Opened 15 months ago

Closed 15 months ago

#15864 closed defect (duplicate)

Crash on Mac waking from sleep

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

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001f9e78f40 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


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  "uptime" : 240000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1977797578,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 49585,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
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  "captureTime" : "2024-09-02 12:03:21.2860 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "04958DED-A103-4253-8DB2-67569B735966",
  "pid" : 93105,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-09-02 11:08:36.5787 +0100",
  "procStartAbsTime" : 5703640981221,
  "procExitAbsTime" : 5770464206773,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"895C887E-B06F-58A4-8DF1-1D7B64F5832B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "6FBB8B18-4F3C-128F-09FB-635FBB942532",
  "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=="},
  "wakeTime" : 1,
  "sleepWakeUUID" : "A5A3F206-9B03-4AA3-B2B3-66353A304A8F",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4336533143\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1027a4000-1027a8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.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":93105},
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_decodeAndInvokeMessageWithEvent:reply:flags:]","symbolLocation":324,"imageIndex":170},{"imageOffset":8910056,"symbol":"message_handler_message","symbolLocation":88,"imageIndex":170},{"imageOffset":129204,"symbol":"message_handler","symbolLocation":152,"imageIndex":170},{"imageOffset":61300,"symbol":"_xpc_connection_call_event_handler","symbolLocation":144,"imageIndex":171},{"imageOffset":55016,"symbol":"_xpc_connection_mach_event","symbolLocation":1404,"imageIndex":171},{"imageOffset":17576,"symbol":"_dispatch_client_callout4","symbolLocation":20,"imageIndex":163},{"imageOffset":133256,"symbol":"_dispatch_mach_msg_invoke","symbolLocation":468,"imageIndex":163},{"imageOffset":47256,"symbol":"_dispatch_lane_serial_drain","symbolLocation":368,"imageIndex":163},{"imageOffset":136664,"symbol":"_dispatch_mach_invoke","symbolLocation":444,"imageIndex":163},{"imageOffset":47256,"symbol":"_dispatch_lane_serial_drain","symbolLocation":368,"imageIndex":163},{"imageOffset":50552,"symbol":"_dispatch_lane_invoke","symbolLocation":432,"imageIndex":163},{"imageOffset":94928,"symbol":"_dispatch_root_queue_drain_deferred_wlh","symbolLocation":288,"imageIndex":163},{"imageOffset":92996,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":404,"imageIndex":163},{"imageOffset":12300,"symbol":"_pthread_wqthread","symbolLocation":288,"imageIndex":158},{"imageOffset":7464,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":158}]}],
  "usedImages" : [
[deleted to fit within ticket limits]
],
  "sharedCache" : {
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           160K        9 \nColorSync                          640K       30 \nCoreAnimation                     1456K       91 \nCoreGraphics                        48K        3 \nCoreUI image data                 2224K       20 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.4G       85 \nMALLOC guard page                  192K       12 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        560K       35 \nStack                            153.8M       36 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      238.0M      276 \nVM_ALLOCATE (reserved)           128.0M        3         reserved VM address space (unallocated)\n__AUTH                            1864K      374 \n__AUTH_CONST                      29.6M      586 \n__CTF                               824        1 \n__DATA                            21.4M      740 \n__DATA_CONST                      40.2M      749 \n__DATA_DIRTY                      1873K      223 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       555.4M      158 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2200K        1 \n__TEXT                           901.9M      766 \ndyld private memory                320K        3 \nmapped file                      530.1M       80 \nshared memory                     3168K       25 \n===========                     =======  ======= \nTOTAL                              5.1G     4321 \nTOTAL, minus reserved VM space     5.0G     4321 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/gomezdd/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Mla3_mimicry/Figure_mimicry/mimicry.cxs

Log from Mon May 20 11:49:05 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/gomezdd/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/MPMI/Structures_Mla3_HIPP.cxs format session

Log from Sat Jul 15 14:34:47 2023UCSF ChimeraX version: 1.5rc202210312311
(2022-10-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/gomezdd/Downloads/Pwl2delta_LRR_rec6_b0207/Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/gomezdd/Downloads/Pwl2delta_LRR_rec6_b0207/Pwl2delta_LRR_rec6_b0207_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

4105 atoms, 521 residues, atom bfactor range 17.4 to 98.3  

> alphafold contacts #1/A toResidues #1/B distance 3

> open
> /Users/gomezdd/Downloads/Bgh3682_LRR_rec6_9e0a6/Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> open
> /Users/gomezdd/Downloads/Bgh3682_LRR_rec6_9e0a6/Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select add #3

4107 atoms, 4186 bonds, 517 residues, 1 model selected  

> select subtract #3

Nothing selected  

> hide #2 models

> show #2 models

> hide #2 models

> close #3

> show #2 models

> ui tool show Matchmaker

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> /Users/gomezdd/Downloads/Bgh3682_LRR_rec6_9e0a6/Bgh3682_LRR_rec6_9e0a6_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json

> color bfactor #2 palette alphafold

4107 atoms, 517 residues, atom bfactor range 27.4 to 98.1  

> alphafold contacts #2/A toResidues #1/2 distance 3

No to residues specified for alphafold contacts  

> alphafold contacts #2/A toResidues #2/B distance 3

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with
Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#2), sequence alignment score = 2164.7  
RMSD between 414 pruned atom pairs is 0.686 angstroms; (across all 429 pairs:
1.007)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

Alignment identifier is 1/A  
Alignment identifier is 1  
Alignment identifier is 2/A  

> select #1/B:138-184 #2/B:138-184

722 atoms, 724 bonds, 94 residues, 2 models selected  

> select #1/B:138-420 #2/B:138-420

4420 atoms, 4500 bonds, 566 residues, 2 models selected  
1 [ID: 1] region 2 chains [138-420] RMSD: 1.066  
  

> select add #1

6315 atoms, 6436 bonds, 21 pseudobonds, 804 residues, 3 models selected  

> select subtract #1

2210 atoms, 2250 bonds, 283 residues, 1 model selected  

> select add #2

4107 atoms, 4186 bonds, 19 pseudobonds, 517 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] RMSD: 0.836  
  

> select #1/B:402 #2/B:402

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/B:402 #2/B:402

14 atoms, 12 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [402] RMSD: 0.797  
  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] RMSD: 0.836  
  

> select #1/B:407 #2/B:407

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/B:407 #2/B:407

16 atoms, 14 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [407] RMSD: 0.371  
  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] RMSD: 0.836  
  

> select #1/B:406 #2/B:406

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/B:406 #2/B:406

12 atoms, 10 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] RMSD: 0.540  
  

> select #1/B:404,406 #2/B:404,406

36 atoms, 34 bonds, 4 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 1 other block RMSD: 0.704  
  

> select #1/B:404,406,408 #2/B:404,406,408

54 atoms, 50 bonds, 6 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 2 other blocks RMSD: 0.600  
  

> select #1/B:404,406,408,412 #2/B:404,406,408,412

76 atoms, 70 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 3 other blocks RMSD: 0.639  
  

> select #1/B:338,404,406,408,412 #2/B:338,404,406,408,412

86 atoms, 78 bonds, 10 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 4 other blocks RMSD: 0.676  
  

> select #1/B:338,340,404,406,408,412 #2/B:338,340,404,406,408,412

108 atoms, 98 bonds, 12 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 5 other blocks RMSD: 0.634  
  

> select #1/B:315,338,340,404,406,408,412 #2/B:315,338,340,404,406,408,412

124 atoms, 112 bonds, 14 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 6 other blocks RMSD: 0.634  
  

> select #1/B:266,315,338,340,404,406,408,412
> #2/B:266,315,338,340,404,406,408,412

146 atoms, 134 bonds, 16 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 7 other blocks RMSD: 0.621  
  

> select #1/B:266,315,338,340,404,406,408,412,426
> #2/B:266,315,338,340,404,406,408,412,426

174 atoms, 164 bonds, 18 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 8 other blocks RMSD: 0.601  
  

> select #1/B:266,315,338,340,404,406,408,412,426,428
> #2/B:266,315,338,340,404,406,408,412,426,428

190 atoms, 178 bonds, 20 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 9 other blocks RMSD: 0.892  
  

> select #1/B:266,315,338,340,384-429 #2/B:266,315,338,340,384-429

820 atoms, 830 bonds, 100 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 10 other blocks RMSD: 0.969  
  

> select #1/B:266,315,338,340,384-429 #2/B:266,315,338,340,384-429

820 atoms, 830 bonds, 100 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 11 other blocks RMSD: 0.977  
  

> select #1/B:266,315,338,340,384-429 #2/B:266,315,338,340,384-429

820 atoms, 830 bonds, 100 residues, 2 models selected  
1 [ID: 1] region 2 chains [406] + 12 other blocks RMSD: 1.038  
  

> select #1/B:388 #2/B:388

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #1/B:388-390 #2/B:388-390

38 atoms, 36 bonds, 6 residues, 2 models selected  
1 [ID: 1] region 2 chains [388-390] RMSD: 0.747  
  

> select #1/B:388-390,404 #2/B:388-390,404

62 atoms, 60 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 2 chains [388-390] + 1 other block RMSD: 0.770  
  

> select #1/B:394 #2/B:394

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/B:394 #2/B:394

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [394] RMSD: 0.766  
  

> select #1/B:394 #2/B:394

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/B:394 #2/B:394

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [394] RMSD: 0.766  
  

> select add #1

4116 atoms, 4196 bonds, 21 pseudobonds, 522 residues, 3 models selected  

> select subtract #1

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #2

4107 atoms, 4186 bonds, 19 pseudobonds, 517 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/B:404 #2/B:404

