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Opened 4 months ago
Closed 4 months ago
#18019 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x0000000326343000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000325337000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032432b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032331f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000322313000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000321307000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003202fb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031f2ef000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e2e3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d2d7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c2cb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b2bf000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a2b3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f7f84f40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 60)
{"app_name":"ChimeraX","timestamp":"2025-06-17 19:44:58.00 -0700","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"3C51D5D2-A163-4763-B20C-D1B33C4CD766"}
{
"uptime" : 2400000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 380068,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-06-17 19:44:49.5479 -0700",
"codeSigningMonitor" : 1,
"incident" : "3C51D5D2-A163-4763-B20C-D1B33C4CD766",
"pid" : 44518,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-16 09:57:53.5425 -0700",
"procStartAbsTime" : 57588966328005,
"procExitAbsTime" : 58945643896767,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5962B24-73D9-5811-802C-5EC5A9E388C3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B7523C58-130A-FA01-2B0B-DC12327FC980",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "9075E200-434F-4817-A1E8-F715399212EF",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4311318167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100f98000-100f9c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":44518},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4311318167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100f98000-100f9c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.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" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/Footprints1A1_vs_6G1.cxs"
Log from Mon Dec 9 13:25:32 2024UCSF ChimeraX version: 1.8.dev202311280534
(2023-11-28)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1_H_and_L.cxs"
Log from Thu Dec 5 12:26:01 2024UCSF ChimeraX version: 1.8.dev202311280534
(2023-11-28)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1.cxs"
Log from Wed Dec 4 17:01:57 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/ModelsFromPhilip/H5+12G1_coot-0-coot-32_real_space_refined_036.pdb"
Chain information for H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #1
---
Chain | Description
A C | No description available
B | No description available
H | No description available
L | No description available
a b c | No description available
> hide cartoons
> hide atoms
> show cartoons
> set bgColor white
> lighting soft
> graphics silhouettes true
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 26163 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select /B
4986 atoms, 5055 bonds, 316 residues, 1 model selected
> color sel light grey
> select clear
> select /b:153
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
2582 atoms, 2611 bonds, 165 residues, 1 model selected
> select up
26421 atoms, 26767 bonds, 1685 residues, 1 model selected
> select down
2582 atoms, 2611 bonds, 165 residues, 1 model selected
> color sel light grey
> select /c:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /A:88
23 atoms, 21 bonds, 2 residues, 1 model selected
> select up
7550 atoms, 7646 bonds, 481 residues, 1 model selected
> select clear
> select /c:90
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add /C:289
25 atoms, 23 bonds, 2 residues, 1 model selected
> select up
7550 atoms, 7646 bonds, 481 residues, 1 model selected
> color sel grey
> select /a:97
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add /A:312
29 atoms, 27 bonds, 2 residues, 1 model selected
> select up
7550 atoms, 7646 bonds, 481 residues, 1 model selected
> color sel dark grey
> select clear
> select /C:280
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add /c:89
41 atoms, 39 bonds, 2 residues, 1 model selected
> select up
7550 atoms, 7646 bonds, 481 residues, 1 model selected
> color sel dark grey
Drag select of 6 residues
> select /a:93
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add /A:49
21 atoms, 19 bonds, 2 residues, 1 model selected
> select up
7550 atoms, 7646 bonds, 481 residues, 1 model selected
> color sel grey
> select clear
> select ::name="NAG"
258 atoms, 258 bonds, 12 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
Drag select of 168 atoms, 1256 residues, 170 bonds
> select clear
Drag select of 97 atoms, 599 residues, 97 bonds
> select up
9676 atoms, 9757 bonds, 605 residues, 1 model selected
> select up
9688 atoms, 9770 bonds, 605 residues, 1 model selected
> select up
22697 atoms, 22989 bonds, 1445 residues, 1 model selected
> show sel surfaces
> select clear
> select /L:41
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1348 atoms, 1364 bonds, 87 residues, 1 model selected
> select up
1709 atoms, 1730 bonds, 112 residues, 1 model selected
> color sel light blue
> select /H:20
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
95 atoms, 94 bonds, 7 residues, 1 model selected
> select up
1867 atoms, 1894 bonds, 122 residues, 1 model selected
> color sel blue
> color sel dark blue
> select /B:173@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #1/H:32,100E,100G,96,100C,100E,100D,100B,100C,100B,100A,100B
142 atoms, 143 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select H
12931 atoms, 1680 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/B:128
14 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/12G1.cxs" includeMaps true
> select #1/B
4986 atoms, 5055 bonds, 316 residues, 1 model selected
> mlp sel
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_B
SES surface": minimum -26.4, mean -4.411, maximum 25.25
To also show corresponding color key, enter the above mlp command and add key
true
> select #1/B:125B
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:166
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /H:100F
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:126
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Side View"
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/12G1_hydrophob_groove.png" width
> 965 height 830 supersample 4 transparentBackground true
> save 12G1_hydrophob_groove.png supersample 8 transparentBackground true
> mlp
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_A
SES surface": minimum -27.45, mean -4.283, maximum 24.92
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_B
SES surface": minimum -26.4, mean -4.411, maximum 25.25
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_C
SES surface": minimum -26.09, mean -4.143, maximum 25.32
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_H
SES surface": minimum -27.55, mean -4.03, maximum 24.65
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_L
SES surface": minimum -24.86, mean -2.588, maximum 24.9
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_a
SES surface": minimum -27.38, mean -3.167, maximum 24.57
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_b
SES surface": minimum -28.19, mean -3.158, maximum 24.83
Map values for surface "H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_c
SES surface": minimum -26.9, mean -3.236, maximum 23.26
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide surfaces
Drag select of 8 atoms, 425 residues, 7 bonds
> select /B:147
20 atoms, 20 bonds, 1 residue, 1 model selected
Drag select of 21 atoms, 507 residues, 22 bonds
> select up
8187 atoms, 8263 bonds, 510 residues, 7 models selected
> select up
8205 atoms, 8282 bonds, 510 residues, 7 models selected
> select up
22628 atoms, 22916 bonds, 1441 residues, 7 models selected
> select up
22845 atoms, 23143 bonds, 1451 residues, 7 models selected
> select up
26421 atoms, 26767 bonds, 1685 residues, 7 models selected
> select down
22845 atoms, 23143 bonds, 1451 residues, 9 models selected
> show sel surfaces
> select /B:122@CD1
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
4905 atoms, 4970 bonds, 312 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select /C:25@H
1 atom, 1 residue, 1 model selected
> select add /C:273@CB
2 atoms, 2 residues, 2 models selected
> select up
32 atoms, 30 bonds, 2 residues, 2 models selected
> select up
4968 atoms, 5035 bonds, 316 residues, 2 models selected
> select up
5063 atoms, 5134 bonds, 320 residues, 2 models selected
> select up
26421 atoms, 26767 bonds, 1685 residues, 2 models selected
> select down
5063 atoms, 5134 bonds, 320 residues, 9 models selected
> color (#!1 & sel) gray
> select /a:14@NE1
1 atom, 1 residue, 1 model selected
> select add /A:285@HB
2 atoms, 2 residues, 2 models selected
> select up
40 atoms, 40 bonds, 2 residues, 3 models selected
> select up
7550 atoms, 7646 bonds, 481 residues, 3 models selected
> select up
7632 atoms, 7732 bonds, 485 residues, 3 models selected
> select up
26421 atoms, 26767 bonds, 1685 residues, 3 models selected
> select down
7632 atoms, 7732 bonds, 485 residues, 9 models selected
> color (#!1 & sel) dim gray
> select clear
> select /c:34@CE1
1 atom, 1 residue, 1 model selected
> select add /C:44@OE1
2 atoms, 2 residues, 2 models selected
> select up
36 atoms, 35 bonds, 2 residues, 3 models selected
