74 | 30.92 | 96 | 1.34 | 0.45
8.2.32 | | 20.74 | 41.19 | 96 | 0 | 0
8.2.51 | | 19.87 | 37.54 | 92 | 1.8 | 0.56
8.2.99 | | 19.87 | 36.19 | 92 | 0 | 0
8.2.103 | | 19.87 | 36.19 | 92 | 0 | 0
8.2.167 | | 19.66 | 29.04 | 91 | 2.47 | 1.01
8.2.88 | | 19.22 | 23.84 | 89 | 1.2 | 0.3
8.2.189 | | 19.22 | 29.52 | 89 | 1.99 | 0.71
8.2.70 | | 18.14 | 28.67 | 84 | 1.7 | 0.53
8.2.83 | | 17.71 | 42.04 | 82 | 3.7 | 1.77
8.2.27 | | 17.28 | 36.68 | 80 | 0 | 0
8.2.25 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.42 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.47 | | 16.85 | 34.43 | 78 | 1.34 | 0.4
8.2.62 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.87 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.112 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.132 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.149 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.179 | | 16.85 | 32.3 | 78 | 0 | 0
8.2.151 | | 15.98 | 27.31 | 74 | 1.7 | 0.72
8.2.9 | | 15.55 | 30.03 | 72 | 2.47 | 1.21
8.2.173 | | 15.34 | 26.99 | 71 | 2.16 | 1
8.2.59 | | 15.12 | 26.99 | 70 | 2.16 | 0.99
8.2.196 | | 15.12 | 27.16 | 70 | 1.34 | 0.5
8.2.153 | | 14.69 | 28.12 | 68 | 1.2 | 0.22
8.2.185 | | 14.69 | 27.15 | 68 | 1.2 | 0.28
8.2.48 | | 14.04 | 25.21 | 65 | 1.2 | 0.31
8.2.120 | | 14.04 | 25.74 | 65 | 1.34 | 0.44
8.2.160 | | 13.82 | 24.53 | 64 | 1.2 | 0.22
8.2.46 | | 13.61 | 23.84 | 63 | 1.04 | 0.4
8.2.28 | | 13.18 | 21.81 | 61 | 0.85 | 0.22
8.2.131 | | 13.18 | 19.85 | 61 | 0.85 | 0.26
8.2.134 | | 13.18 | 22.33 | 61 | 1.7 | 0.61
8.2.33 | | 12.96 | 19.73 | 60 | 1.34 | 0.5
8.2.39 | | 12.74 | 17.9 | 59 | 1.2 | 0.26
8.2.54 | | 12.53 | 25.88 | 58 | 2.16 | 1.01
8.2.22 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.60 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.61 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.64 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.75 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.76 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.84 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.101 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.108 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.135 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.148 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.154 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.159 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.166 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.177 | | 12.31 | 29.54 | 57 | 0 | 0
8.2.194 | | 10.8 | 19.46 | 50 | 0.6 | 0.11
8.2.94 | | 10.58 | 20.24 | 49 | 1.2 | 0.39