24 atoms, 24 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] RMSD: 0.836  
  

> select #1/B:404,406 #2/B:404,406

36 atoms, 34 bonds, 4 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 1 other block RMSD: 0.704  
  

> select #1/B:404,406,408 #2/B:404,406,408

54 atoms, 50 bonds, 6 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 2 other blocks RMSD: 0.600  
  

> select #1/B:404,406,408,412 #2/B:404,406,408,412

76 atoms, 70 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 3 other blocks RMSD: 0.639  
  

> select #1/B:404,406,408,412 #2/B:404,406,408,412

76 atoms, 70 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 3 other blocks RMSD: 0.639  
  

> select #1/B:404,406,408,412 #2/B:404,406,408,412

76 atoms, 70 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 3 other blocks RMSD: 0.639  
  

> select #1/B:404,406,408,412,426 #2/B:404,406,408,412,426

104 atoms, 100 bonds, 10 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 4 other blocks RMSD: 0.599  
  

> select #1/B:404,406,408,412,426,429 #2/B:404,406,408,412,426,429

126 atoms, 122 bonds, 12 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 5 other blocks RMSD: 1.403  
  

> select #1/B:338,404,406,408,412,426,429 #2/B:338,404,406,408,412,426,429

136 atoms, 130 bonds, 14 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 6 other blocks RMSD: 1.335  
  

> select #1/B:315,338,404,406,408,412,426,429
> #2/B:315,338,404,406,408,412,426,429

152 atoms, 144 bonds, 16 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 7 other blocks RMSD: 1.269  
  

> select #1/B:315,338,340,404,406,408,412,426,429
> #2/B:315,338,340,404,406,408,412,426,429

174 atoms, 164 bonds, 18 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 8 other blocks RMSD: 1.202  
  

> select #1/B:266,315,338,340,404,406,408,412,426,429
> #2/B:266,315,338,340,404,406,408,412,426,429

196 atoms, 186 bonds, 20 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 9 other blocks RMSD: 1.152  
  

> select #1/B:266,293,315,338,340,404,406,408,412,426,429
> #2/B:266,293,315,338,340,404,406,408,412,426,429

214 atoms, 202 bonds, 22 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 10 other blocks RMSD: 1.105  
  

> select #1/B:240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:240,266,293,315,338,340,404,406,408,412,426,429

242 atoms, 232 bonds, 24 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 11 other blocks RMSD: 1.125  
  

> select #1/B:239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:239-240,266,293,315,338,340,404,406,408,412,426,429

254 atoms, 244 bonds, 26 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 12 other blocks RMSD: 1.095  
  

> select #1/B:239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:239-240,266,293,315,338,340,404,406,408,412,426,429

254 atoms, 244 bonds, 26 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 13 other blocks RMSD: 1.068  
  

> select #1/B:181,239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:181,239-240,266,293,315,338,340,404,406,408,412,426,429

270 atoms, 258 bonds, 28 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 14 other blocks RMSD: 1.046  
  

> select #1/B:111,181,239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:111,181,239-240,266,293,315,338,340,404,406,408,412,426,429

288 atoms, 274 bonds, 30 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 15 other blocks RMSD: 1.016  
  

> select #1/B:88,111,181,239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:88,111,181,239-240,266,293,315,338,340,404,406,408,412,426,429

306 atoms, 290 bonds, 32 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 16 other blocks RMSD: 0.989  
  

> select
> #1/B:60,88,111,181,239-240,266,293,315,338,340,404,406,408,412,426,429
> #2/B:60,88,111,181,239-240,266,293,315,338,340,404,406,408,412,426,429

328 atoms, 310 bonds, 34 residues, 2 models selected  
1 [ID: 1] region 2 chains [404] + 17 other blocks RMSD: 0.965  
  

> color (#!2 & sel) cyan

> select #1/B:239 #2/B:239

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/B:239 #2/B:239

12 atoms, 10 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [239] RMSD: 0.626  
  

> color (#!2 & sel) cornflower blue

> select #1/B:197 #2/B:197

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/B:197 #2/B:197

16 atoms, 14 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [197] RMSD: 0.523  
  

> color (#!2 & sel) cyan

> undo

> select #1/B:114 #2/B:114

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/B:114 #2/B:114

20 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [114] RMSD: 0.444  
  

> color (#!2 & sel) cyan

> select #2/A:1-2

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #2/A

726 atoms, 746 bonds, 88 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select clear

> hide #!2 models

> show #!2 models

> interfaces #!2 & ~solvent

1 buried areas: B A 1379  
Drag select of 3 residues  
[Repeated 1 time(s)]

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file
> /Users/gomezdd/Downloads/Bgh3682_LRR_rec6_9e0a6/Bgh3682_LRR_rec6_9e0a6_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json

> color #2/B:76-223 lime

> color #2/B:14-60 lime

> color #2/B:118-163 magenta

> color #2/A:17-68 lime

> color #2/B:82-141 magenta

> color #2/A:18-56 lime

> color #2/B:87-98 magenta

> color #2/A:26-31 lime

> color #2/B:89-94 magenta

> color #2/A:28-32 lime

> color #2/B:93-97 magenta

> help help:user/tools/alphafold.html#pae

> color bfactor #2 palette alphafold

4107 atoms, 517 residues, atom bfactor range 27.4 to 98.1  

> open
> /Users/gomezdd/Downloads/Bgh3125_LRR_rec6_f73e6/Bgh3125_LRR_rec6_f73e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb

Chain information for
Bgh3125_LRR_rec6_f73e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select add #3

4688 atoms, 4759 bonds, 597 residues, 2 models selected  

> select add #2

8773 atoms, 8945 bonds, 19 pseudobonds, 1111 residues, 3 models selected  

> hide #!2 models

> select subtract #2

4666 atoms, 4759 bonds, 594 residues, 1 model selected  

> select subtract #3

Nothing selected  

> alphafold pae #3 file
> /Users/gomezdd/Downloads/Bgh3125_LRR_rec6_f73e6/Bgh3125_LRR_rec6_f73e6_scores_rank_001_alphafold2_multimer_v3_model_2_seed_000.json

> color bfactor #3 palette alphafold

4666 atoms, 594 residues, atom bfactor range 15.8 to 98.2  

> select add #3

4666 atoms, 4759 bonds, 594 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hide #3 models

> show #3 models

> select subtract #3

Nothing selected  

> interfaces #3 & ~solvent

1 buried areas: B A 1421  

> alphafold contacts #3/A toResidues #3/B distance 3

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with
Bgh3125_LRR_rec6_f73e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#3), sequence alignment score = 2168.3  
RMSD between 415 pruned atom pairs is 0.596 angstroms; (across all 429 pairs:
0.807)  
  

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> undo

> hide sel atoms

> select add #3

4666 atoms, 4759 bonds, 16 pseudobonds, 594 residues, 2 models selected  

> hide sel atoms

> open
> /Users/gomezdd/Downloads/AVRPikD_LRR_rec6_c9a3b/AVRPikD_LRR_rec6_c9a3b_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
AVRPikD_LRR_rec6_c9a3b_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!3 models

> hide #!2 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with
AVRPikD_LRR_rec6_c9a3b_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4), sequence alignment score = 2180.9  
RMSD between 426 pruned atom pairs is 0.315 angstroms; (across all 429 pairs:
0.380)  
  

> hide #4 models

> select #1/A:92

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> open /Users/gomezdd/Downloads/01_Sequences/PWL2.fasta

Summary of feedback from opening
/Users/gomezdd/Downloads/01_Sequences/PWL2.fasta  
---  
notes | Alignment identifier is PWL2.fasta  
Associated
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
chain B to PWL2 with 0 mismatches  
Associated
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
chain A to PWL2 with 0 mismatches  
Associated
Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
chain B to PWL2 with 0 mismatches  
Associated
Bgh3125_LRR_rec6_f73e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
chain B to PWL2 with 0 mismatches  
Associated
AVRPikD_LRR_rec6_c9a3b_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
chain B to PWL2 with 0 mismatches  
  
Opened 1 sequences from PWL2.fasta  

> show #4 models

> hide #!1 models

> select add #4

4857 atoms, 4964 bonds, 613 residues, 2 models selected  

> select add #1

8238 atoms, 8404 bonds, 21 pseudobonds, 1042 residues, 3 models selected  

> select subtract #1

4133 atoms, 4218 bonds, 521 residues, 1 model selected  

> alphafold pae #4 file
> /Users/gomezdd/Downloads/AVRPikD_LRR_rec6_c9a3b/AVRPikD_LRR_rec6_c9a3b_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json

> color bfactor #4 palette alphafold

4133 atoms, 521 residues, atom bfactor range 20.2 to 97.7  

> alphafold contacts #4/A toResidues #4/B distance 3

> hide #!4 models

> show #!1 models

> open
> /Users/gomezdd/Downloads/Blugr2_4964_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Blugr2_4964_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> close #5

> open
> /Users/gomezdd/Downloads/Blugr2_3682_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Blugr2_3682_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> alphafold pae #5 file
> /Users/gomezdd/Downloads/Blugr2_3682_scores_rank_001_alphafold2_multimer_v3_model_1_seed_000.json