> select up
7550 atoms, 7646 bonds, 481 residues, 3 models selected
> select up
7645 atoms, 7745 bonds, 485 residues, 3 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #919191ff
> select clear
> select /H:48
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
700 atoms, 714 bonds, 44 residues, 2 models selected
> select up
1867 atoms, 1894 bonds, 122 residues, 2 models selected
> hide sel atoms
> select clear
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/ModelsFromPhilip/H5_6G1-coot-11_renumbered_real_space_refined_018.pdb"
Chain information for H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
a b c | No description available
> hide atoms
> show cartoons
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 26126 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select /A:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /a:45
26 atoms, 24 bonds, 2 residues, 1 model selected
> select up
3391 atoms, 3432 bonds, 216 residues, 1 model selected
> select up
7653 atoms, 7752 bonds, 484 residues, 1 model selected
> color sel light grey
> select /b:97
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add /B:300
34 atoms, 32 bonds, 2 residues, 1 model selected
> select up
1623 atoms, 1638 bonds, 101 residues, 1 model selected
> select up
7638 atoms, 7738 bonds, 484 residues, 1 model selected
> color sel tin
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> select /B:21
13 atoms, 12 bonds, 1 residue, 1 model selected
> select add /b:93
27 atoms, 25 bonds, 2 residues, 1 model selected
> select up
1676 atoms, 1686 bonds, 104 residues, 1 model selected
> select up
7638 atoms, 7738 bonds, 484 residues, 1 model selected
> color sel #929292ff
> color sel #919191ff
> select /c:86
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add /C:285
28 atoms, 26 bonds, 2 residues, 1 model selected
> select up
4886 atoms, 4949 bonds, 305 residues, 1 model selected
> select up
7640 atoms, 7739 bonds, 484 residues, 1 model selected
> color sel dim gray
> select clear
> select /H:8
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
213 atoms, 214 bonds, 15 residues, 1 model selected
> select up
1900 atoms, 1928 bonds, 125 residues, 1 model selected
> color sel #009051ff
> color sel #008f00ff
> color sel #4f8f00ff
> color sel #009051ff
> select /L:41
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1674 atoms, 1696 bonds, 111 residues, 1 model selected
> select up
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> select down
1674 atoms, 1696 bonds, 111 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
> color sel #8efa00ff
> color sel #73fa79ff
> color sel lime
> select clear
> select ::name="NAG"
379 atoms, 379 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel byhetero
Drag select of 78 residues
> select up
15409 atoms, 15587 bonds, 961 residues, 1 model selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/6G1.cxs" includeMaps true
——— End of log from Wed Dec 4 17:01:57 2024 ———
opened ChimeraX session
> select
> #1/H:100C,100C,31,32,100E,100G,101,96,101,100G,100E,100E,100G,100D,100B,100C,100B,100B
148 atoms, 146 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select /A:125@CG
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 2 models selected
> select up
221 atoms, 223 bonds, 12 residues, 2 models selected
> select up
4285 atoms, 4343 bonds, 269 residues, 2 models selected
> mlp sel
Map values for surface "H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A
SES surface": minimum -26.3, mean -4.312, maximum 25.79
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> save 6G1_H_A_hydrophobicGrooveFromRight.png supersample 8
> transparentBackground true
> save 6G1_H_A_hydrophobicGrooveFromLeft.png supersample 8
> transparentBackground true
> select H
12980 atoms, 1686 residues, 1 model selected
> hide sel atoms
> select clear
> save 6G1_H_A_hydrophobicGrooveHeadOn.png supersample 8 transparentBackground
> true
> select clear
> select #1/L:57,49,56,49,30,50,28,28,28,28,53,28
111 atoms, 109 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select H
12980 atoms, 1686 residues, 1 model selected
> hide sel atoms
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1_H_and_L.cxs" includeMaps
> true
——— End of log from Thu Dec 5 12:26:01 2024 ———
opened ChimeraX session
> select clear
Drag select of H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A SES
surface, 51162 of 345860 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_B SES surface, 129488 of
352546 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_C SES
surface, 106496 of 351158 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_a SES surface, 103612 of
239464 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_b SES
surface, 89353 of 244122 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_c SES surface, 106063 of
233634 triangles, 110 atoms, 497 residues, 112 bonds
> select up
7812 atoms, 7876 bonds, 505 residues, 7 models selected
> select up
7890 atoms, 7954 bonds, 505 residues, 7 models selected
> select up
16851 atoms, 17042 bonds, 1068 residues, 7 models selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 7 models selected
> show sel surfaces
> ui tool show "Side View"
> hide sel surfaces
> select clear
Drag select of 129 atoms, 596 residues, 128 bonds
> select up
9407 atoms, 9491 bonds, 606 residues, 7 models selected
> select up
17313 atoms, 17513 bonds, 1097 residues, 7 models selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 7 models selected
> ui tool show "Color Actions"
> open /Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln-clustalw
Unrecognized file suffix '.aln-clustalw'
> open /Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln
Summary of feedback from opening
/Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln
---
notes | Alignment identifier is Jiangsu_RTH_gisAID_H5_alignment.aln
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment Jiangsu_RTH_gisAID_H5_alignment.aln
Opened 808 sequences from Jiangsu_RTH_gisAID_H5_alignment.aln
> color sel byattr seq_conservation palette royal blue:pale turquoise:light
> grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byattr seq_conservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel by seq_conservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byattr seq_conservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byattribute seq_conservation
26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to
0.353
Fetching compressed palette royal from
https://www.colourlovers.com/api/palettes?keywords=royal&format=json&numResults=100
Could not find palette royal at COLOURlovers.com using keyword search
> color byattribute seq_conservation palette snow:moccasin:navy
26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to
0.353
> toolshed show
> color byattribute seq_conservation palette cyanmaroon key true
> key cyan-white-maroon :-5.461 :-2.554 :0.353 showTool true
> ui mousemode right "color key"
26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to
0.353
> key cyan-white-maroon :-5.461 ":\\\" :0.353
> key cyan-white-maroon :-5.461 : :0.353
> key cyan-white-maroon :-5.461 : :C
> key cyan-white-maroon :-5.461 : :Co
> key cyan-white-maroon :-5.461 : :Con
> key cyan-white-maroon :-5.461 : :Cons
> key cyan-white-maroon :-5.461 : :Conse
> key cyan-white-maroon :-5.461 : :Conser
> key cyan-white-maroon :-5.461 : :Conserv
> key cyan-white-maroon :-5.461 : :Conserve
> key cyan-white-maroon :-5.461 : :Conserver
> key cyan-white-maroon :-5.461 : :Conserverd
> key cyan-white-maroon :-5.461 : :Conserver
> key cyan-white-maroon :-5.461 : :Conserve
> key cyan-white-maroon :-5.461 : :Conserved
> key cyan-white-maroon :V : :Conserved
> key cyan-white-maroon : : :Conserved
> key cyan-white-maroon :V : :Conserved
> key cyan-white-maroon :Va : :Conserved
> key cyan-white-maroon :Var : :Conserved
> key cyan-white-maroon :Vari : :Conserved
> key cyan-white-maroon :Varia : :Conserved
> key cyan-white-maroon :Variab : :Conserved
> key cyan-white-maroon :Variabl : :Conserved
> key cyan-white-maroon :Variable : :Conserved
> key ^cyan-white-maroon :Conserved : :Variable
> key labelColor #bfbfbf
> key labelColor default
> select /A-C:125B
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /A-C:125B-126
66 atoms, 63 bonds, 6 residues, 1 model selected
> select /A:131
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:132
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:131
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A-C:132
42 atoms, 39 bonds, 3 residues, 1 model selected
> select /A-C:132
42 atoms, 39 bonds, 3 residues, 1 model selected
> select /C:125B
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:169
13 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:166 /B:166 /C:166
57 atoms, 54 bonds, 3 residues, 1 model selected
> select /A:169 /B:169 /C:169
39 atoms, 36 bonds, 3 residues, 1 model selected
> select /A:168 /B:168 /C:168
63 atoms, 63 bonds, 3 residues, 1 model selected
> select clear
> key spectral-3 :Conserved : :Variable
> key accent-3 :Conserved : :Variable
> key blues-3 :Conserved : :Variable
> color byattribute seq_conservation palette blues key true
> key blues :-5.461 :-4.008 :-2.554 :-1.101 :0.353 showTool true
26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to
0.353