8.2.171 | | 10.37 | 20.06 | 48 | 0.6 | 0.17
8.2.18 | | 10.15 | 15.9 | 47 | 0.6 | 0.18
8.2.180 | | 10.15 | 18.67 | 47 | 1.2 | 0.38
8.2.98 | | 9.29 | 17.38 | 43 | 0.85 | 0.33
8.2.68 | | 9.07 | 17.34 | 42 | 0.6 | 0.11
8.2.123 | | 8.42 | 17.5 | 39 | 0.85 | 0.25
8.2.197 | | 8.21 | 19.51 | 38 | 1.34 | 0.49
8.2.7 | | 7.78 | 14.79 | 36 | 0.6 | 0.18
8.2.82 | | 7.78 | 11.32 | 36 | 0.6 | 0.13
8.2.110 | | 7.56 | 14.05 | 35 | 1.2 | 0.38
8.2.115 | | 7.56 | 14.48 | 35 | 1.2 | 0.28
8.2.5 | | 7.34 | 16.24 | 34 | 1.34 | 0.52
8.2.16 | | 7.34 | 14.79 | 34 | 0.6 | 0.14
8.2.30 | | 6.7 | 14.51 | 31 | 0.6 | 0.12
8.2.147 | | 6.7 | 14.81 | 31 | 0.85 | 0.35
8.2.161 | | 6.7 | 12.94 | 31 | 0.6 | 0.19
8.2.205 | | 6.7 | 14.97 | 31 | 0.85 | 0.25
8.2.142 | | 6.05 | 15.32 | 28 | 0.6 | 0.02
8.2.203 | | 5.83 | 12.28 | 27 | 0.6 | 0.13
8.2.67 | | 5.62 | 13.81 | 26 | 0.85 | 0.3
193 cavities found for MenV L Homology NiV L Elongation.pdb #12
MenV L Homology NiV L Elongation.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
12.2.16 | | 3560.76 | 3118.97 | 16485 | 14.93 | 4.2
12.2.53 | | 3130.49 | 2383.45 | 14493 | 12.21 | 4.5
12.2.117 | | 1376.35 | 1189.3 | 6372 | 4.37 | 1.11
12.2.89 | | 798.55 | 565.65 | 3697 | 4.69 | 1.31
12.2.68 | | 738.29 | 633.56 | 3418 | 7.64 | 1.87
12.2.143 | | 707.83 | 631.19 | 3277 | 8.51 | 1.83
12.2.22 | | 657.07 | 687.17 | 3042 | 7.05 | 3.28
12.2.4 | | 428.54 | 372.54 | 1984 | 6.26 | 2.45
12.2.172 | | 395.28 | 342.8 | 1830 | 5.79 | 1.65
12.2.5 | | 326.59 | 317.94 | 1512 | 13.25 | 3.67
12.2.59 | | 323.35 | 325.36 | 1497 | 0 | 0
12.2.30 | | 301.97 | 334.63 | 1398 | 7.02 | 1.71
12.2.189 | | 287.06 | 350.04 | 1329 | 7.73 | 3.21
12.2.95 | | 283.61 | 230.66 | 1313 | 6.15 | 1.95
12.2.13 | | 280.15 | 227.85 | 1297 | 5.69 | 1.75
12.2.32 | | 276.7 | 346.46 | 1281 | 7.85 | 2.61
12.2.116 | | 253.58 | 210.01 | 1174 | 4.41 | 1.82
12.2.56 | | 228.31 | 239.9 | 1057 | 0 | 0
12.2.79 | | 221.4 | 215.04 | 1025 | 0 | 0
12.2.63 | | 217.51 | 235.87 | 1007 | 0 | 0
12.2.76 | | 192.24 | 228.5 | 890 | 5.66 | 1.99
12.2.174 | | 176.9 | 154.15 | 819 | 5.5 | 1.69
12.2.176 | | 166.32 | 176.04 | 770 | 5.82 | 2.48
12.2.11 | | 158.33 | 153.54 | 733 | 5.4 | 2.08
12.2.102 | | 143.86 | 195.18 | 666 | 10.56 | 5.2
12.2.101 | | 140.62 | 183.06 | 651 | 0 | 0
12.2.145 | | 139.75 | 139.24 | 647 | 6.24 | 2.43
12.2.119 | | 131.98 | 163.25 | 611 | 9.18 | 4.59
12.2.159 | | 131.11 | 164.37 | 607 | 7.73 | 3.77
12.2.124 | | 124.2 | 117.92 | 575 | 4.33 | 1.43
12.2.61 | | 122.47 | 144.06 | 567 | 0 | 0
12.2.109 | | 115.78 | 60.94 | 536 | 1.2 | 0.32
12.2.81 | | 108.86 | 157.21 | 504 | 7.8 | 3.13