> color bfactor #5 palette alphafold

4113 atoms, 518 residues, atom bfactor range 30.3 to 98.1  

> alphafold contacts #5/A toResidues #5/B distance 3

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #!5 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Bgh3682_LRR_rec6_9e0a6_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#2) with
Blugr2_3682_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#5), sequence alignment score = 2162.3  
RMSD between 421 pruned atom pairs is 0.316 angstroms; (across all 429 pairs:
0.604)  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 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

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!2 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

> hide #!5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!5 models

> select #1/B:1 #2/B:1

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/B #2/B

6762 atoms, 6880 bonds, 858 residues, 2 models selected  
1 [ID: 1] region 2 chains [1-429] RMSD: 1.007  
  

> show sel & #!1 surfaces

> select add #2

7488 atoms, 7626 bonds, 19 pseudobonds, 946 residues, 4 models selected  

> select subtract #2

3381 atoms, 3440 bonds, 429 residues, 2 models selected  

> color (#!1 & sel) hot pink

> color (#!1 & sel) #fec6ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #ffa7f9ff

[Repeated 1 time(s)]

> color (#!1 & sel) #c681c1ff

[Repeated 1 time(s)]

> color (#!1 & sel) #aa6fa6ff

[Repeated 1 time(s)]

> lighting flat

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting soft

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 3 models selected  

> select subtract #1

1 model selected  

> select #2/A:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A

726 atoms, 746 bonds, 88 residues, 1 model selected  

> select #1/A:1

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

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> show sel surfaces

> color (#!1 & sel) cyan

> color (#!1 & sel) #79a6aaff

> color (#!1 & sel) #78a6aaff

> color (#!1 & sel) #94cdd1ff

[Repeated 1 time(s)]

> color (#!1 & sel) #5bd1c2ff

> color (#!1 & sel) #5bd1c3ff

> color (#!1 & sel) #5acfd1ff

[Repeated 1 time(s)]

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 3 models selected  

> hide #!1 models

> select subtract #1

2 models selected  

> select add #5

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 2 models selected  
Alignment identifier is 5/A  
Alignment identifier is 5/B  

> show #!1 models

> hide #!1 models

> show #!1 models

> select #5/B:1-2

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/B:1-7

52 atoms, 51 bonds, 7 residues, 1 model selected  

> select #5/B:1

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

> select #5/B:1-410

3221 atoms, 3275 bonds, 410 residues, 1 model selected  

> select #1/B:1 #2/B:1

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/B #2/B

6762 atoms, 6880 bonds, 858 residues, 2 models selected  
1 [ID: 1] region 2 chains [1-429] RMSD: 1.007  
  

> show sel & #!1 surfaces

> hide #!5 models

> show #!5 models

> select #5/B:1

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

> select #5/B

3387 atoms, 3446 bonds, 430 residues, 1 model selected  

> show sel surfaces

> color (#!5 & sel) hot pink

> color (#!5 & sel) #935e8fff

> select #5/B:1-2

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/B:1

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

> select add #5

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 3 models selected  

> select subtract #5

1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #5/A:1-2

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #5/A

726 atoms, 746 bonds, 88 residues, 1 model selected  

> show sel surfaces

> show #!1 models

> hide #!5 models

> select #1/A:1

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

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> ui tool show "Side View"

> close #4

> close #3

> close #2

> transparency (#!1 & sel) 40

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 5 models selected  

> transparency (#!1 & sel) 50

> show #!5 models

> select add #5

8218 atoms, 8378 bonds, 40 pseudobonds, 1039 residues, 10 models selected  

> select subtract #1

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 8 models selected  

> select add #1

8218 atoms, 8378 bonds, 40 pseudobonds, 1039 residues, 10 models selected  

> hide #!1 models

> select subtract #1

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 8 models selected  

> transparency (#!5 & sel) 50

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #5

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 8 models selected  

> hide #!5 models

> select subtract #5

2 models selected  

> show #!5 models

> hide #!1 models

> show #!1 models

> select add #5

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 2 models selected  

> select add #1

8218 atoms, 8378 bonds, 40 pseudobonds, 1039 residues, 7 models selected  

> hide sel surfaces

> select subtract #1

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 6 models selected  

> select subtract #5

2 models selected  

> hide #!1 models

> select #5/B:413

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #5/B:413

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #5/B:405,413

23 atoms, 22 bonds, 2 residues, 1 model selected  

> select #5/B:371,405,413

31 atoms, 29 bonds, 3 residues, 1 model selected  

> select #5/B:316,371,405,413

39 atoms, 36 bonds, 4 residues, 1 model selected  

> select #5/B:267,316,371,405,413

50 atoms, 47 bonds, 5 residues, 1 model selected  

> select #5/B:267,316,341,371,405,413

61 atoms, 57 bonds, 6 residues, 1 model selected  

> select #5/B:267,316,341,371,405,413

61 atoms, 57 bonds, 6 residues, 1 model selected  

> select #5/B:267,316,341,371,405,413

61 atoms, 57 bonds, 6 residues, 1 model selected  

> select #5/B:112,267,316,341,371,405,413

70 atoms, 65 bonds, 7 residues, 1 model selected  

> select #5/B:89,112,267,316,341,371,405,413

79 atoms, 73 bonds, 8 residues, 1 model selected  

> select #5/B:89,112,116,267,316,341,371,405,413

87 atoms, 80 bonds, 9 residues, 1 model selected  

> select #5/B:89,112,115-116,267,316,341,371,405,413

97 atoms, 91 bonds, 10 residues, 1 model selected  

> select #5/B:89,112,115-116,267,316,341,371,405,413

97 atoms, 91 bonds, 10 residues, 1 model selected  

> select #5/B:89,112,115-116,267,316,341,371,405,413

97 atoms, 91 bonds, 10 residues, 1 model selected  

> select #5/B:89,112,115-116,241,267,316,341,371,405,413

111 atoms, 106 bonds, 11 residues, 1 model selected  

> select #5/B:89,112,115-116,182,241,267,316,341,371,405,413

119 atoms, 113 bonds, 12 residues, 1 model selected  

> select #5/B:61,89,112,115-116,182,241,267,316,341,371,405,413

130 atoms, 123 bonds, 13 residues, 1 model selected  

> color (#!5 & sel) purple

> select #5/B:116

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/B:116

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color (#!5 & sel) #935e8fff

> select #5/B:116

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/B:116

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #!5 models

> show #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> select add #5

4113 atoms, 4192 bonds, 19 pseudobonds, 518 residues, 3 models selected  

> select subtract #5

2 models selected  

> hide #!5 models

> show #!5 models

> hide #!1 models

> show #!1 models

> hide #!5 models

> open /Users/gomezdd/Downloads/drive-
> download-20230705T100529Z-001/Blugr2_3919_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb

Chain information for
Blugr2_3919_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> ui tool show "AlphaFold Error Plot"

> alphafold pae #2 file /Users/gomezdd/Downloads/drive-
> download-20230705T100529Z-001/Blugr2_3919_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json

> color bfactor #2 palette alphafold

4103 atoms, 519 residues, atom bfactor range 26.1 to 98  

> alphafold contacts #2/A toResidues #2/B distance 3

> show #!5 models

> ui tool show Matchmaker

> matchmaker #!2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Blugr2_3682_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain B (#5) with
Blugr2_3919_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain B (#2), sequence alignment score = 2173.5  
RMSD between 423 pruned atom pairs is 0.662 angstroms; (across all 430 pairs:
1.033)  
  

> hide #!2 models

> show #!1 models

> hide #!5 models

> open
> /Users/gomezdd/Documents/Bioinformatics/PWL2/PWL2_structure/PWL2_HIPP43_12-11-2020-final.pdb

PWL2_HIPP43_12-11-2020-final.pdb title:  
\--- [more info...]  
  
Chain information for PWL2_HIPP43_12-11-2020-final.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 5/A  
Alignment identifier is 5/A  
Alignment identifier is 2  
Alignment identifier is 2/A  
Alignment identifier is 3/A  
Alignment identifier is 3/B  

> close #2

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> color sel orange

> color sel #935d58ff

[Repeated 1 time(s)]

> color sel #936d6aff

> color sel #936e6aff

> color sel #c0908bff

> color sel #c1908bff

> color sel #c1985dff

[Repeated 1 time(s)]

> color sel #c17657ff

[Repeated 1 time(s)]

> color sel #ec906bff

[Repeated 1 time(s)]

> color sel #ec9278ff

[Repeated 1 time(s)]

> color sel #ec959eff

[Repeated 1 time(s)]

> color sel #ec809fff

[Repeated 1 time(s)]

> color sel #ec6483ff

> color sel #ec7f75ff

[Repeated 1 time(s)]

> select #3/B:23

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

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> color sel light sea green

> color sel #ccece7ff

[Repeated 1 time(s)]

> color sel #abecc0ff

[Repeated 1 time(s)]

> color sel #a8e0ecff

[Repeated 1 time(s)]

> color sel #83aeb8ff

> color sel #89b7c1ff

[Repeated 1 time(s)]

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PWL2_HIPP43_12-11-2020-final.pdb, chain B (#3) with
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 489.1  
RMSD between 78 pruned atom pairs is 0.672 angstroms; (across all 91 pairs:
7.882)  
  

> ui tool show Matchmaker

> matchmaker #3 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with PWL2_HIPP43_12-11-2020-final.pdb, chain A (#3), sequence
alignment score = 50.5  
RMSD between 5 pruned atom pairs is 1.438 angstroms; (across all 64 pairs:
14.187)  
  