> key gnbu-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key greys-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key paired-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key paecontacts :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key pastel2-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key piyg-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key prgn-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key pubu :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key prgn-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key set3-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key set1-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key ylorrd :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key spectral :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key spectral-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353
[Repeated 1 time(s)]
> key esmfold :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key blues :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> key greys :-5.461 :-4.008 :-2.554 :-1.101 :0.353
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/SequenceConservation.cxs"
> includeMaps true
> close all
> ui mousemode right translate
> open /Users/aleon/Downloads/H5_1A1.pdb
Chain information for H5_1A1.pdb #1
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
a b c | No description available
Associated H5_1A1.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain c to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Drag select of 26476 atoms, 394 bonds
> select up
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> select /L:83@HG21
1 atom, 1 residue, 1 model selected
> select add /H:108@O
2 atoms, 2 residues, 2 models selected
> select up
30 atoms, 29 bonds, 2 residues, 3 models selected
> select up
2614 atoms, 2646 bonds, 173 residues, 3 models selected
> hide sel surfaces
> select /H:10@N
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
213 atoms, 214 bonds, 15 residues, 2 models selected
> select up
1900 atoms, 1928 bonds, 125 residues, 2 models selected
> hide sel surfaces
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/ModelsFromPhilip/H5_6G1-coot-11_renumbered_real_space_refined_018.pdb"
Chain information for H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #2
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
a b c | No description available
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain c to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
> select add #2
28405 atoms, 28781 bonds, 1813 residues, 3 models selected
> select add #1
53010 atoms, 53706 bonds, 3376 residues, 3 models selected
> select subtract #1
26505 atoms, 26853 bonds, 1688 residues, 9 models selected
> select clear
> select add #2
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #1/A:278@HA
1 atom, 1 residue, 1 model selected
> select add #1/a:38@CD
2 atoms, 2 residues, 2 models selected
> select up
36 atoms, 34 bonds, 2 residues, 3 models selected
> select up
3391 atoms, 3432 bonds, 216 residues, 3 models selected
> select up
7653 atoms, 7752 bonds, 484 residues, 3 models selected
> color sel light grey
> select #1/b:14@CE3
1 atom, 1 residue, 1 model selected
> select add #1/B:22@OG
2 atoms, 2 residues, 2 models selected
> select up
35 atoms, 35 bonds, 2 residues, 3 models selected
> select up
1326 atoms, 1340 bonds, 90 residues, 3 models selected
> select up
7638 atoms, 7738 bonds, 484 residues, 3 models selected
> color sel dark grey
> select #1/c:34@CE1
1 atom, 1 residue, 1 model selected
> select add #1/C:292@CE
2 atoms, 2 residues, 2 models selected
> select up
38 atoms, 37 bonds, 2 residues, 3 models selected
> select up
4536 atoms, 4603 bonds, 291 residues, 3 models selected
> select up
7640 atoms, 7739 bonds, 484 residues, 3 models selected
> color sel grey
> select clear
> select #2/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #009051ff
> select clear
> select #1/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> color (#!1 & sel) #ff2600ff
> color (#!1 & sel) red
> select clear
> select #1/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> ui tool show "Color Actions"
> ui tool show "Color Zone"
No surface chosen for color zoning
> select sel : select sel : select #1/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select sel : select clear
> select #2/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select sel : select #2/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select sel : select #2/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select sel : select #1/B:51@CD1
1 atom, 1 residue, 1 model selected
> select add #1/b:28@N
2 atoms, 2 residues, 2 models selected
> select up
33 atoms, 31 bonds, 2 residues, 3 models selected
> select up
1326 atoms, 1340 bonds, 90 residues, 3 models selected
> select up
7638 atoms, 7738 bonds, 484 residues, 3 models selected
> color sel tin
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ui tool show "Color Actions"
> color (#!1 & sel) #919191ff
> select #1/c:15@NE2
1 atom, 1 residue, 1 model selected
> select add #1/C:60@CG2
2 atoms, 2 residues, 2 models selected
> select up
36 atoms, 34 bonds, 2 residues, 3 models selected
> select up
1327 atoms, 1341 bonds, 90 residues, 3 models selected
> select up
7640 atoms, 7739 bonds, 484 residues, 3 models selected
> color sel dim grey
> select clear
> select sel : select #2/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select sel : color (#!1-2 & sel) #009051ff
> select #1/H/L
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> color sel red
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/Footprints1A1_vs_6G1.cxs"
> includeMaps true
——— End of log from Mon Dec 9 13:25:32 2024 ———
opened ChimeraX session
> lighting soft
> select clear
> select #1/A-C:13-321/a-c:2-166 #2/A-C:13-321/a-c:2-166
45104 atoms, 45670 bonds, 2874 residues, 2 models selected
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/ForGarazi/EditsDec18AL/H5_final.aln"
Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre
Leon/Flu Andre/GaraziH5/ForGarazi/EditsDec18AL/H5_final.aln
---
notes | Alignment identifier is H5_final.aln
Associated H5_1A1.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_1A1.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment H5_final.aln
Opened 18 sequences from H5_final.aln
> select clear
> select #1/B:274@N
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> select up
772 atoms, 781 bonds, 51 residues, 2 models selected
> select up
5030 atoms, 5100 bonds, 318 residues, 2 models selected
> select up
26505 atoms, 26853 bonds, 1688 residues, 2 models selected
> select down
5030 atoms, 5100 bonds, 318 residues, 9 models selected
> select #1/b:32@HG
1 atom, 1 residue, 1 model selected
> select add #1/B:292@SD
2 atoms, 2 residues, 2 models selected
> select up
28 atoms, 26 bonds, 2 residues, 3 models selected
> select up
1273 atoms, 1292 bonds, 87 residues, 3 models selected
> select up
7638 atoms, 7738 bonds, 484 residues, 3 models selected
> color sel grey
> select #1/a:42@NE2
1 atom, 1 residue, 1 model selected
> select add #1/A:304@OE2
2 atoms, 2 residues, 2 models selected
> select up
32 atoms, 30 bonds, 2 residues, 3 models selected
> select up
3391 atoms, 3432 bonds, 216 residues, 3 models selected
> select up
7653 atoms, 7752 bonds, 484 residues, 3 models selected
> color sel light grey grey
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
Drag select of 16 residues
> select up
1674 atoms, 1696 bonds, 111 residues, 2 models selected
> select up
26505 atoms, 26853 bonds, 1688 residues, 2 models selected
> select down
1674 atoms, 1696 bonds, 111 residues, 9 models selected
> select clear
> select #1/H:13
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/L:10
33 atoms, 31 bonds, 2 residues, 2 models selected
> select up
1887 atoms, 1910 bonds, 126 residues, 3 models selected
> select up
3574 atoms, 3624 bonds, 236 residues, 3 models selected
> color sel #FFBF00
> select clear
> select #1/B:51@CD1
1 atom, 1 residue, 1 model selected
> select #1/b:34@CZ
1 atom, 1 residue, 1 model selected
> select add #1/B:57@NZ
2 atoms, 2 residues, 2 models selected
> select up
43 atoms, 42 bonds, 2 residues, 3 models selected
> select up
1326 atoms, 1340 bonds, 90 residues, 3 models selected
> select up
7638 atoms, 7738 bonds, 484 residues, 3 models selected
> color sel grey
> select #1/B:142@C
1 atom, 1 residue, 1 model selected
> select clear
> select add #1/H:62
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/L:14
25 atoms, 23 bonds, 2 residues, 2 models selected
> select up
1718 atoms, 1740 bonds, 114 residues, 3 models selected
> select up
3574 atoms, 3624 bonds, 236 residues, 3 models selected
> ui tool show "Surface Color"
> select sel @ select sel @ color sel #FFBF00
> select clear
> select #1/L:3
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1/H:62
27 atoms, 25 bonds, 2 residues, 2 models selected
> select up
1718 atoms, 1740 bonds, 114 residues, 3 models selected
> select up
3574 atoms, 3624 bonds, 236 residues, 3 models selected
> select sel : color sel #FFBF00
> select clear
> select ::name="NAG"
758 atoms, 758 bonds, 30 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select clear
Drag select of 164 residues
> select up
5248 atoms, 5319 bonds, 347 residues, 4 models selected
> select up
7148 atoms, 7248 bonds, 472 residues, 4 models selected
> hide
> ~hide
Unknown command: ~hide
> select clear
Drag select of 80 residues
> select down
1154 atoms, 80 residues, 3 models selected
> select up
5050 atoms, 5118 bonds, 334 residues, 3 models selected
> select up
5248 atoms, 5320 bonds, 347 residues, 3 models selected
> select up
53010 atoms, 53706 bonds, 3376 residues, 3 models selected
> select down
5248 atoms, 5320 bonds, 347 residues, 10 models selected
> select clear
Drag select of 215 residues
> select up
7069 atoms, 7167 bonds, 467 residues, 4 models selected
> select up
7148 atoms, 7248 bonds, 472 residues, 4 models selected
> hide sel cartoons
> center
Unknown command: center