12.2.167 | | 106.92 | 136.8 | 495 | 4.33 | 1.84
12.2.183 | | 106.49 | 119.9 | 493 | 5.16 | 1.6
12.2.6 | | 102.6 | 125.59 | 475 | 0 | 0
12.2.135 | | 99.14 | 117.96 | 459 | 0 | 0
12.2.104 | | 97.42 | 121.07 | 451 | 0 | 0
12.2.168 | | 95.69 | 112.13 | 443 | 3.5 | 1.12
12.2.93 | | 93.96 | 128.83 | 435 | 7.64 | 2.79
12.2.158 | | 85.1 | 114.35 | 394 | 5.69 | 1.93
12.2.149 | | 81.86 | 131.57 | 379 | 7.15 | 2.43
12.2.21 | | 78.62 | 108.14 | 364 | 7.02 | 2.62
12.2.9 | | 78.19 | 93.56 | 362 | 4.57 | 1.44
12.2.169 | | 74.74 | 95.67 | 346 | 4.49 | 1.78
12.2.190 | | 74.09 | 78.11 | 343 | 3.7 | 1.42
12.2.118 | | 71.93 | 97.31 | 333 | 0 | 0
12.2.57 | | 70.42 | 84.66 | 326 | 3.65 | 1.42
12.2.127 | | 64.8 | 75.29 | 300 | 3 | 0.89
12.2.48 | | 64.37 | 103.28 | 298 | 3.55 | 0.92
12.2.123 | | 63.72 | 84.62 | 295 | 0 | 0
12.2.44 | | 63.07 | 77.79 | 292 | 4.57 | 1.84
12.2.182 | | 60.26 | 92.8 | 279 | 0 | 0
12.2.41 | | 56.38 | 58.11 | 261 | 2.68 | 0.74
12.2.110 | | 55.73 | 81.02 | 258 | 3.5 | 1.08
12.2.121 | | 55.51 | 91.02 | 257 | 6.15 | 2.67
12.2.153 | | 54.43 | 74.68 | 252 | 0 | 0
12.2.113 | | 53.57 | 76.45 | 248 | 2.24 | 0.81
12.2.96 | | 52.92 | 71.94 | 245 | 0 | 0
12.2.83 | | 52.49 | 73.4 | 243 | 0 | 0
12.2.77 | | 52.06 | 69.57 | 241 | 5.37 | 2.27
12.2.75 | | 50.54 | 79.85 | 234 | 1.9 | 0.55
12.2.152 | | 48.82 | 66.49 | 226 | 0 | 0
12.2.134 | | 47.3 | 61.43 | 219 | 1.8 | 0.54
12.2.137 | | 46.66 | 67.73 | 216 | 5.02 | 2.21
12.2.155 | | 46.66 | 66.57 | 216 | 4.37 | 1.82
12.2.36 | | 45.14 | 70.71 | 209 | 5.4 | 2.52
12.2.114 | | 44.06 | 72.27 | 204 | 5.16 | 1.82
12.2.14 | | 43.42 | 52.17 | 201 | 1.47 | 0.52
12.2.73 | | 42.34 | 50.96 | 196 | 2.4 | 0.55
12.2.154 | | 42.34 | 75.85 | 196 | 2.75 | 0.8
12.2.67 | | 42.12 | 62.35 | 195 | 3.55 | 1.65
12.2.18 | | 41.9 | 45.58 | 194 | 3 | 0.92
12.2.50 | | 40.61 | 53.55 | 188 | 1.8 | 0.51
12.2.84 | | 39.31 | 57.96 | 182 | 4.02 | 1.9
12.2.65 | | 38.23 | 59.56 | 177 | 0 | 0
12.2.86 | | 36.72 | 43.02 | 170 | 3 | 0.84
12.2.108 | | 35.42 | 58.84 | 164 | 0 | 0
12.2.150 | | 35.21 | 53.37 | 163 | 0 | 0
12.2.62 | | 34.56 | 52.11 | 160 | 0 | 0
12.2.17 | | 32.83 | 53.5 | 152 | 0 | 0
12.2.130 | | 32.62 | 51.72 | 151 | 4.02 | 2.14
12.2.148 | | 32.62 | 56.39 | 151 | 0 | 0
12.2.33 | | 32.18 | 65.73 | 149 | 0 | 0
12.2.25 | | 31.75 | 29.87 | 147 | 1.2 | 0.31
12.2.55 | | 31.75 | 42.76 | 147 | 1.34 | 0.42
12.2.88 | | 31.75 | 42.56 | 147 | 1.2 | 0.3
12.2.161 | | 31.75 | 42.3 | 147 | 2.47 | 0.81
12.2.157 | | 31.54 | 52.72 | 146 | 3 | 1.24
12.2.111 | | 31.1 | 47.85 | 144 | 0 | 0
12.2.43 | | 30.02 | 38.93 | 139 | 1.8 | 0.55
12.2.51 | | 29.38 | 36.09 | 136 | 1.47 | 0.42