> undo

> show #!1 models

> ui tool show Matchmaker

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

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PWL2_HIPP43_12-11-2020-final.pdb, chain A (#3) with
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1), sequence alignment score = 50.5  
RMSD between 5 pruned atom pairs is 1.438 angstroms; (across all 64 pairs:
14.187)  
  

> open
> /Users/gomezdd/Documents/Bioinformatics/PWL2/PWL2_structure/V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb

Chain information for V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Destroying pre-existing alignment with identifier 3/B  
Alignment identifier is 3/B  

> show #!5 models

Destroying pre-existing alignment with identifier 3/B  
Alignment identifier is 3/B  

> hide #!5 models

> hide #3 models

> hide #!1 models

> select add #3

1640 atoms, 1506 bonds, 362 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #2

1606 atoms, 1651 bonds, 205 residues, 1 model selected  
Alignment identifier is 2/B  
Alignment identifier is 2/C  

> select #2/B:1

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/B

711 atoms, 724 bonds, 91 residues, 1 model selected  

> color sel hot pink

> color sel #ac90c1ff

[Repeated 1 time(s)]

> color sel #c19bb1ff

[Repeated 1 time(s)]

> color sel #c18cb9ff

[Repeated 1 time(s)]

> color sel #c1aab4ff

[Repeated 1 time(s)]

> color sel #c180b6ff

[Repeated 1 time(s)]

> color sel #e295d5ff

[Repeated 1 time(s)]

> color sel #e27bd2ff

[Repeated 1 time(s)]

> color sel #e285bbff

[Repeated 1 time(s)]

> color sel #f38fc8ff

[Repeated 1 time(s)]

> color sel #f384d1ff

[Repeated 1 time(s)]

> color sel #f37fadff

[Repeated 1 time(s)]

> color sel #f3a4e0ff

[Repeated 1 time(s)]

> color sel #b97eabff

[Repeated 1 time(s)]

> color sel #c284b3ff

[Repeated 1 time(s)]

> color sel #db95caff

[Repeated 1 time(s)]

> select #2/C:1-2

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #2/C

895 atoms, 927 bonds, 114 residues, 1 model selected  

> show #!1 models

> ui tool show Matchmaker

> matchmaker #2/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb, chain B
(#2), sequence alignment score = 439.6  
RMSD between 70 pruned atom pairs is 0.683 angstroms; (across all 91 pairs:
2.020)  
  

> select #2/C:83-84

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select #2/C:83-114

241 atoms, 253 bonds, 32 residues, 1 model selected  

> hide sel cartoons

> show #3 models

> ui tool show Matchmaker

> matchmaker #3/A to #2/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb, chain B (#2) with
PWL2_HIPP43_12-11-2020-final.pdb, chain A (#3), sequence alignment score =
36.7  
RMSD between 14 pruned atom pairs is 0.651 angstroms; (across all 56 pairs:
14.321)  
  

> hide #2 models

> select #2/C:80

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/C:80-82

26 atoms, 27 bonds, 3 residues, 1 model selected  

> select #3/B:103

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:103-134

241 atoms, 253 bonds, 32 residues, 1 model selected  

> hide sel cartoons

> select #3/B:103-104

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select #3/B:103-110

54 atoms, 55 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select add #1

4159 atoms, 4241 bonds, 21 pseudobonds, 529 residues, 3 models selected  

> select add #3

5745 atoms, 5692 bonds, 21 pseudobonds, 883 residues, 5 models selected  

> show sel surfaces

> hide #!1 models

> select #3/B:23

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

> select #3/B:23-105

663 atoms, 683 bonds, 83 residues, 1 model selected  

> select #3/B:111-112

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/B:111-134

187 atoms, 197 bonds, 24 residues, 1 model selected  

> hide sel surfaces

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> color (#!3 & sel) #9ddbcaff

[Repeated 1 time(s)]

> color (#!3 & sel) #92cadbff

[Repeated 1 time(s)]

> color (#!3 & sel) #92cadbc7

> color (#!3 & sel) #92cadbae

[Repeated 1 time(s)]

> color (#!3 & sel) #92cadbad

> show sel cartoons

[Repeated 1 time(s)]

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> show sel cartoons

> color (#!3 & sel) #92cadbad

> color (#!3 & sel) #92cadbae

> color (#!3 & sel) #92cadbdf

> color (#!3 & sel) #92cadbff

> transparency (#!3 & sel) 50

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> color (#!3 & sel) #db9d9cff

[Repeated 1 time(s)]

> color (#!3 & sel) #db93a4ff

[Repeated 1 time(s)]

> color (#!3 & sel) #db607cff

[Repeated 1 time(s)]

> color (#!3 & sel) #db7989ff

[Repeated 1 time(s)]

> transparency (#!3 & sel) 50

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> show #!1 models

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #1/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> show #!5 models

> hide #!5 models

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> show sel surfaces

> show sel cartoons

> select #1/A:1

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

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> show sel surfaces

> show sel cartoons

> hide #!1 models

> view sel

> show #!1 models

> hide #!3 models

> select #1/A:87-88

12 atoms, 12 bonds, 2 residues, 1 model selected  

> select #1/A:87-92

45 atoms, 46 bonds, 6 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #1/A:85

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:85-86

12 atoms, 11 bonds, 2 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #3/B:23

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

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> hide sel surfaces

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> transparency (#!3 & sel) 60

> show #!1 models

> select #1/B:1

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

> select #1/B:1-149

1178 atoms, 1194 bonds, 149 residues, 1 model selected  

> select #1/B:1

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

> select #1/B:1-200

1574 atoms, 1593 bonds, 200 residues, 1 model selected  

> select #1/B:1-2

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/B:1-245

1944 atoms, 1975 bonds, 245 residues, 1 model selected  

> select #1/B:1

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

> select #1/B:1-288

2281 atoms, 2317 bonds, 288 residues, 1 model selected  

> hide sel cartoons

> hide sel surfaces

> select #1/B:289

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

> select #1/B:289-315

221 atoms, 224 bonds, 27 residues, 1 model selected  

> select #1/B:288-289

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/B:289-324

288 atoms, 293 bonds, 36 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #1/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #1/A:1-90

712 atoms, 734 bonds, 90 residues, 1 model selected  

> select #1/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel surfaces

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 3 models selected  

> select subtract #1

2 models selected  

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 2 models selected  

> ~hbonds

> select subtract #1

2 models selected  

> hide #!1 models

> show #!1 models

> hide #!3 models

> interfaces #!1 & ~solvent

1 buried areas: B A 1408  

> select #1/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #1/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #5/B:330

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/B:330-430

776 atoms, 791 bonds, 101 residues, 1 model selected  

> show #!1 cartoons

> hide #!1 atoms

> select #5/B:1-2

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #5/B:1-196

1544 atoms, 1563 bonds, 196 residues, 1 model selected  

> select
> #1/B:25-30,38-43,47-49,70-78,97-101,121-125,146-148,163-171,187-199,219-227,246-254,256-259,275-283,321-323,345-350,382-397

874 atoms, 866 bonds, 115 residues, 1 model selected  

> select #1/B:1

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

> select #1/B:1-331

2625 atoms, 2669 bonds, 331 residues, 1 model selected  

> select #1/B:1

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

> select #1/B:1-324

2569 atoms, 2611 bonds, 324 residues, 1 model selected  

> hide sel cartoons

> select #1/B:325-326

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/B:325-429

812 atoms, 828 bonds, 105 residues, 1 model selected  

> select add #1

4105 atoms, 4186 bonds, 21 pseudobonds, 521 residues, 3 models selected  

> select subtract #1

2 models selected  

> interfaces #!1 & ~solvent

1 buried areas: B A 1408  

> select #1/B:325-326

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/B:325-429

812 atoms, 828 bonds, 105 residues, 1 model selected  

> hide contacts #1

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide contacts #1/A to #1/B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide alphafold contacts #1/A to #1/B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide alphafold contacts #1/A to #1/B distance 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide contacts #1/A to #1/B distance 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide contacts #1/A to #1/B distance 3

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> open
> /Users/gomezdd/Downloads/Pwl2delta_LRR_rec6_b0207/Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1) with
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4), sequence alignment score = 2184.5  
RMSD between 429 pruned atom pairs is 0.000 angstroms; (across all 429 pairs:
0.000)  
  

> hide #!1 models

> close #1

> view

Alignment identifier is 5/A  
Alignment identifier is 5/B  
Alignment identifier is 3/A  
Alignment identifier is 3/B  
Alignment identifier is 2/B  
Alignment identifier is 2/C  
Alignment identifier is 4/A  
Alignment identifier is 4/B  

> select #4/B:419

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:419-429

96 atoms, 98 bonds, 11 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> show #2 models

> hide #2 models

> show #!3 models

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel surfaces

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> select #4/B:1

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

> select #4/B:1-283

2242 atoms, 2278 bonds, 283 residues, 1 model selected  

> select #4/B:1

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

> select #4/B:1-324

2569 atoms, 2611 bonds, 324 residues, 1 model selected  

> hide sel cartoons

> select #3/A:92-93

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select #3/A:92-100

82 atoms, 87 bonds, 9 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> color (#!3 & sel) #db84d5ff

[Repeated 1 time(s)]

> color (#!3 & sel) #d572dbff

[Repeated 1 time(s)]

> color (#!3 & sel) #c183dbff

[Repeated 1 time(s)]

> color (#!3 & sel) #db6ad0ff

> color (#!3 & sel) #db95d5ff

[Repeated 1 time(s)]

> color (#!3 & sel) #b77cb2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #c586bfff

[Repeated 1 time(s)]