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/H5_Footprints.cxs" includeMaps true
> close
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/20D10/20D10.cxs"
opened ChimeraX session
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/12G1/12G1_all_residues.cxs"
opened ChimeraX session
Drag select of 62 residues
> select up
3047 atoms, 3089 bonds, 200 residues, 1 model selected
> select down
886 atoms, 62 residues, 1 model selected
> select down
886 atoms, 62 residues, 1 model selected
> select clear
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/20D10/20D10.cxs"
opened ChimeraX session
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/overlays/Overlays_HCDRs_shown_noH.cxs"
opened ChimeraX session
> show #2 models
> show #!3 models
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/1A1_overlay/H5_1A1.pdb"
Chain information for H5_1A1.pdb #4
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
a b c | No description available
> select clear
> hide #!1 models
> hide #2 models
> hide #!3 models
> select add #4
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
Drag select of 943 residues
> select up
19538 atoms, 19766 bonds, 1242 residues, 1 model selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 1 model selected
> color sel grey
> select clear
> select #4/b:119
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/B:258
42 atoms, 42 bonds, 2 residues, 1 model selected
> select up
904 atoms, 910 bonds, 53 residues, 1 model selected
> select up
7638 atoms, 7738 bonds, 484 residues, 1 model selected
> color sel light grey
> select clear
Drag select of 146 residues
> select up
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> color sel #FFBF00
> select clear
> show #!3 models
> show #2 models
> show #!1 models
> hide #!1 models
> hide #2 models
> hide #!3 models
> hide #4 models
> show #!1 models
> show #2 models
> show #!3 models
Drag select of 233 residues
> select up
9754 atoms, 9886 bonds, 642 residues, 3 models selected
> select up
10699 atoms, 10845 bonds, 704 residues, 3 models selected
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #2#!1,3 atoms
> select clear
Drag select of 211 residues
> select up
9706 atoms, 9838 bonds, 639 residues, 3 models selected
> select up
10699 atoms, 10845 bonds, 704 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 26126 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
> hide #!3 models
> hide #2 models
Drag select of 91 atoms, 674 residues, 90 bonds
> select up
21558 atoms, 21790 bonds, 1386 residues, 9 models selected
> select up
21656 atoms, 21891 bonds, 1386 residues, 9 models selected
> select up
29336 atoms, 29703 bonds, 1884 residues, 9 models selected
> select up
33630 atoms, 34074 bonds, 2156 residues, 9 models selected
> select clear
Drag select of 127 atoms, 808 residues, 128 bonds
> select up
12863 atoms, 12978 bonds, 818 residues, 7 models selected
> select up
12978 atoms, 13095 bonds, 818 residues, 7 models selected
> select up
19098 atoms, 19328 bonds, 1209 residues, 7 models selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 7 models selected
> show sel surfaces
> select clear
> show #2 models
> show #!3 models
> show #4 models
> hide #4 models
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs" includeMaps
> true
> show #4 models
> hide #4 models
> hide #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> select #2/a:46
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/A:119
27 atoms, 25 bonds, 2 residues, 1 model selected
> select up
404 atoms, 403 bonds, 25 residues, 1 model selected
> select up
7658 atoms, 7758 bonds, 485 residues, 1 model selected
> color sel light grey
> select add #2/b:90
7670 atoms, 7769 bonds, 486 residues, 1 model selected
> select clear
> select add #2/b:90
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/c:86
24 atoms, 22 bonds, 2 residues, 1 model selected
> select add #2/B:179
43 atoms, 40 bonds, 3 residues, 1 model selected
> select add #2/C:148
54 atoms, 50 bonds, 4 residues, 1 model selected
> select up
2360 atoms, 2383 bonds, 142 residues, 1 model selected
> select up
15315 atoms, 15515 bonds, 970 residues, 1 model selected
> color sel grey
> select clear
Drag select of 356 residues
> select up
10972 atoms, 11070 bonds, 703 residues, 1 model selected
> select up
22973 atoms, 23273 bonds, 1455 residues, 1 model selected
> show sel surfaces
> select clear
> select ::name="NAG"
1340 atoms, 1340 bonds, 54 residues, 4 models selected
> show sel & #!2 atoms
> color sel & #!2 byhetero
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!2 atoms
> select clear
> show #!3 models
> show #!1 models
> select add #1
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> hide sel surfaces
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs" includeMaps
> true
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
Drag select of 243 residues
> select up
14841 atoms, 15040 bonds, 944 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> show #!1 models
> hide #!2 models
Drag select of 3 atoms, 273 residues, 2 bonds
> select up
4404 atoms, 4446 bonds, 274 residues, 4 models selected
> select up
10420 atoms, 10568 bonds, 659 residues, 4 models selected
> select up
15107 atoms, 15315 bonds, 954 residues, 4 models selected
> hide sel cartoons
> select clear
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> select add #1
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> select add #3
52926 atoms, 53620 bonds, 3373 residues, 8 models selected
> hide sel atoms
> select clear
> select #1/H:1-95
1490 atoms, 1510 bonds, 98 residues, 1 model selected
> transparency sel 75 cartoons
> select #2/H:1-95
1467 atoms, 1486 bonds, 97 residues, 1 model selected
> transparency sel 75 cartoons
> select #3/H:1-95
1499 atoms, 1519 bonds, 98 residues, 1 model selected
> transparency sel 75 cartoons
> select clear
> select #3/H:100H-113
167 atoms, 168 bonds, 12 residues, 1 model selected
> transparency sel 75 cartoons
> select #2/H:100H-113
185 atoms, 186 bonds, 13 residues, 1 model selected
> transparency sel 75 cartoons
> select #1/H:100H-113
204 atoms, 206 bonds, 15 residues, 1 model selected
> select #1/H:100I-113
197 atoms, 199 bonds, 14 residues, 1 model selected
> transparency sel 75 cartoons
> select clear
> select #1/L:1-17
236 atoms, 238 bonds, 16 residues, 1 model selected
> select #1/L:127
Nothing selected
> select #1/L:1-27
372 atoms, 375 bonds, 26 residues, 1 model selected
> transparency sel 75 cartoons
> select #2/L:1-27
389 atoms, 392 bonds, 27 residues, 1 model selected
> transparency sel 75 cartoons
> select #3/L:1-27
389 atoms, 392 bonds, 27 residues, 1 model selected
> transparency sel 75 cartoons
> select #3/L:33-113
1154 atoms, 1166 bonds, 75 residues, 1 model selected
> transparency sel 75 cartoons
> select #2/L:33-113
1164 atoms, 1178 bonds, 75 residues, 1 model selected
> transparency sel 75 cartoons
> select up
1712 atoms, 1734 bonds, 112 residues, 1 model selected
> select clear
> select #1/L:33-113
1151 atoms, 1165 bonds, 75 residues, 1 model selected
> transparency sel 75 cartoons
> select clear
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save overlay_zoom_H5.png supersample 8 transparentBackground true
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs_transparencies.cxs"
> includeMaps true
> hide #!3 models
> hide #!2 models
> select add #1
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> show sel cartoons
> select clear
> 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
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #1/H:32,96,100B,100C,100E
90 atoms, 88 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!1 atoms
> select clear
> ~transparency
Unknown command: ~transparency
> transparency all -
Missing or invalid "percent" argument: Expected a number
> transparency all 0
> transparency all c 0
Missing or invalid "percent" argument: Expected a number
> transparency all 0 cartoons
Drag select of 102 residues
> select up
3539 atoms, 3589 bonds, 234 residues, 1 model selected
> select up
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> select down
3539 atoms, 3589 bonds, 234 residues, 1 model selected
> select up
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> hide sel cartoons
> select #1/H:95-100H,30-34
313 atoms, 320 bonds, 19 residues, 1 model selected
> show sel cartoons
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
7 hydrogen bonds found
> select clear
> select #1/L:32@CZ
1 atom, 1 residue, 1 model selected
> select add #1/H:97@CD
2 atoms, 2 residues, 1 model selected
> select add #1/H:100F@CD2
3 atoms, 3 residues, 1 model selected
> select add #1/L:34@CG
4 atoms, 4 residues, 1 model selected
> select subtract #1/L:34@CG
3 atoms, 3 residues, 1 model selected
> select add #1/L:34@CG
4 atoms, 4 residues, 1 model selected
> select add #1/L:32@CG
5 atoms, 4 residues, 1 model selected
> select up
78 atoms, 76 bonds, 4 residues, 1 model selected
> select up
2614 atoms, 2646 bonds, 173 residues, 1 model selected
> select down
78 atoms, 76 bonds, 4 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/H:100E
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:125B,128,169,124,167
68 atoms, 64 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/H:32@HH
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> select clear
> select #1/H:100C@CD1
1 atom, 1 residue, 1 model selected
> select add #1/H:100C@CD1
1 atom, 1 bond, 1 residue, 1 model selected
> ui tool show Distances
> select add #1/A:124@CG1
2 atoms, 1 bond, 2 residues, 1 model selected
> distance #1/H:100C@CD1 #1/A:124@CG1
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H LEU
100C CD1 and /A ILE 124 CG1: 5.076
> distance style color #ffd479
> select clear