12.2.162 | | 29.38 | 63.66 | 136 | 0 | 0
12.2.105 | | 28.08 | 54.13 | 130 | 0 | 0
12.2.34 | | 27.43 | 49.72 | 127 | 0 | 0
12.2.180 | | 25.49 | 40.78 | 118 | 0 | 0
12.2.99 | | 24.62 | 58.13 | 114 | 0 | 0
12.2.2 | | 23.54 | 34.25 | 109 | 2.47 | 0.9
12.2.78 | | 23.54 | 34.15 | 109 | 1.34 | 0.32
12.2.91 | | 23.54 | 44.22 | 109 | 0 | 0
12.2.12 | | 23.11 | 40.33 | 107 | 0 | 0
12.2.115 | | 23.11 | 42.35 | 107 | 0 | 0
12.2.188 | | 23.11 | 40.33 | 107 | 0 | 0
12.2.39 | | 22.9 | 34.66 | 106 | 1.7 | 0.48
12.2.72 | | 22.9 | 41.28 | 106 | 0 | 0
12.2.120 | | 22.9 | 39.3 | 106 | 0 | 0
12.2.87 | | 22.68 | 38.41 | 105 | 2.62 | 1.56
12.2.144 | | 21.82 | 40.63 | 101 | 0 | 0
12.2.24 | | 21.38 | 37.45 | 99 | 0 | 0
12.2.74 | | 21.38 | 37.45 | 99 | 0 | 0
12.2.140 | | 21.38 | 37.45 | 99 | 0 | 0
12.2.19 | | 21.17 | 39.07 | 98 | 0 | 0
12.2.35 | | 21.17 | 39.07 | 98 | 0 | 0
12.2.151 | | 21.17 | 39.07 | 98 | 0 | 0
12.2.7 | | 20.95 | 37.32 | 97 | 0.6 | 0.16
12.2.156 | | 20.74 | 41.19 | 96 | 0 | 0
12.2.49 | | 20.3 | 36.62 | 94 | 0.85 | 0.21
12.2.185 | | 20.3 | 35.44 | 94 | 1.2 | 0.24
12.2.94 | | 19.87 | 36.19 | 92 | 0 | 0
12.2.1 | | 19.44 | 24.43 | 90 | 1.2 | 0.34
12.2.107 | | 19.01 | 38.34 | 88 | 0 | 0
12.2.160 | | 19.01 | 40.78 | 88 | 3.06 | 1.52
12.2.27 | | 18.58 | 30.85 | 86 | 0.85 | 0.25
12.2.10 | | 17.71 | 25.79 | 82 | 1.2 | 0.36
12.2.178 | | 17.71 | 27.89 | 82 | 1.2 | 0.45
12.2.54 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.60 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.66 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.71 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.85 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.122 | | 17.28 | 36.68 | 80 | 0 | 0
12.2.138 | | 17.28 | 25.7 | 80 | 1.2 | 0.3
12.2.47 | | 16.85 | 32.3 | 78 | 0 | 0
12.2.69 | | 16.85 | 32.3 | 78 | 0 | 0
12.2.141 | | 16.85 | 32.3 | 78 | 0 | 0
12.2.147 | | 16.85 | 32.3 | 78 | 0 | 0
12.2.26 | | 16.63 | 25.6 | 77 | 1.34 | 0.41
12.2.181 | | 16.2 | 32.87 | 75 | 1.8 | 0.62
12.2.192 | | 15.98 | 24.07 | 74 | 1.2 | 0.39
12.2.31 | | 15.77 | 25.79 | 73 | 1.34 | 0.3
12.2.165 | | 15.34 | 24.88 | 71 | 2.16 | 0.87
12.2.3 | | 13.18 | 22.36 | 61 | 0.6 | 0.21
12.2.175 | | 13.18 | 22.63 | 61 | 1.7 | 0.72
12.2.23 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.29 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.42 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.45 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.46 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.52 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.58 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.70 