> color (#!3 & sel) #b9a8c5ff

[Repeated 1 time(s)]

> color (#!3 & sel) #c281c5ff

> color (#!3 & sel) #c280c5ff

> color (#!3 & sel) #c571b4ff

[Repeated 1 time(s)]

> color (#!3 & sel) #76c566ff

> color (#!3 & sel) #75c566ff

> color (#!3 & sel) #94c599ff

> color (#!3 & sel) #95c599ff

> color (#!3 & sel) #61c58dff

[Repeated 1 time(s)]

> color (#!3 & sel) #79c5a3ff

[Repeated 1 time(s)]

> color (#!3 & sel) #79c56fff

> color (#!3 & sel) #62c59cff

[Repeated 1 time(s)]

> color (#!3 & sel) #61c581ff

[Repeated 1 time(s)]

> color (#!3 & sel) #69d58cff

[Repeated 1 time(s)]

> color (#!3 & sel) #a1ffa0ff

> select #4/B:325-326

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:325-429

812 atoms, 828 bonds, 105 residues, 1 model selected  

> color sel #fbc9ffff

[Repeated 1 time(s)]

> color sel #ffa0e0ff

> color sel #ffa0dfff

> color sel #cd81b4ff

[Repeated 1 time(s)]

> color sel #dc8ac0ff

[Repeated 1 time(s)]

> color sel #c77caeff

[Repeated 1 time(s)]

> color sel #e08cc4ff

[Repeated 1 time(s)]

> color sel #e062a4ff

[Repeated 1 time(s)]

> color sel #e09abeff

[Repeated 1 time(s)]

> color sel #e08dd2ff

[Repeated 1 time(s)]

> color sel #e0a9cbff

[Repeated 1 time(s)]

> color sel #e0a7ccff

[Repeated 2 time(s)]

> color sel #e0a6ccff

> color sel #e0a5ccff

> color sel #e0a3cbff

> color sel #e0a1cbff

> color sel #e0a0cbff

> color sel #e09fcbff

> color sel #c68db3ff

[Repeated 1 time(s)]

> color sel #d296bfff

[Repeated 1 time(s)]

> color sel #d29cc1ff

[Repeated 1 time(s)]

> color sel #d29bc1ff

> color sel #d29ac2ff

> color sel #d298c4ff

> color sel #d298c5ff

> color sel #d29ac9ff

> color sel #d29ccdff

> color sel #d29ed1ff

> color sel #cfa0d2ff

> color sel #cea2d2ff

> color sel #cda5d2ff

> color sel #cca8d2ff

> color sel #ccaad2ff

> color sel #ccabd2ff

> color sel #cbacd2ff

> color sel #cbadd2ff

> color sel #caadd2ff

> color sel #caaed2ff

[Repeated 2 time(s)]

> color sel #cbadd2ff

> color sel #cfacd2ff

> color sel #d2abceff

> color sel #d2aaccff

> color sel #d2a9caff

> color sel #d2a8c9ff

> color sel #d2a7c8ff

> color sel #d2a6c7ff

> color sel #d2a4c4ff

> color sel #d2a1c1ff

[Repeated 1 time(s)]

> select #4/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> color sel light sea green

> color sel cyan

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #!3 models

> select #4/A:84-85

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #4/A:84-92

61 atoms, 62 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> show #2 models

> hide #4 models

> show #4 models

> hide #4 models

> hide #2 models

> show #2 models

> hide #2 models

> show #4 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> view sel

> ui tool show "Side View"

> show #2 models

> hide #2 models

> show #4 models

> hide #!3 models

> show #2 models

> hide #2 models

> show #!3 models

> hide #4 models

> show #2 models

> hide #2 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!3 models

> show #2 models

> show #4 models

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #4 models

> view

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #4 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/C-term_Pwl2.png" width 2000 height 1562 supersample 3
> transparentBackground true

> show #2 models

> hide #4 models

> hide #2 models

> show #!3 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/HIPP_Pwl2.png" width 2000 height 1562 supersample 3
> transparentBackground true

> show #4 models

> select #4/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel cartoons

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> select #3/B:23

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

> select #3/B:23-100

626 atoms, 644 bonds, 78 residues, 1 model selected  

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> select #3/B:111

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:111-112

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> color (#!3 & sel) #93cbd2ff

> color (#!3 & sel) #79b9d2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #70cfd2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #4bd2c1ff

[Repeated 1 time(s)]

> color (#!3 & sel) #4ed2cbff

[Repeated 1 time(s)]

> color (#!3 & sel) #63d0d2ff

> color (#!3 & sel) #63cfd2ff

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-87

472 atoms, 475 bonds, 62 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #3/A:88

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:88-91

28 atoms, 27 bonds, 4 residues, 1 model selected  

> select #3/A:87

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

> select #3/A:87-94

61 atoms, 63 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select #3/A:91

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:91-94

38 atoms, 40 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-90

491 atoms, 494 bonds, 65 residues, 1 model selected  

> hide sel cartoons

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/C-term_Pwl2_v1.png" width 2000 height 1562 supersample 3
> transparentBackground true

> select #3/B:23

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

> select #3/B:23-113

720 atoms, 742 bonds, 91 residues, 1 model selected  

> show sel surfaces

> select #3/B:111

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:111-113

24 atoms, 24 bonds, 3 residues, 1 model selected  

> hide sel surfaces

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> transparency (#!3 & sel) 60

> hide sel cartoons

> show sel cartoons

> transparency (#!3 & sel) 70

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:26-90

491 atoms, 494 bonds, 65 residues, 1 model selected  

> show sel cartoons

> select #4/B:411-412

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #4/B:411-429

155 atoms, 159 bonds, 19 residues, 1 model selected  

> hide sel cartoons

> select #4/B:411

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:411-418

59 atoms, 60 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select #4/B:411

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:411-414

31 atoms, 31 bonds, 4 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #4/B:415

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:415-429

124 atoms, 127 bonds, 15 residues, 1 model selected  

> hide sel cartoons

> select #4/B:411

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:411-412

18 atoms, 18 bonds, 2 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

Nothing selected  

> interfaces #4#!3 & ~solvent

6 buried areas: #3/B #4/A 3126, #4/B #3/A 2267, #4/B #3/B 2131, #3/B #3/A
1995, #4/B #4/A 1408, #4/A #3/A 1249  

> undo

> hide #!3 models

> show #!3 models

> hide sel atoms

> select add #3

5745 atoms, 5692 bonds, 883 residues, 2 models selected  

> show sel cartoons

> select #4/B:46-47

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #4/B:46-329

2250 atoms, 2287 bonds, 284 residues, 1 model selected  

> hide sel cartoons

> select #4/B:1-2

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/B:1-45

364 atoms, 369 bonds, 45 residues, 1 model selected  

> hide sel cartoons

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

Nothing selected  

> interfaces #4#!3 & ~solvent

6 buried areas: #3/B #4/A 3126, #4/B #3/A 2267, #4/B #3/B 2131, #3/B #3/A
1995, #4/B #4/A 1408, #4/A #3/A 1249  

> show sel atoms

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> show sel atoms

> select #3/A:91

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:91-100

91 atoms, 96 bonds, 10 residues, 1 model selected  

> select #4/B:1-2

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/B:1-259

2059 atoms, 2094 bonds, 259 residues, 1 model selected  

> hide sel atoms

> select #4/B:260

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

> select #4/B:260-315

443 atoms, 447 bonds, 56 residues, 1 model selected  

> hide sel atoms

> select #4/A:1

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

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #3/B:23

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

> select #3/B:23-113

720 atoms, 742 bonds, 91 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide #!3 models

> select #4/B:317

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #4/B:317

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #4/B:423

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

> select #4/B:423-429

64 atoms, 66 bonds, 7 residues, 1 model selected  

> select #4/B:421-422

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/B:421-429

80 atoms, 82 bonds, 9 residues, 1 model selected  

> select #4/B:419

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:419-429

96 atoms, 98 bonds, 11 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!3 models

> select #3/B:114

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:114-134

163 atoms, 172 bonds, 21 residues, 1 model selected  

> hide sel cartoons

> hide #4 models

> show #4 models

> hide #!3 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 3 time(s)]

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!3 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-41

125 atoms, 125 bonds, 16 residues, 1 model selected  

> select #3/A:87-88

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:87-100

114 atoms, 119 bonds, 14 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!3 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/B:23

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

> select #3/B:23-113

720 atoms, 742 bonds, 91 residues, 1 model selected  

> show sel surfaces

> show sel cartoons

> select #3/B:109

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

> select #3/B:109-112

30 atoms, 30 bonds, 4 residues, 1 model selected  

> select #3/B:110

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:110-134

196 atoms, 206 bonds, 25 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #3/A:52

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

> select #3/A:52-55

29 atoms, 28 bonds, 4 residues, 1 model selected  

> select #3/A:63

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:63-66

31 atoms, 31 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select #3/A:63

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:63-65

25 atoms, 25 bonds, 3 residues, 1 model selected  

> select #3/B:23

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

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> hide sel cartoons

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/A:78

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:78

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47,51

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:47,51

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/A:43,47,51,56

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #3/A:43,47,51,56,59

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select #3/A:43,47,51,56,59,61

48 atoms, 42 bonds, 6 residues, 1 model selected  

> show #4 models

> hide #!3 models

> show #!3 models

> view sel

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> color (#!3 & sel) #c38ed2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #d29e97ff

[Repeated 1 time(s)]

