Opened 4 months ago

Last modified 4 months ago

#18019 closed defect

Crash on Mac waking from sleep — at Version 1

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-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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(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 (1)

comment:1 by Eric Pettersen, 4 months ago

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