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.82 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.90 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.92 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.112 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.125 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.126 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.128 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.136 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.146 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.163 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.177 | | 12.31 | 29.54 | 57 | 0 | 0
12.2.179 | | 12.1 | 21.75 | 56 | 1.2 | 0.23
12.2.20 | | 11.66 | 26.66 | 54 | 1.8 | 0.98
12.2.166 | | 11.66 | 18.98 | 54 | 0.6 | 0.2
12.2.100 | | 11.45 | 20.11 | 53 | 0.85 | 0.11
12.2.184 | | 11.02 | 19.24 | 51 | 1.04 | 0.27
12.2.191 | | 11.02 | 20.67 | 51 | 1.34 | 0.4
12.2.106 | | 10.58 | 23.58 | 49 | 0.85 | 0.37
12.2.171 | | 10.37 | 23.04 | 48 | 1.7 | 0.72
12.2.103 | | 10.15 | 16.02 | 47 | 0.85 | 0.23
12.2.186 | | 10.15 | 17.02 | 47 | 1.2 | 0.29
12.2.131 | | 9.94 | 19.56 | 46 | 1.34 | 0.42
12.2.133 | | 9.94 | 19.13 | 46 | 1.2 | 0.3
12.2.98 | | 9.07 | 14.69 | 42 | 1.2 | 0.29
12.2.142 | | 8.86 | 19.53 | 41 | 0.85 | 0.21
12.2.139 | | 8.64 | 15.82 | 40 | 1.2 | 0.35
12.2.173 | | 8.64 | 15.26 | 40 | 0.6 | 0.11
12.2.37 | | 8.42 | 19.26 | 39 | 1.2 | 0.48
12.2.164 | | 8.42 | 16.13 | 39 | 1.2 | 0.34
12.2.193 | | 8.21 | 16.03 | 38 | 0.6 | 0.13
12.2.8 | | 7.99 | 17.1 | 37 | 0.6 | 0.23
12.2.40 | | 7.78 | 17.01 | 36 | 1.2 | 0.44
12.2.28 | | 7.34 | 16.6 | 34 | 0.85 | 0.28
12.2.38 | | 6.48 | 9.55 | 30 | 0.6 | 0.12
12.2.132 | | 6.48 | 13.05 | 30 | 0.6 | 0.12
12.2.170 | | 6.05 | 14.18 | 28 | 0.85 | 0.24
12.2.187 | | 6.05 | 13.72 | 28 | 0.85 | 0.25
12.2.15 | | 5.62 | 12.34 | 26 | 0.6 | 0.16
12.2.64 | | 5.62 | 12.9 | 26 | 0.6 | 0.18
12.2.80 | | 5.62 | 10.71 | 26 | 0.6 | 0.18
12.2.129 | | 5.62 | 11.34 | 26 | 0.6 | 0.18
12.2.97 | | 5.18 | 11.86 | 24 | 0.6 | 0.12
121 cavities found for MenV L Homology RSV L promoter Elongation.pdb #13
MenV L Homology RSV L promoter Elongation.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
13.2.46 | | 1399.9 | 1032.29 | 6481 | 10.7 | 3.22
13.2.73 | | 1189.3 | 993.83 | 5506 | 10.48 | 2.31
13.2.8 | | 673.92 | 608.46 | 3120 | 9.71 | 2.47
13.2.49 | | 433.08 | 426.57 | 2005 | 6.81 | 2.74
13.2.50 | | 427.25 | 453.31 | 1978 | 6.29 | 1.44
13.2.81 | | 405.22 | 464.98 | 1876 | 8.07 | 2.25
13.2.20 | | 385.78 | 366.09 | 1786 | 5.56 | 1.69
13.2.25 | | 348.41 | 349.6 | 1613 | 6.38 | 1.3