> distance style color #73fdff
> distance style color #76d6ff
> distance style color #73fdff
> distance style color #00fdff
> select #1/H:96@CG
1 atom, 1 residue, 1 model selected
> select add #1/A:128@CG
2 atoms, 2 residues, 1 model selected
> distance #1/H:96@CG #1/A:128@CG
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H LEU
96 CG and /A PRO 128 CG: 3.739
> distance style color #73fdff
> distance style color #00fdff
> select clear
> select H
51907 atoms, 6741 residues, 4 models selected
> select clear
> select #1/H:32@OH
1 atom, 1 residue, 1 model selected
> select add #1/A:125B
12 atoms, 10 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select #1/A:125B
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/A:125B@O
1 atom, 1 residue, 1 model selected
> select add #1/H:32@OH
2 atoms, 2 residues, 2 models selected
> distance #1/A:125B@O #1/H:32@OH
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A SER
125B O and /H TYR 32 OH: 3.186
> select add #1/A:125B@CA
3 atoms, 2 residues, 2 models selected
> select #1/A:125B@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
44 atoms, 43 bonds, 3 residues, 2 models selected
> show sel cartoons
> select #1/H:100D
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #1/A:167
25 atoms, 23 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #1/H:100D@O
1 atom, 1 residue, 1 model selected
> select add #1/A:167@N
2 atoms, 2 residues, 1 model selected
> distance #1/H:100D@O #1/A:167@N
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H ASN
100D O and /A SER 167 N: 2.867
> select add #1/A:167@CB
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
25 atoms, 23 bonds, 2 residues, 2 models selected
> show sel cartoons
> select #1/A:169
13 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/H:100B
23 atoms, 21 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #1/H:100B@O
1 atom, 1 residue, 1 model selected
> select add #1/A:169@H
2 atoms, 2 residues, 1 model selected
> select add #1/A:169@N
3 atoms, 2 residues, 2 models selected
> select subtract #1/A:169@H
2 atoms, 2 residues, 2 models selected
> distance #1/H:100B@O #1/A:169@N
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H ALA
100B O and /A ASN 169 N: 2.933
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
23 atoms, 21 bonds, 2 residues, 2 models selected
> show sel cartoons
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!1 atoms
> select clear
> label delete
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5.cxs" includeMaps true
Drag select of 71 residues
> select up
3283 atoms, 3327 bonds, 216 residues, 1 model selected
> hide sel cartoons
Drag select of 14 residues
> select up
3549 atoms, 3597 bonds, 234 residues, 1 model selected
> select up
26522 atoms, 26870 bonds, 1689 residues, 1 model selected
> select down
3549 atoms, 3597 bonds, 234 residues, 7 models selected
> hide sel cartoons
> select clear
> select #2/H:32,96,100A,100B,100C,100F
115 atoms, 115 bonds, 6 residues, 1 model selected
> show sel atoms
> select #2/A:125B,128,169,124,167,164
87 atoms, 82 bonds, 6 residues, 1 model selected
> show sel atoms
> select up
536 atoms, 542 bonds, 33 residues, 2 models selected
> select clear
> select #2/H:95-100H,30-34
305 atoms, 312 bonds, 19 residues, 1 model selected
> show sel cartoons
> select #2/H:32,96,100A,100B,100C,100F
115 atoms, 115 bonds, 6 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
5 hydrogen bonds found
> select #2/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
Unsupported scale factor (0.000000) detected on Display1
> select #2/A:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/H:100C
32 atoms, 31 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #2/A:167@O
1 atom, 1 residue, 1 model selected
> select add #2/H:100C@N
2 atoms, 1 bond, 2 residues, 2 models selected
> distance #2/A:167@O #2/H:100C@N
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A SER 167 O
and /H TYR 100C N: 3.145
> select #2/A:167@CA
1 atom, 1 residue, 1 model selected
Drag select of 8 residues
> select clear
> select add #2/H:100C@H
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
32 atoms, 31 bonds, 2 residues, 2 models selected
> show sel cartoons
Drag select of 5 residues
> select #2/B:96
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
Drag select of 1 residues
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #2/H:100C
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/A:167
32 atoms, 31 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #2/A:169
13 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/H:100A
27 atoms, 26 bonds, 2 residues, 2 models selected
> hide sel cartoons
> select #2/A:169@H
1 atom, 1 residue, 1 model selected
> select add #2/H:100A@O
2 atoms, 2 residues, 2 models selected
> select add #2/A:169@N
3 atoms, 2 residues, 2 models selected
> select subtract #2/A:169@H
2 atoms, 2 residues, 2 models selected
> distance #2/H:100A@O #2/A:169@N
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H PRO 100A O
and /A ASN 169 N: 2.681
> select up
27 atoms, 26 bonds, 2 residues, 2 models selected
> show sel cartoons
> select #2/A:164
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/A:164@O
1 atom, 1 residue, 1 model selected
> select add #2/H:100F@OH
2 atoms, 2 residues, 2 models selected
> distance #2/A:164@O #2/H:100F@OH
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A ILE 164 O
and /H TYR 100F OH: 2.667
> select #2/A:164@CA
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> show sel cartoons
> select #2/A:126
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:125B
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/A:125B@O
1 atom, 1 residue, 1 model selected
> select add #2/H:32@OH
2 atoms, 2 residues, 2 models selected
> distance #2/A:125B@O #2/H:32@OH
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A SER 125B O
and /H TYR 32 OH: 2.433
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> show sel cartoons
> select #2/H:96@CG
1 atom, 1 residue, 1 model selected
> select add #2/A:128@CG
2 atoms, 2 residues, 1 model selected
> distance #2/H:96@CG #2/A:128@CG
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H LEU 96 CG
and /A PRO 128 CG: 4.188
> distance #2/H:96@CG #2/A:128@CG
Window position QRect(2388,390 600x300) outside any known screen, using
primary screen
Distance already exists; modify distance properties with 'distance style'
> distance style color #0096ff
> distance style color #00fdff
> distance style color #797979
> distance style color #00fdff
> distance style color #797979
> select clear
> distance style color #00fdff
> distance style color #797979
> color sel turquoise
> select #2/a:125
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/H:100B@CG
1 atom, 1 residue, 1 model selected
> select add #2/A:124@CG1
2 atoms, 2 residues, 1 model selected
> distance #2/H:100B@CG #2/A:124@CG1
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H LEU 100B CG
and /A ILE 124 CG1: 4.851
> color sel turquoise
Drag select of 7 residues
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!2 atoms
> select clear
> label delete
> select clear
> select #2/A:125B,128,169,124,167,164
87 atoms, 82 bonds, 6 residues, 1 model selected
> color sel byhetero
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
Drag select of 369 residues
> select up
22587 atoms, 22873 bonds, 1439 residues, 1 model selected
> color sel grey
> select clear
> select #3/B:175
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/b:50
26 atoms, 24 bonds, 2 residues, 1 model selected
> select up
7487 atoms, 7581 bonds, 477 residues, 1 model selected
> select up
7568 atoms, 7666 bonds, 481 residues, 1 model selected
> color sel light grey
> select clear
Drag select of 60 residues
> select up
3095 atoms, 3137 bonds, 203 residues, 1 model selected
> select up
3576 atoms, 3624 bonds, 234 residues, 1 model selected
> hide sel cartoons
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5.cxs" includeMaps true
> select #3/H:32,100B,100C,100D
72 atoms, 72 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/H:95-100H,30-34
310 atoms, 317 bonds, 19 residues, 1 model selected
> show sel cartoons
> select #3/B:9125B,169,166,167
43 atoms, 41 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/H:32,100B,100C,100D
72 atoms, 72 bonds, 4 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
3 hydrogen bonds found
> select #3/B:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/H:100D
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/B:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/H:100D
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/B:167
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #3/L:32@CE2
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:167
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/H:100D
32 atoms, 31 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #3/B:167@O
1 atom, 1 residue, 1 model selected
> select add #3/H:100D@N
2 atoms, 2 residues, 1 model selected
> distance #3/B:167@O #3/H:100D@N
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B SER
167 O and /H TYR 100D N: 3.491
> select add #3/B:167@CA
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
32 atoms, 31 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #3/H:100B
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/B:169
24 atoms, 22 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #3/B:169@N
1 atom, 1 residue, 1 model selected
> select add #3/H:100B@O
2 atoms, 2 residues, 1 model selected
> distance #3/B:169@N #3/H:100B@O
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B ASN
169 N and /H SER 100B O: 2.530
> select #3/B:169@CB
1 atom, 1 residue, 1 model selected
> select add #3/H:100B@CA
2 atoms, 2 residues, 1 model selected