> color (#!3 & sel) #d27670ff

[Repeated 1 time(s)]

> color (#!3 & sel) #d25957ff

[Repeated 1 time(s)]

> color (#!3 & sel) #d2706eff

[Repeated 1 time(s)]

> color (#!3 & sel) #394bd2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #5a70d2ff

[Repeated 1 time(s)]

> color (#!3 & sel) #667feeff

[Repeated 1 time(s)]

> color (#!3 & sel) #accaeeff

> color (#!3 & sel) #9b9eeeff

[Repeated 1 time(s)]

> color (#!3 & sel) #948beeff

[Repeated 1 time(s)]

> color (#!3 & sel) #7a72c3ff

[Repeated 1 time(s)]

> hide #4 models

> select #3/A:73

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:73-100

226 atoms, 232 bonds, 28 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel atoms

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56,59

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61-62

29 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56,59

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #3/A:51,56,59,61

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A:46,51,56,59,61

37 atoms, 32 bonds, 5 residues, 1 model selected  

> select #3/A:43,46,51,56,59,61

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select #3/A:43,46,51,56,59,61

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:43,47

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:59,61

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #3/A:47,56,59,61

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A:43,47,56,59,61

39 atoms, 34 bonds, 5 residues, 1 model selected  

> select #3/A:43,47,51,56,59,61

48 atoms, 42 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide #!3 models

> show #!3 models

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> view

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/A:35

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:35-41

51 atoms, 50 bonds, 7 residues, 1 model selected  

> select #3/A:36

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:36-41

44 atoms, 43 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> show #4 models

> select #4/B:315

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:315-429

887 atoms, 905 bonds, 115 residues, 1 model selected  

> hide sel atoms

> select #4/B:402

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:402

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:402,405

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select #4/B:402,405,407

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select #4/B:384,402,405,407

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #4/B:384,386,402,405,407

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:393,397

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #4/B:389,393,397

29 atoms, 26 bonds, 3 residues, 1 model selected  

> select #4/B:389,393,397,402

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #4/B:389,393,397,402,405

44 atoms, 39 bonds, 5 residues, 1 model selected  

> select #4/B:389,393,397,402,405,407

52 atoms, 46 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel #7a72c3ff

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #4/B:350-351

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:351-369

140 atoms, 140 bonds, 19 residues, 1 model selected  

> hide sel surfaces

> hide sel atoms

> hide sel cartoons

> select #4/B:377-378

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #4/B:377-381

26 atoms, 25 bonds, 5 residues, 1 model selected  

> select #4/B:345

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:345-350

48 atoms, 47 bonds, 6 residues, 1 model selected  

> select #4/B:338

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

> select #4/B:338-344

52 atoms, 52 bonds, 7 residues, 1 model selected  

> select #4/B:331-332

9 atoms, 8 bonds, 2 residues, 1 model selected  

> select #4/B:331-337

44 atoms, 44 bonds, 7 residues, 1 model selected  

> select #4/B:329-330

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:330-337

51 atoms, 52 bonds, 8 residues, 1 model selected  

> hide sel cartoons

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> select #4/B:338

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

> select #4/B:338-351

108 atoms, 108 bonds, 14 residues, 1 model selected  

> select #4/B:352

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

> select #4/B:338-352

112 atoms, 112 bonds, 15 residues, 1 model selected  

> hide sel cartoons

> hide #!3 models

> show #!3 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56-76

153 atoms, 154 bonds, 21 residues, 1 model selected  

> select #3/A:42

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

> select #3/A:42-72

231 atoms, 231 bonds, 31 residues, 1 model selected  

> show sel cartoons

> select #3/A:73

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:73-75

28 atoms, 28 bonds, 3 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47,51

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:43,47,51,56

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #3/A:43,47,51,56,59

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select #3/A:43,47,51,56,59,61-62

56 atoms, 50 bonds, 7 residues, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:59,61

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #3/A:51,56,59,61

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A:47,51,56,59,61

39 atoms, 34 bonds, 5 residues, 1 model selected  

> select #3/A:43,47,51,56,59,61

48 atoms, 42 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> select #3/A:38

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:38-41

27 atoms, 26 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #3/A:35-36

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/A:35-37

24 atoms, 23 bonds, 3 residues, 1 model selected  

> show sel cartoons

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> hide #4 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> show sel cartoons

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> select #3/B:107

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

> select #3/B:107-110

25 atoms, 25 bonds, 4 residues, 1 model selected  

> select #3/B:105

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

> select #3/B:105-110

37 atoms, 37 bonds, 6 residues, 1 model selected  

> select #3/B:111

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:111-112

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/B:114

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:114-115

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #3/B:108-109

12 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/B:108-110

21 atoms, 21 bonds, 3 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #3/B:102

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:102-107

45 atoms, 46 bonds, 6 residues, 1 model selected  

> select #3/B:108

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/B:108-110

21 atoms, 21 bonds, 3 residues, 1 model selected  

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #4 models

> view

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #4 models

> select #4/B:173

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:173-175

28 atoms, 27 bonds, 3 residues, 1 model selected  

> select #4/B:139

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:139-141

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select #3/A:35-36

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/A:35-37

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #3/A:35

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:35-36

16 atoms, 15 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show #4 models

> hide #!3 models

> show #!3 models

> hide #4 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Interface_HIPP.png" width 2000 height 1177 supersample 3
> transparentBackground true

> select #3/B:23

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

> select #3/B:23-106

671 atoms, 691 bonds, 84 residues, 1 model selected  

> transparency (#!3 & sel) 50

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Interface_HIPP_v1.png" width 2000 height 1177 supersample 3
> transparentBackground true

> show #4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Interface_Cterm.png" width 2000 height 1177 supersample 3
> transparentBackground true

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:26-62

283 atoms, 284 bonds, 37 residues, 1 model selected  

> select #3/A:26-30

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select #3/A:26-72

356 atoms, 358 bonds, 47 residues, 1 model selected  

> show sel cartoons

> select #3/A:68

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

> select #3/A:68

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

> select #3/A:63-64

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:63-72

73 atoms, 73 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-37

98 atoms, 98 bonds, 12 residues, 1 model selected  

> hide sel cartoons

> hide #4 models

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47,51

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select #3/A:43,47,51,56

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #3/A:43,47,51,56,59

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select #3/A:43,47,51,56,59,61

48 atoms, 42 bonds, 6 residues, 1 model selected  

> show sel atoms

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Interface_HIPP_v2.png" width 2000 height 1177 supersample 3
> transparentBackground true

> show #4 models

> hide #4 models

> show #4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Interface_Cterm_v1.png" width 2000 height 1177 supersample 3
> transparentBackground true

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:393,397

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #4/B:393,397

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select
> #4/B:25-30,38-43,47-49,70-78,97-101,121-125,146-148,163-171,187-199,219-227,246-254,256-259,275-283,321-323,345-350,382-397

874 atoms, 866 bonds, 115 residues, 1 model selected  

> select
> #4/B:7-10,33-36,55-57,84-86,107-109,131-133,154-160,177-182,205-210,236-239,264-267,289-293,302-305,315-319,325-328,338-344,370-376,404-410

705 atoms, 702 bonds, 86 residues, 1 model selected  

> select
> #4/B:25-30,38-43,47-49,70-78,97-101,121-125,146-148,163-171,187-199,219-227,246-254,256-259,275-283,321-323,345-350,382-397

874 atoms, 866 bonds, 115 residues, 1 model selected  

> select #4/B:389

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:389

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:363-393

237 atoms, 239 bonds, 31 residues, 1 model selected  

> select #4/B:389

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:389

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:389,397

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:389,393,397

29 atoms, 26 bonds, 3 residues, 1 model selected  

> select #4/B:389,393,397,402

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #4/B:389,393,397,402,405

44 atoms, 39 bonds, 5 residues, 1 model selected  

> select #4/B:389,393,397,402,405,407

52 atoms, 46 bonds, 6 residues, 1 model selected  

> color sel orange red

> color sel orange

> color sel #c351acff

> color sel #c350acff

> turn y 4 270

> turn y 270

> select #4/B:1

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

> select #4/B

3381 atoms, 3440 bonds, 429 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> color sel #e3acd1ff

> view sel

> hide #4 models

> show #4 models

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

Nothing selected  

> turn y 315

> turn y 45

> turn y 330

> turn y 60

> turn y 330

> turn y 320

> turn y 15

> turn y 20

> lighting full

> lighting soft

> view

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/full_LRR.png" width 2000 height 1177 supersample 3
> transparentBackground true

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select #4/B:1-2

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/B:1-418

3285 atoms, 3341 bonds, 418 residues, 1 model selected  

> hide sel cartoons

> select #4/B:419

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:419-429

96 atoms, 98 bonds, 11 residues, 1 model selected  

> hide sel cartoons

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> color (#!3 & sel) #a8ffa7ff

> view sel

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> view

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/full_HIPP.png" width 2000 height 1177 supersample 3
> transparentBackground true

> select #4/B:1

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

> select #4/B

3381 atoms, 3440 bonds, 429 residues, 1 model selected  

> show sel cartoons

> view

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/full_LRR_v1.png" width 2000 height 1177 supersample 3
> transparentBackground true

> open
> /Users/gomezdd/Downloads/AvrPikD_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb

Chain information for
AvrPikD_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!3 models

> hide #4 models

> show #!3 models

> show #4 models

> hide #1 models

> view

> select #4/B:1-2

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/B:1-417

3275 atoms, 3330 bonds, 417 residues, 1 model selected  

> select #4/B

3381 atoms, 3440 bonds, 429 residues, 1 model selected  

> show sel surfaces

> color (#!4 & sel) #ffc6ecff

[Repeated 1 time(s)]