13.2.109 | | 332.42 | 296.47 | 1539 | 5.5 | 1.41
13.2.4 | | 319.9 | 266.93 | 1481 | 8.05 | 2.37
13.2.79 | | 294.62 | 254.05 | 1364 | 4.57 | 1.49
13.2.29 | | 278.42 | 239.34 | 1289 | 3 | 0.96
13.2.2 | | 242.35 | 267.12 | 1122 | 5.26 | 1.63
13.2.31 | | 232.85 | 233.38 | 1078 | 6.63 | 3.35
13.2.51 | | 191.81 | 212.42 | 888 | 4.02 | 1.09
13.2.28 | | 184.68 | 140.72 | 855 | 4.84 | 1.16
13.2.112 | | 161.35 | 159.81 | 747 | 4.24 | 1.82
13.2.45 | | 156.6 | 159.27 | 725 | 7.32 | 3.07
13.2.17 | | 155.95 | 185.76 | 722 | 8.51 | 4.46
13.2.47 | | 152.93 | 199.46 | 708 | 10.95 | 4.47
13.2.54 | | 150.12 | 164.36 | 695 | 3.6 | 0.87
13.2.30 | | 134.14 | 145.16 | 621 | 3.89 | 1.57
13.2.63 | | 122.26 | 110.61 | 566 | 3.23 | 0.84
13.2.67 | | 108.86 | 87.02 | 504 | 3 | 0.94
13.2.60 | | 97.42 | 111.4 | 451 | 0 | 0
13.2.111 | | 92.23 | 129.22 | 427 | 0 | 0
13.2.3 | | 88.13 | 94.16 | 408 | 4.57 | 2.02
13.2.37 | | 83.16 | 114.11 | 385 | 0 | 0
13.2.77 | | 82.08 | 97.31 | 380 | 0 | 0
13.2.56 | | 74.09 | 100.89 | 343 | 7.27 | 4.14
13.2.91 | | 73.66 | 100.58 | 341 | 4.28 | 2.3
13.2.27 | | 62.86 | 76.3 | 291 | 5.13 | 2.1
13.2.15 | | 56.59 | 77.08 | 262 | 2.4 | 0.6
13.2.44 | | 56.59 | 76.8 | 262 | 0 | 0
13.2.88 | | 55.3 | 68.52 | 256 | 3.39 | 1.29
13.2.23 | | 54.22 | 74.57 | 251 | 0 | 0
13.2.103 | | 50.76 | 64.17 | 235 | 0 | 0
13.2.119 | | 49.25 | 43.91 | 228 | 2.62 | 0.69
13.2.38 | | 47.74 | 70.88 | 221 | 0 | 0
13.2.113 | | 43.2 | 64.3 | 200 | 0 | 0
13.2.41 | | 42.98 | 63.94 | 199 | 0 | 0
13.2.76 | | 42.55 | 58.88 | 197 | 4.28 | 2.13
13.2.95 | | 42.55 | 61.3 | 197 | 0 | 0
13.2.105 | | 41.69 | 60.45 | 193 | 0 | 0
13.2.87 | | 41.04 | 59.47 | 190 | 0 | 0
13.2.12 | | 40.82 | 62.98 | 189 | 1.7 | 0.51
13.2.32 | | 40.61 | 64.68 | 188 | 0 | 0
13.2.93 | | 37.58 | 74.68 | 174 | 0 | 0
13.2.98 | | 37.37 | 45.43 | 173 | 2.16 | 0.64
13.2.52 | | 35.86 | 52.67 | 166 | 3.7 | 1.46
13.2.68 | | 34.78 | 53.01 | 161 | 1.34 | 0.38
13.2.71 | | 34.78 | 40.13 | 161 | 1.9 | 0.61
13.2.16 | | 33.26 | 51.84 | 154 | 1.8 | 0.41
13.2.96 | | 33.26 | 45.99 | 154 | 1.34 | 0.27
13.2.19 | | 32.83 | 44.58 | 152 | 2.47 | 0.81
13.2.83 | | 32.83 | 50.74 | 152 | 0 | 0
13.2.21 | | 31.97 | 55.8 | 148 | 0 | 0
13.2.24 | | 31.75 | 43.86 | 147 | 1.2 | 0.29
13.2.100 | | 31.54 | 52.01 | 146 | 0 | 0
13.2.86 | | 31.1 | 54.35 | 144 | 0 | 0
13.2.117 | | 31.1 | 44.32 | 144 | 2.47 | 1.12
13.2.85 | | 29.16 | 60.41 | 135 | 0 | 0
13.2.106 | | 28.73 | 44.94 | 133 | 3.06 | 1.61
13.2.110 | | 27.86 | 44.27 | 129 | 0 | 0
13.2.33 | | 27.65 | 34.66 | 128 | 1.7 | 0.61
13.2.57 | | 26.35 | 42.67 | 122 | 2.16 | 0.97
13.2.61 | | 26.14 | 46.8 | 121 | 0 | 0