> select up
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #3/B:125B
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/B:125B@O
1 atom, 1 residue, 1 model selected
> select add #3/H:32@OH
2 atoms, 2 residues, 1 model selected
> distance #3/B:125B@O #3/H:32@OH
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B SER
125B O and /H TYR 32 OH: 2.529
> select #3/B:125B@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3/H:100C@CD1
1 atom, 1 residue, 1 model selected
> select add #3/B:166@CG2
2 atoms, 2 residues, 1 model selected
> distance #3/H:100C@CD1 #3/B:166@CG2
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/H LEU
100C CD1 and /B ILE 166 CG2: 3.613
> color sel turquoise
> select clear
> select H
51907 atoms, 6741 residues, 4 models selected
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!3 atoms
> select clear
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> delete labels
Missing or invalid "atoms" argument: invalid atoms specifier
> labels delete
Unknown command: labels delete
> label delete
> select #3/b:78
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #3/H:100C
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/B:166
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #3/H:100C
38 atoms, 36 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs" includeMaps
> true
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> select ::name="NAG"
1340 atoms, 1340 bonds, 54 residues, 4 models selected
> show sel & #!1-3 atoms
> color sel & #!1-3 byhetero
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!1-3 atoms
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs" includeMaps
> true
> show #4 models
> hide #4 models
> hide #!3 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #!3 models
> show #4 models
> hide #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/H:100G
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!1 atoms
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> select #3/H:100G
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!3 atoms
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> select #1/H:100C
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/H:96
38 atoms, 36 bonds, 2 residues, 1 model selected
> select add #1/H:95
50 atoms, 47 bonds, 3 residues, 1 model selected
> select add #1/H:97
74 atoms, 70 bonds, 4 residues, 1 model selected
> select add #1/H:98
89 atoms, 84 bonds, 5 residues, 1 model selected
> select add #1/H:99
113 atoms, 109 bonds, 6 residues, 1 model selected
> select add #1/H:100
124 atoms, 119 bonds, 7 residues, 1 model selected
> select add #1/H:100A
131 atoms, 125 bonds, 8 residues, 1 model selected
> select add #1/H:100B
141 atoms, 134 bonds, 9 residues, 1 model selected
> select add #1/H:100G
162 atoms, 155 bonds, 10 residues, 1 model selected
> select add #1/H:100H
169 atoms, 161 bonds, 11 residues, 1 model selected
> select add #1/H:100E
190 atoms, 182 bonds, 12 residues, 1 model selected
> select add #1/H:100F
211 atoms, 203 bonds, 13 residues, 1 model selected
> select add #1/H:100D
225 atoms, 216 bonds, 14 residues, 1 model selected
> transparency 50 selection
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 selected
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 selected c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency c 50 selected
Missing or invalid "percent" argument: Expected a number
> transparency select 50 c
Missing or invalid "percent" argument: Expected a number
> transparency 50 selection c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 select c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 selected c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 target c
> transparency 0 target c
> transparency sel 50 target c
> select clear
> show #!2 models
> hide #!2 models
> select #1/H:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/H:100H
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/H:100B
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> select clear
> select add #1/A:144
10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected
> select subtract #1/A:144
1 pseudobond, 2 models selected
> select add #1/A:144
10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected
> select subtract #1/A:144
1 pseudobond, 2 models selected
> select add #1/A:144
10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected
> color sel turquoise
> select clear
> select #1/A:144
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel light grey
> select clear
> save 6G1_Hbond.png supersample 8 transparentBackground true
> hide #!1 models
> show #!2 models
> show #!1 models
> select #2/H:95
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #2/H:100G
22 atoms, 20 bonds, 2 residues, 1 model selected
> select add #2/H:100H
39 atoms, 36 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #2/H:100F
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/H:100E
42 atoms, 42 bonds, 2 residues, 1 model selected
> select add #2/H:100D
63 atoms, 63 bonds, 3 residues, 1 model selected
> select add #2/H:100C
84 atoms, 84 bonds, 4 residues, 1 model selected
> select add #2/H:100B
103 atoms, 102 bonds, 5 residues, 1 model selected
> select add #2/H:100A
117 atoms, 116 bonds, 6 residues, 1 model selected
> select add #2/H:100
124 atoms, 122 bonds, 7 residues, 1 model selected
> select add #2/H:99
138 atoms, 135 bonds, 8 residues, 1 model selected
> select add #2/H:98
149 atoms, 145 bonds, 9 residues, 1 model selected
> select add #2/H:97
159 atoms, 154 bonds, 10 residues, 1 model selected
> select add #2/H:96
178 atoms, 172 bonds, 11 residues, 1 model selected
> transparency sel 50 target c
> select clear
> save 20D10_Hbond.png supersample 8 transparentBackground true
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> select #3/H:95
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #3/H:100H
21 atoms, 19 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #3/H:96
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/H:97
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #3/H:98
28 atoms, 26 bonds, 2 residues, 1 model selected
> select add #3/H:99
52 atoms, 49 bonds, 3 residues, 1 model selected
> select add #3/H:100
59 atoms, 55 bonds, 4 residues, 1 model selected
> select add #3/H:100A
73 atoms, 69 bonds, 5 residues, 1 model selected
> select add #3/H:100B
84 atoms, 79 bonds, 6 residues, 1 model selected
> select add #3/H:100C
103 atoms, 97 bonds, 7 residues, 1 model selected
> select add #3/H:100D
124 atoms, 118 bonds, 8 residues, 1 model selected
> select add #3/H:100E
145 atoms, 139 bonds, 9 residues, 1 model selected
> select add #3/H:100F
166 atoms, 160 bonds, 10 residues, 1 model selected
> select add #3/H:100G
187 atoms, 181 bonds, 11 residues, 1 model selected
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> transparency sel 50 target c
> select clear
> save 12G1_Hbond.png supersample 8 transparentBackground true
> show #!2 models
> hide #!2 models
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs" includeMaps
> true
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/FigureMakingChimeraXSessions/Conservation/sequenceCons_sameClade_2024_allGaraziSequences.cxs"
opened ChimeraX session
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/H5_11SequencesAlignment.aln"
Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre
Leon/Flu Andre/GaraziH5/RevisionsWard/H5_11SequencesAlignment.aln
---
notes | Alignment identifier is H5_11SequencesAlignment.aln
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment H5_11SequencesAlignment.aln
Opened 10 sequences from H5_11SequencesAlignment.aln
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"
Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre
Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln
---
notes | Alignment identifier is H5_12sequences.aln
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment H5_12sequences.aln
Opened 10 sequences from H5_12sequences.aln
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"
Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre
Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln
---
notes | Alignment identifier is H5_12sequences.aln
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to
A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment H5_12sequences.aln
Opened 10 sequences from H5_12sequences.aln
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"
Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre
Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln
---
notes | Alignment identifier is H5_12sequences.aln
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to
A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with
0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment H5_12sequences.aln
Opened 12 sequences from H5_12sequences.aln
> select #1/A:125@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 2 models selected
> select up
221 atoms, 223 bonds, 12 residues, 2 models selected
> select up
4285 atoms, 4343 bonds, 269 residues, 2 models selected
> select up
5018 atoms, 5086 bonds, 317 residues, 2 models selected
> select up
5045 atoms, 5114 bonds, 318 residues, 2 models selected
> select clear
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> select add #1
26505 atoms, 26853 bonds, 1688 residues, 1 model selected
> select subtract #1
6 models selected
Drag select of H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A SES
surface, 143751 of 345860 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_B SES surface, 139576 of
352546 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_C SES
surface, 130568 of 351158 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_a SES surface, 122587 of