> color (#!4 & sel) #ff98feff

[Repeated 1 time(s)]

> color (#!4 & sel) #e084ffff

> color (#!4 & sel) #e184ffff

> color (#!4 & sel) #ff79fdff

[Repeated 1 time(s)]

> color (#!4 & sel) #fd9fffff

> color (#!4 & sel) #fda0ffff

> color (#!4 & sel) #ba75bbff

[Repeated 1 time(s)]

> color (#!4 & sel) #c57dc7ff

[Repeated 1 time(s)]

> color (#!4 & sel) #c779b1ff

[Repeated 1 time(s)]

> transparency (#!4 & sel) 50

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> select add #4

4105 atoms, 4186 bonds, 521 residues, 2 models selected  

> select subtract #4

1 model selected  

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> show sel cartoons

> show sel surfaces

> hide #!4 models

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> transparency (#!3 & sel) 50

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> view

> select add #3

1640 atoms, 1506 bonds, 362 residues, 1 model selected  

> transparency (#!3 & sel) 0

> lighting flat

> lighting full

> lighting flat

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting flat

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> show #2 models

> hide #2 models

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B:23-44

179 atoms, 182 bonds, 22 residues, 1 model selected  

> select #3/B:114

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:114-134

163 atoms, 172 bonds, 21 residues, 1 model selected  

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:26-36

90 atoms, 90 bonds, 11 residues, 1 model selected  

> select #3/A:87

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

> select #3/A:87-100

114 atoms, 119 bonds, 14 residues, 1 model selected  

> select #3/A:92

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:92-100

82 atoms, 87 bonds, 9 residues, 1 model selected  

> select #3/A:94-95

19 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:94-100

60 atoms, 63 bonds, 7 residues, 1 model selected  

> select #3/A:96

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:96-100

41 atoms, 42 bonds, 5 residues, 1 model selected  

> select #3/A:95

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:95-100

53 atoms, 55 bonds, 6 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> hide sel surfaces

> show sel surfaces

> select #3/A:96

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:96-100

41 atoms, 42 bonds, 5 residues, 1 model selected  

> hide sel surfaces

> select #4/B:338

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

> select #4/B:338-429

716 atoms, 729 bonds, 92 residues, 1 model selected  

> show #!3 surfaces

> hide #!3 surfaces

> show #!3 surfaces

> select add #4

4105 atoms, 4186 bonds, 521 residues, 2 models selected  

> select #4/A:1

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

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide #!3 surfaces

[Repeated 1 time(s)]

> show #!3 surfaces

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

1 model selected  

> show #!4 models

> select #4/A:1

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

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> hide sel surfaces

> select #4/B:338

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

> select #4/B:338-429

716 atoms, 729 bonds, 92 residues, 1 model selected  

> hide sel cartoons

> transparency (#!4 & sel) 0

> select #4/B:1

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

> select #4/B:1-222

1748 atoms, 1770 bonds, 222 residues, 1 model selected  

> hide sel cartoons

> hide sel surfaces

> select #4/B:223

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:223-337

917 atoms, 939 bonds, 115 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #4/B:326

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:326-337

87 atoms, 89 bonds, 12 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select #4/A:1

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

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> hide sel surfaces

> open
> /Users/gomezdd/Downloads/Blugr2_3_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
Blugr2_3_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!4 models

> show #!5 models

> hide #6 models

> show #6 models

> hide #!5 models

> show #!5 models

> hide #6 models

> show #6 models

> hide #!5 models

> show #!5 models

> hide #6 models

> open
> /Users/gomezdd/Downloads/Blugr2_3818_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb

Chain information for
Blugr2_3818_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!5 models

> alphafold pae #7 file
> /Users/gomezdd/Downloads/Blugr2_3818_scores_rank_001_alphafold2_multimer_v3_model_5_seed_000.json

> color bfactor #7 palette alphafold

4173 atoms, 525 residues, atom bfactor range 23.9 to 98.1  

> alphafold contacts #7/A toResidues #7/B 3

Expected a keyword  

> alphafold contacts #7/A toResidues #7/B distance 3

> alphafold contacts #7/B toResidues #7/A distance 3

> alphafold contacts #7/A toResidues #7/B distance 3

> alphafold contacts #7/B toResidues #7/B distance 3

> color bfactor #5 palette alphafold

4113 atoms, 518 residues, 2 surfaces, atom bfactor range 30.3 to 98.1  

> color bfactor #5 palette alphafold

4113 atoms, 518 residues, 2 surfaces, atom bfactor range 30.3 to 98.1  

> color bfactor #7 palette alphafold

4173 atoms, 525 residues, atom bfactor range 23.9 to 98.1  

> alphafold contacts #7/B toResidues #7/A distance 3

> alphafold contacts #7/A toResidues #7/B distance 3

> show #!5 models

> hide #!7 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> show sel surfaces

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-36

90 atoms, 90 bonds, 11 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B:23-113

720 atoms, 742 bonds, 91 residues, 1 model selected  

> show sel surfaces

> select #3/B:23

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

> select #3/B:23-111

708 atoms, 730 bonds, 89 residues, 1 model selected  

> select #3/B:111

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:111-113

24 atoms, 24 bonds, 3 residues, 1 model selected  

> hide sel surfaces

> show #!4 models

> select #4/B:326-327

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/B:326-429

803 atoms, 819 bonds, 104 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> view

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-39

112 atoms, 112 bonds, 14 residues, 1 model selected  

> select #3/A:41

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

> select #3/A:26-41

125 atoms, 125 bonds, 16 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select #4/B:326-429

803 atoms, 819 bonds, 104 residues, 1 model selected  

> select #4/B:326-327

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/B:326-350

187 atoms, 190 bonds, 25 residues, 1 model selected  

> hide sel cartoons

> select #4/B:351

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:351-368

129 atoms, 129 bonds, 18 residues, 1 model selected  

> hide sel cartoons

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:26-41

125 atoms, 125 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #3/A:26-27

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:26-39

112 atoms, 112 bonds, 14 residues, 1 model selected  

> hide sel cartoons

> select #3/A:87-88

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:87-100

114 atoms, 119 bonds, 14 residues, 1 model selected  

> hide sel cartoons

> select #3/A:76-77

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/A:76-85

77 atoms, 76 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> select #3/A:86

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:86-87

11 atoms, 10 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select #3/A:74

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:74-75

16 atoms, 15 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select #3/A:73

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:73

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #4/B:421-422

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/B:421-429

80 atoms, 82 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> select #4/B:419

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:419-420

16 atoms, 15 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:47,51

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:43,47,51

27 atoms, 24 bonds, 3 residues, 1 model selected  

> color (#!3 & sel) #aa7ac7ff

[Repeated 1 time(s)]

> color (#!3 & sel) #877fd9ff

> color (#!3 & sel) #d99b9fff

[Repeated 1 time(s)]

> color (#!3 & sel) #7a71c3ff

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:393,397

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select #4/B:389,393,397

29 atoms, 26 bonds, 3 residues, 1 model selected  

> color (#!4 & sel) #7a71c3ff

> select #3/B:25-31,37-44,48-52,62-70,73-75,82-85

304 atoms, 305 bonds, 36 residues, 1 model selected  

> select #3/B:23

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

> select #3/B:23-110

696 atoms, 717 bonds, 88 residues, 1 model selected  

> show sel cartoons

> transparency (#!3 & sel) 50

> select add #3

1640 atoms, 1506 bonds, 362 residues, 2 models selected  

> select subtract #3

2 models selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting soft

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/K_HIPP43.png" width 2000 height 1648 supersample 3
> transparentBackground true

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56,59

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61-62

29 atoms, 26 bonds, 4 residues, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:61

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:59,61

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:56,59,61

21 atoms, 18 bonds, 3 residues, 1 model selected  

> color (#!3 & sel) #7a71c3ff

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/K_HIPP43_v1.png" width 2000 height 1648 supersample 3
> transparentBackground true

> show #!4 models

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #4/B:402

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:402

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:402,406

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select #4/B:406

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

> select #4/B:406

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

> select #4/B:406

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

> select #4/B:406

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

> select #4/B:405

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:405

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:405,407

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #4/B:402,405,407

23 atoms, 20 bonds, 3 residues, 1 model selected  

> color (#!4 & sel) #7a71c3ff

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:397

9 atoms, 8 bonds, 1 residue, 1 model selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/K_Mla3.png" width 2000 height 1648 supersample 3
> transparentBackground true

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #2 models

> hide #!4 models

> hide #2 models

> show #!4 models

> show #!5 models

> hide #!4 models

> hide #!3 models

> view

> select #4/B:340

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #4/B:340

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show #!4 models

> hide #!5 models

> select #4/B:1

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

> select #4/B

3381 atoms, 3440 bonds, 429 residues, 1 model selected  

> show sel cartoons

> select #4/A:1-2

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #4/A

724 atoms, 746 bonds, 92 residues, 1 model selected  

> show sel cartoons

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!4 models

> close #5

> close #6

> close #7

> close #1

> show #2 models

> show #!3 models

> show #!4 models

> select #4/B:338-339

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #4/B:338-429

716 atoms, 729 bonds, 92 residues, 1 model selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/MPMI/Structures_Mla3_HIPP.cxs"