13.2.13 | | 25.92 | 44.39 | 120 | 0 | 0
13.2.116 | | 25.92 | 35.6 | 120 | 1.2 | 0.29
13.2.97 | | 25.7 | 51.61 | 119 | 0 | 0
13.2.35 | | 24.84 | 37.71 | 115 | 3 | 1.38
13.2.101 | | 24.84 | 40.56 | 115 | 0 | 0
13.2.1 | | 24.62 | 41.26 | 114 | 2.24 | 0.92
13.2.53 | | 23.76 | 38.74 | 110 | 1.2 | 0.36
13.2.10 | | 22.9 | 40.08 | 106 | 0 | 0
13.2.58 | | 22.9 | 41.28 | 106 | 0 | 0
13.2.62 | | 22.9 | 39.3 | 106 | 0 | 0
13.2.48 | | 21.38 | 37.45 | 99 | 0 | 0
13.2.115 | | 21.38 | 37.45 | 99 | 0 | 0
13.2.69 | | 21.17 | 35.98 | 98 | 1.34 | 0.39
13.2.22 | | 20.52 | 34.88 | 95 | 2.55 | 1.07
13.2.92 | | 19.66 | 35.17 | 91 | 1.34 | 0.34
13.2.89 | | 19.22 | 43.32 | 89 | 3.29 | 1.41
13.2.94 | | 19.01 | 38.34 | 88 | 0 | 0
13.2.18 | | 17.28 | 36.68 | 80 | 0 | 0
13.2.64 | | 17.28 | 36.68 | 80 | 0 | 0
13.2.80 | | 17.28 | 36.68 | 80 | 0 | 0
13.2.114 | | 17.28 | 36.68 | 80 | 0 | 0
13.2.36 | | 16.85 | 32.3 | 78 | 0 | 0
13.2.104 | | 16.42 | 26.2 | 76 | 1.7 | 0.47
13.2.9 | | 16.2 | 27.07 | 75 | 1.8 | 0.84
13.2.34 | | 15.77 | 26.82 | 73 | 2.4 | 1.05
13.2.108 | | 14.9 | 27.19 | 69 | 1.2 | 0.29
13.2.99 | | 12.53 | 21.98 | 58 | 1.2 | 0.41
13.2.6 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.7 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.11 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.65 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.74 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.75 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.78 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.82 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.90 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.102 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.118 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.120 | | 12.31 | 29.54 | 57 | 0 | 0
13.2.55 | | 12.1 | 20.4 | 56 | 1.34 | 0.29
13.2.121 | | 11.88 | 23.61 | 55 | 0.85 | 0.25
13.2.72 | | 11.66 | 23.87 | 54 | 1.8 | 0.78
13.2.84 | | 11.45 | 26.34 | 53 | 1.9 | 0.97
13.2.26 | | 11.02 | 21.91 | 51 | 1.2 | 0.29
13.2.14 | | 9.72 | 14.63 | 45 | 0.85 | 0.29
13.2.66 | | 9.5 | 18.53 | 44 | 0.6 | 0.11
13.2.59 | | 8.86 | 20.08 | 41 | 1.34 | 0.6
13.2.43 | | 8.64 | 17.63 | 40 | 0.6 | 0.16
13.2.40 | | 8.42 | 15.58 | 39 | 1.2 | 0.28
13.2.42 | | 7.34 | 12.79 | 34 | 0.85 | 0.25
13.2.70 | | 6.91 | 9.73 | 32 | 0.85 | 0.26
13.2.107 | | 6.05 | 16.17 | 28 | 0.6 | 0.15
13.2.39 | | 5.83 | 12.61 | 27 | 0.6 | 0.18
13.2.5 | | 5.4 | 12.59 | 25 | 0 | 0
> transparency #8,12-13 80
> hide #!8 models
> hide #!13 models
> hide #!12 models
> show #!8 models
> open "/Users/michael/Downloads/caver_3.0/caver/out/data/tunnels/tunnels_MenV