239464 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_b SES
surface, 128984 of 244122 triangles,
H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_c SES surface, 143182 of
233634 triangles, 42 atoms, 631 residues, 42 bonds
> select up
9829 atoms, 9907 bonds, 634 residues, 7 models selected
> select up
18234 atoms, 18443 bonds, 1158 residues, 7 models selected
> select up
22931 atoms, 23229 bonds, 1452 residues, 7 models selected
> color byattribute seq_conservation sel palette "dark slate gray:sandy
> brown:moccasin:light yellow:white" key true
> key darkslategrey:-4.895 sandybrown:-3.595 moccasin:-2.294
> lightyellow:-0.994 white:0.306 showTool true
> ui mousemode right "color key"
22931 atoms, 1452 residues, 6 surfaces, atom seq_conservation range -4.89 to
0.306
> key white:0.306 lightyellow:-0.994 moccasin:-2.294 sandybrown:-3.595
> darkslategrey:-4.895
> key colorTreatment distinct
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select #1/A:240@CG
1 atom, 1 residue, 1 model selected
> select clear
> key pos 0.683575,0.807168 size 0,0
> select #1-3/H:100A-102
516 atoms, 526 bonds, 32 residues, 3 models selected
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"
> includeMaps true
> transparency sel 15 target c
> select clear
> hide #2 models
> show #2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #1/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/H:100C
26 atoms, 24 bonds, 2 residues, 1 model selected
> select add #1/H:100B
36 atoms, 33 bonds, 3 residues, 1 model selected
> select add #1/H:100D
50 atoms, 46 bonds, 4 residues, 1 model selected
> select add #1/H:100E
71 atoms, 67 bonds, 5 residues, 1 model selected
> select add #1/H:100F
92 atoms, 88 bonds, 6 residues, 1 model selected
> select add #1/H:100G
113 atoms, 109 bonds, 7 residues, 1 model selected
> select add #1/H:100H
120 atoms, 115 bonds, 8 residues, 1 model selected
> select add #1/H:100I
137 atoms, 131 bonds, 9 residues, 1 model selected
> select add #1/H:101
149 atoms, 142 bonds, 10 residues, 1 model selected
> select add #1/H:102
165 atoms, 157 bonds, 11 residues, 1 model selected
> select clear
> show #2 models
> show #!3 models
> ui tool show "Side View"
> select #1-3/H:100A-102
516 atoms, 526 bonds, 32 residues, 3 models selected
> transparency sel 20
> transparency sel 20 target ac
> select clear
> select #1-3/H:100A-102
516 atoms, 526 bonds, 32 residues, 3 models selected
> transparency sel 40 target ac
> transparency sel 50 target ac
> select clear
> save seqConsTransCDRH3.png supersample 8 tranparentBackground true
Expected a keyword
> save seqConsTransCDRH3.png supersample 8 transparentBackground true
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"
> hide #!3 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> select #1/H:100A
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/H:100C
26 atoms, 24 bonds, 2 residues, 1 model selected
> select add #1/H:100B
36 atoms, 33 bonds, 3 residues, 1 model selected
> select add #1/H:100D
50 atoms, 46 bonds, 4 residues, 1 model selected
> select add #1/H:100E
71 atoms, 67 bonds, 5 residues, 1 model selected
> select add #1/H:100F
92 atoms, 88 bonds, 6 residues, 1 model selected
> select add #1/H:100H
99 atoms, 94 bonds, 7 residues, 1 model selected
> select add #1/H:100G
120 atoms, 115 bonds, 8 residues, 1 model selected
> select add #1/H:100I
137 atoms, 131 bonds, 9 residues, 1 model selected
> select add #1/H:101
149 atoms, 142 bonds, 10 residues, 1 model selected
> select add #1/H:102
165 atoms, 157 bonds, 11 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #2 models
> save seqConsTransCDRH3_clone1Only.png supersample 8 transparentBackground
> true
> select #1-3/H:100A-102
516 atoms, 526 bonds, 32 residues, 3 models selected
> transparency sel 0 target ac
> select clear
> save seqConsNotTransCDRH3_clone1Only.png supersample 8 transparentBackground
> true
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"
> ui mousemode right translate
opened ChimeraX session
> select #1-3/H:100A-102
516 atoms, 526 bonds, 32 residues, 3 models selected
> transparency sel 0 target ac
> select clear
> save seqConsNotTransCDRH3_AllClones.png supersample 8 transparentBackground
> true
> open "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs"
opened ChimeraX session
> lighting soft
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!1-3 surfaces
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!2 models
> hide #!1 models
Drag select of 500 residues
> select up
22587 atoms, 22873 bonds, 1439 residues, 1 model selected
> select up
22845 atoms, 23143 bonds, 1451 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> show #!1 models
> hide #!1 models
Drag select of 69 atoms, 466 residues, 70 bonds
> select up
7568 atoms, 7632 bonds, 471 residues, 7 models selected
> select up
7633 atoms, 7697 bonds, 471 residues, 7 models selected
> select up
12311 atoms, 12424 bonds, 771 residues, 7 models selected
> select up
22973 atoms, 23273 bonds, 1455 residues, 7 models selected
> hide sel cartoons
> hide #!2 models
> show #!1 models
> show #!2 models
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> select clear
Drag select of 286 residues
> select up
9799 atoms, 9933 bonds, 645 residues, 3 models selected
> select up
10699 atoms, 10845 bonds, 704 residues, 3 models selected
> select clear
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> select add #2
26522 atoms, 26870 bonds, 1689 residues, 1 model selected
> show sel cartoons
> select add #3
52943 atoms, 53637 bonds, 3374 residues, 8 models selected
> select subtract #2
26421 atoms, 26767 bonds, 1685 residues, 7 models selected
> hide #!2 models
> show sel cartoons
> select clear
Drag select of 607 residues
> select up
22587 atoms, 22873 bonds, 1439 residues, 1 model selected
> select up
22845 atoms, 23143 bonds, 1451 residues, 1 model selected
> color sel grey
> select clear
> select #3/b:59
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #3/B:239
31 atoms, 30 bonds, 2 residues, 1 model selected
> select up
7487 atoms, 7581 bonds, 477 residues, 1 model selected
> select up
7568 atoms, 7666 bonds, 481 residues, 1 model selected
> color sel light grey
> select clear
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> select #2/L:56,49,53,27E,28
77 atoms, 75 bonds, 5 residues, 1 model selected
> show sel atoms
> select clear
Drag select of 70 residues
> select up
3204 atoms, 3248 bonds, 211 residues, 1 model selected
> select up
3549 atoms, 3597 bonds, 234 residues, 1 model selected
> hide sel cartoons
> select #2/L:56,49,53,27E,28
77 atoms, 75 bonds, 5 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
5 hydrogen bonds found
> select #2/L:49-56,27D-29
175 atoms, 176 bonds, 12 residues, 1 model selected
> show sel cartoons
> color sel byhetero
> select #2/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #2/B:220
38 atoms, 36 bonds, 2 residues, 2 models selected
> select subtract #2/B:220
14 atoms, 13 bonds, 1 residue, 3 models selected
> select add #2/B:227
38 atoms, 36 bonds, 2 residues, 2 models selected
> color sel byhetero
> select clear
> select #2/A:162
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #2/L:27D
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/L:56@CG
1 atom, 1 residue, 1 model selected
> select add #2/A:162@CG
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #2/L:56@CG #2/A:162@CG
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L PRO 56 CG
and /A PRO 162 CG: 3.693
> select #2/L:53@OD1
1 atom, 1 residue, 1 model selected
> select add #2/A:163@OG1
2 atoms, 2 residues, 1 model selected
> distance #2/L:53@OD1 #2/A:163@OG1
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L ASP 53 OD1
and /A THR 163 OG1: 3.224
> select #2/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/A:163@O
1 atom, 1 residue, 1 model selected
> select add #2/L:49@OH
2 atoms, 2 residues, 2 models selected
> distance #2/A:163@O #2/L:49@OH
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A THR 163 O
and /L TYR 49 OH: 2.735
> select #2/A:163@C
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/B:227@NH2
1 atom, 1 residue, 1 model selected
> select add #2/L:27E@O
2 atoms, 2 residues, 2 models selected
> distance #2/B:227@NH2 #2/L:27E@O
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH2
and /L SER 27E O: 3.130
> select #2/B:227@NH1
1 atom, 1 residue, 1 model selected
> select add #2/L:27E@O
2 atoms, 2 residues, 2 models selected
> distance #2/B:227@NH1 #2/L:27E@O
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH1
and /L SER 27E O: 3.344
> select #2/L:27E@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/L:28
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/B:227@NH1
1 atom, 1 residue, 1 model selected
> select add #2/L:28@O
2 atoms, 2 residues, 2 models selected
> distance #2/B:227@NH1 #2/L:28@O
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH1
and /L ILE 28 O: 3.083
> select #2/L:28@CB
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!2 atoms
> label delete
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> hide #!2 models
> show #!1 models
> select #1/L:49,30,28,53,67,28
85 atoms, 83 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
6 hydrogen bonds found
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
6 hydrogen bonds found
Drag select of 143 residues
> select up
3539 atoms, 3589 bonds, 234 residues, 1 model selected
> select up
3574 atoms, 3624 bonds, 236 residues, 1 model selected
> hide sel cartoons
> select #1/L:28-31,66-68,49-53
157 atoms, 157 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/L:27-31,66-68,49-53
251 atoms, 252 bonds, 18 residues, 1 model selected
> show sel cartoons
> select #1/L:27A