> L Homology PIV5 APO.pdb.obj"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 355, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/__init__.py", line 44, in open
return obj.read_obj(session, data, file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/obj.py", line 73, in read_obj
for line_num, line in enumerate(input.readlines()):
^^^^^^^^^^^^^^^^^
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
File "", line 322, in decode
See log for complete Python traceback.
> open "/Users/michael/Downloads/caver_3.0/caver/out/data/MenV L Homology PIV5
> APO.pdb"
MenV L Homology PIV5 APO.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) MenV L [more info...]
Chain information for MenV L Homology PIV5 APO.pdb #14
---
Chain | Description
A | No description available
Non-standard residues in MenV L Homology PIV5 APO.pdb #14
---
ZN — (ZN)
Computing secondary structure
> open "/Users/michael/Downloads/caver_3.0/caver/out/data/tunnels/tunnels_MenV
> L Homology RSV L promoter Elongation.pdb0.obj"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 355, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/__init__.py", line 44, in open
return obj.read_obj(session, data, file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/obj.py", line 73, in read_obj
for line_num, line in enumerate(input.readlines()):
^^^^^^^^^^^^^^^^^
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
File "", line 322, in decode
See log for complete Python traceback.
> open "/Users/michael/Downloads/caver_3.0/caver/out/data/tunnels/tunnels_MenV
> L Homology PIV5 APO.pdb.obj"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
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 816, in dropEvent
_open_dropped_file(self.session, p)
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 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 216, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/__init__.py", line 44, in open
return obj.read_obj(session, data, file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/wavefront_obj/obj.py", line 73, in read_obj
for line_num, line in enumerate(input.readlines()):
^^^^^^^^^^^^^^^^^
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xac in position 0:
invalid start byte
File "", line 322, in decode
See log for complete Python traceback.
> hide #14 models
> ui mousemode right clip
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
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: 14 days, 6 hours, 11 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
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