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
1674 atoms, 1696 bonds, 111 residues, 1 model selected
> hide sel cartoons
> select #1/L:27E-31,66-68,49-53
168 atoms, 168 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/A:165
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/A:169
35 atoms, 33 bonds, 2 residues, 2 models selected
> select add #1/A:246
50 atoms, 47 bonds, 3 residues, 2 models selected
> select add #1/B:187
64 atoms, 60 bonds, 4 residues, 2 models selected
> color sel byhetero
> select clear
> select #1/L:53@OH
1 atom, 1 residue, 1 model selected
> select add #1/A:246@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/L:53@OH #1/A:246@OE2
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/L TYR
53 OH and /A GLU 246 OE2: 2.663
> select #1/B:187@ND2
1 atom, 1 residue, 1 model selected
> select add #1/L:67@OG
2 atoms, 2 residues, 2 models selected
> distance #1/B:187@ND2 #1/L:67@OG
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/B ASN
187 ND2 and /L SER 67 OG: 3.323
> select #1/A:165@NZ
1 atom, 1 residue, 1 model selected
> select add #1/L:30@OG
2 atoms, 2 residues, 2 models selected
> distance #1/A:165@NZ #1/L:30@OG
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A LYS
165 NZ and /L SER 30 OG: 2.526
> select #1/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/A:163@O
1 atom, 1 residue, 1 model selected
> select add #1/L:49@OH
2 atoms, 2 residues, 2 models selected
> distance #1/A:163@O #1/L:49@OH
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A THR
163 O and /L TYR 49 OH: 2.672
> select clear
> select #1/A:163@CA
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1/A:169@ND2
1 atom, 1 residue, 1 model selected
> select add #1/L:28@OH
2 atoms, 2 residues, 2 models selected
> distance #1/A:169@ND2 #1/L:28@OH
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A ASN
169 ND2 and /L TYR 28 OH: 2.563
> select #1/B:227
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
0 hydrogen bonds found
> color sel byhetero
> select #1/L:28
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/B:227@CZ
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol
> false intraRes false reveal true retainCurrent true
0 hydrogen bonds found
> hbonds sel color #797979 dashes 6 interModel false distSlop 0.5 angleSlop
> 100.0 intraMol false intraRes false reveal true retainCurrent true
0 hydrogen bonds found
> select #1/B:227@CD
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false distSlop 0.5 angleSlop
> 200.0 intraMol false intraRes false reveal true retainCurrent true
0 hydrogen bonds found
> hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop
> 100.0 intraMol false intraRes false reveal true retainCurrent true
0 hydrogen bonds found
> select #1/L:28@H
1 atom, 1 residue, 1 model selected
> select add #1/B:227@NH2
2 atoms, 2 residues, 1 model selected
> select #1/L:28@N
1 atom, 1 residue, 1 model selected
> select add #1/B:227@NH2
2 atoms, 2 residues, 1 model selected
> distance #1/L:28@N #1/B:227@NH2
Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/L TYR
28 N and /B ARG 227 NH2: 3.144
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!1 atoms
> select clear
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> delete labels
Missing or invalid "atoms" argument: invalid atoms specifier
> label delete
> select clear
> show #!3 models
> hide #!1 models
> select #3/L:52,53,30,28,56,49,28,27E
108 atoms, 106 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel byhetero
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop
> 100.0 intraMol false intraRes false reveal true retainCurrent true
9 hydrogen bonds found
> select #3/B:129
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #3/B:165
36 atoms, 34 bonds, 2 residues, 1 model selected
> select add #3/B:167
47 atoms, 44 bonds, 3 residues, 1 model selected
> select add #3/C:222
64 atoms, 60 bonds, 4 residues, 1 model selected
> select add #3/B:170
78 atoms, 73 bonds, 5 residues, 1 model selected
> select subtract #3/B:170
64 atoms, 60 bonds, 4 residues, 1 model selected
> select add #3/B:169
77 atoms, 72 bonds, 5 residues, 1 model selected
> color sel byhetero
> select clear
Drag select of 101 residues
> select up
3303 atoms, 3349 bonds, 217 residues, 1 model selected
> select up
3576 atoms, 3624 bonds, 234 residues, 1 model selected
> hide sel cartoons
> select clear
> select #3/L:28@OH
1 atom, 1 residue, 1 model selected
> select add #3/B:169@ND2
2 atoms, 2 residues, 1 model selected
> distance #3/L:28@OH #3/B:169@ND2
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L TYR 28
OH and /B ASN 169 ND2: 2.558
> select #3/L:27E@O
1 atom, 1 residue, 1 model selected
> select add #3/C:222@NE2
2 atoms, 2 residues, 1 model selected
> distance #3/L:27E@O #3/C:222@NE2
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L SER
27E O and /C GLN 222 NE2: 3.268
> select #3/L:30@OH
1 atom, 1 residue, 1 model selected
> select add #3/B:167@OG
2 atoms, 2 residues, 1 model selected
> distance #3/L:30@OH #3/B:167@OG
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L TYR 30
OH and /B SER 167 OG: 2.289
> select #3/L:56@OG
1 atom, 1 residue, 1 model selected
> select add #3/B:129@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/L:56@OG #3/B:129@OD1
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L SER 56
OG and /B ASN 129 OD1: 2.905
> select #3/B:165@NZ
1 atom, 1 residue, 1 model selected
> select add #3/L:52@OG
2 atoms, 2 residues, 1 model selected
> distance #3/B:165@NZ #3/L:52@OG
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B LYS
165 NZ and /L SER 52 OG: 3.058
> select #3/B:165@NZ
1 atom, 1 residue, 1 model selected
> select add #3/L:53@OD2
2 atoms, 2 residues, 1 model selected
> distance #3/B:165@NZ #3/L:53@OD2
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B LYS
165 NZ and /L ASP 53 OD2: 3.296
> select #3/B:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/B:163@O
1 atom, 1 residue, 1 model selected
> select add #3/L:49@OH
2 atoms, 2 residues, 1 model selected
> distance #3/B:163@O #3/L:49@OH
Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B THR
163 O and /L TYR 49 OH: 3.479
> select #3/B:163@C
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
4905 atoms, 4970 bonds, 312 residues, 1 model selected
> select down
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3/L:27E-31,48-56
213 atoms, 214 bonds, 14 residues, 1 model selected
> show sel cartoons
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!3 atoms
> label delete
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> select clear
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> select clear
> delete sel
> ~distance #2/B:227@NH2 #2/L:27E@O
> ~distance #2/B:227@NH1 #2/L:27E@O
> select #2/B:227@NH2
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop
> 100.0 intraMol false intraRes false reveal true retainCurrent true
2 hydrogen bonds found
> select #2/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #2/L:27E@O
1 atom, 1 residue, 1 model selected
> select add #2/B:227@NH2
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #2/L:27E@O #2/B:227@NH2
Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L SER 27E O
and /B ARG 227 NH2: 3.130
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> select H
51907 atoms, 6741 residues, 4 models selected
> hide sel & #!2 atoms
> select clear
> select #2/L:27D@C
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> label delete
> select clear
> color sel turquoise
> select clear
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> select #2/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency sel 50 target c
> select clear
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> select #1/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/L:49
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/L:50
40 atoms, 39 bonds, 2 residues, 1 model selected
> select #1/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/L:49
32 atoms, 31 bonds, 2 residues, 1 model selected
> select add #1/L:50
51 atoms, 49 bonds, 3 residues, 1 model selected
> transparency sel 50 target c
> select clear
> select #1/L:27E
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/L:31
25 atoms, 23 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> select #3/L:48
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/L:49
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/L:53
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/L:49
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/L:50
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #3/L:49
40 atoms, 39 bonds, 2 residues, 1 model selected
> select add #3/L:51
47 atoms, 45 bonds, 3 residues, 1 model selected
> transparency sel 50 target c
> select clear
> select #3/L:31
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> show #!2 models
> hide #!3 models
> select #2/L:49
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/L:50
40 atoms, 39 bonds, 2 residues, 1 model selected
> transparency sel 50 target c
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> save "/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu
> Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs" includeMaps true
> hide #!3 models
> hide #!2 models
> save 6G1_CDRL_H5.png supersample 8 transparentBackground true
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> save 20D10_CDRL_H5.png supersample 8 transparentBackground true
> show #!3 models
> hide #!2 models
> save 12G1_CDRL_H5.png supersample 8 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 77 days, 22 hours, 9 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 4096 x 2304
UI Looks like: 2048 x 1152 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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