——— End of log from Sat Jul 15 14:34:47 2023 ———

opened ChimeraX session  

> select #4/B:1

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

> select #4/B

3381 atoms, 3440 bonds, 429 residues, 1 model selected  

> color (#!4 & sel) #c2a2c9ff

> color (#!4 & sel) #c8a0ccff

[Repeated 1 time(s)]

> color (#!4 & sel) #cca4d1ff

> color (#!4 & sel) #cea5d2ff

[Repeated 1 time(s)]

> color (#!4 & sel) #cea5d3ff

[Repeated 1 time(s)]

> color (#!4 & sel) #cfa6d3ff

> color (#!4 & sel) #d0a6d4ff

> color (#!4 & sel) #d0a7d4ff

> color (#!4 & sel) #d0a7d5ff

> color (#!4 & sel) #d1a8d6ff

> color (#!4 & sel) #d2a8d6ff

> select #1/A:398 #1/B:6, 68,72

Nothing selected  

> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity/MLA23/ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #1: MLA23

No name or id option specified for renaming  

> rename #1 MLA23

> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA3/ranked_0.pdb

Chain information for ranked_0.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #5 MLA3

> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA6/ranked_0.pdb

Chain information for ranked_0.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #6 MLA6

> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA28/ranked_0.pdb

Chain information for ranked_0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #7 MLA28

> ui tool show Matchmaker

> matchmaker #1,5-7 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4) with MLA23, chain B (#1), sequence alignment score = 2045.1  
RMSD between 413 pruned atom pairs is 0.519 angstroms; (across all 423 pairs:
0.624)  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4) with MLA3, chain B (#5), sequence alignment score = 2161.7  
RMSD between 420 pruned atom pairs is 0.517 angstroms; (across all 429 pairs:
0.786)  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4) with MLA6, chain B (#6), sequence alignment score = 1810  
RMSD between 339 pruned atom pairs is 1.027 angstroms; (across all 427 pairs:
1.923)  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4) with MLA28, chain B (#7), sequence alignment score = 1851.1  
RMSD between 402 pruned atom pairs is 0.802 angstroms; (across all 429 pairs:
1.183)  
  

> select add #1

8602 atoms, 8692 bonds, 555 residues, 1 model selected  

> select add #2

10208 atoms, 10343 bonds, 760 residues, 2 models selected  

> select add #3

11848 atoms, 11849 bonds, 1122 residues, 3 models selected  

> select add #4

15953 atoms, 16035 bonds, 1643 residues, 6 models selected  

> select add #5

24685 atoms, 24858 bonds, 2204 residues, 8 models selected  

> select add #6

33402 atoms, 33661 bonds, 2763 residues, 9 models selected  

> select add #7

42299 atoms, 42645 bonds, 3333 residues, 10 models selected  

> select subtract #2

40693 atoms, 40994 bonds, 3128 residues, 9 models selected  

> select subtract #4

36588 atoms, 36808 bonds, 2607 residues, 8 models selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #2 models

Alignment identifier is 3/A  
Alignment identifier is 3/B  
Alignment identifier is 1  
Alignment identifier is 1/B  
Alignment identifier is 5/B  
Alignment identifier is 6/B  
Alignment identifier is 7/B  

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A:1-114 #5/A:1-114 #6/A:1-114 #7/A:1-114

6712 atoms, 6840 bonds, 456 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-114] RMSD: 24.356  
  

> hide #1/A, #6/A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1:A, #6:A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1:A, #6:A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1:A, #6:A cartoon

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1:A, #6:A cartoons

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #1:A, #6:A cartoons

Expected an objects specifier or a keyword  

> select #1/A, #6/A

Expected an objects specifier or a keyword  

> select #1/A #6/A

3666 atoms, 3730 bonds, 248 residues, 2 models selected  

> hide #1/A #6/A

> hide #1/A #6/A cartoons

> hide #1/A #6/A #7/A cartoons

> select #5/B:1

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #5/B:1-249

3982 atoms, 4012 bonds, 249 residues, 1 model selected  

> select #5/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #5/B

6900 atoms, 6959 bonds, 437 residues, 1 model selected  

> color sel #d2a8d6ff

> select #1/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #1/B

6769 atoms, 6827 bonds, 431 residues, 1 model selected  

> color sel #8885d5ff

> select #6/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #6/B

6884 atoms, 6938 bonds, 435 residues, 1 model selected  

> color sel #fb8f7eff

> color sel #dc7e6fff

> select #7/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #7/B

7064 atoms, 7119 bonds, 446 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #a37adcff

> color sel #97c5dcff

> color sel #65dc87ff

> color sel #79dca7ff

> color sel #7edcb8ff

> color sel #1bdc7bff

> color sel #85dc22ff

> color sel #9edc1fff

> color sel #b8dc22ff

> color sel #d0dc27ff

> color sel #dcd77eff

> color sel #dcd5a0ff

> select #5/B

6900 atoms, 6959 bonds, 437 residues, 1 model selected  

> select #5/B

6900 atoms, 6959 bonds, 437 residues, 1 model selected  

> select #5/A

1832 atoms, 1864 bonds, 124 residues, 1 model selected  

> color sel #96cde4ff

> select #1/B

6769 atoms, 6827 bonds, 431 residues, 1 model selected  

> select #1/A:97 #5/A:97 #6/A:97 #7/A:97

68 atoms, 64 bonds, 4 residues, 4 models selected  

> select #1/A:97-124 #5/A:97-124 #6/A:97-124 #7/A:97-124

1711 atoms, 1743 bonds, 112 residues, 4 models selected  
1 [ID: 1] region 4 chains [97-124] RMSD: 32.716  
  

> select #1/A:94 #5/A:94 #6/A:94 #7/A:94

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select #1/A:94-124 #5/A:94-124 #6/A:94-124 #7/A:94-124

1795 atoms, 1827 bonds, 124 residues, 4 models selected  
1 [ID: 1] region 4 chains [94-124] RMSD: 32.593  
  

> select #1/A:45-90 #5/A:45-90 #6/A:45-90 #7/A:45-90

2792 atoms, 2840 bonds, 184 residues, 4 models selected  

> select #1/A:45-124 #5/A:45-124 #6/A:45-124 #7/A:45-124

4739 atoms, 4827 bonds, 320 residues, 4 models selected  
1 [ID: 1] region 4 chains [45-124] RMSD: 28.953  
  

> select #1/A:90 #5/A:90 #6/A:90 #7/A:90

84 atoms, 84 bonds, 4 residues, 4 models selected  

> select #1/A:90-124 #5/A:90-124 #6/A:90-124 #7/A:90-124

2031 atoms, 2071 bonds, 140 residues, 4 models selected  
1 [ID: 1] region 4 chains [90-124] RMSD: 32.853  
  

> hide sel cartoons

> hide #!3 models

> view

> ui tool show "Side View"

> select #1/B:346

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/B:346-431

1282 atoms, 1294 bonds, 86 residues, 1 model selected  

> select #1/B:345

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/B:151-345

3103 atoms, 3131 bonds, 195 residues, 1 model selected  

> hide sel cartoons

> select #1/B:1

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/B:1-150

2384 atoms, 2400 bonds, 150 residues, 1 model selected  

> hide sel cartoons

> select #6/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #6/B:1-350

5577 atoms, 5621 bonds, 350 residues, 1 model selected  

> select #6/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #6/B:1-343

5478 atoms, 5522 bonds, 343 residues, 1 model selected  

> hide sel cartoons

> select #5/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #5/B:1-345

5486 atoms, 5531 bonds, 345 residues, 1 model selected  

> hide sel cartoons

> select #7/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #7/B:1-345

5530 atoms, 5572 bonds, 345 residues, 1 model selected  

> hide sel cartoons

> select #7/B:346

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #7/B:346-446

1534 atoms, 1546 bonds, 101 residues, 1 model selected  

> view sel

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A:1-89 #5/A:1-89 #6/A:1-89 #7/A:1-89

5300 atoms, 5384 bonds, 356 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-89] RMSD: 22.704  
  

> view sel

> show #!3 models

> select add #1

12577 atoms, 12730 bonds, 822 residues, 4 models selected  

> select subtract #1

3975 atoms, 4038 bonds, 267 residues, 3 models selected  

> select add #5

11382 atoms, 11515 bonds, 739 residues, 3 models selected  

> select subtract #5

2650 atoms, 2692 bonds, 178 residues, 2 models selected  

> select add #6

10042 atoms, 10149 bonds, 648 residues, 2 models selected  

> select subtract #6

1325 atoms, 1346 bonds, 89 residues, 1 model selected  

> select add #7

8897 atoms, 8984 bonds, 570 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #3

1640 atoms, 1506 bonds, 362 residues, 1 model selected  

> hide #5 models

> hide #6 models

> show #6 models

> show #5 models

Destroying pre-existing alignment with identifier 3/A  
Alignment identifier is 3/A  
Destroying pre-existing alignment with identifier 3/B  
Alignment identifier is 3/B  

> select #3/A:26

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A

582 atoms, 591 bonds, 75 residues, 1 model selected  

> show sel cartoons

> select #3/A:94

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:94

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56-57

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> view sel

> color (#!3 & sel) #acf9a7ff

> color sel byhetero

> hide #5 models

> hide #6 models

> hide #7 models

> hide #1 models

> select #3/A:56

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:56-57

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/B:23-24

8 atoms, 7 bonds, 2 residues, 1 model selected  

> select #3/B

883 atoms, 915 bonds, 112 residues, 1 model selected  

> show sel cartoons

> select #3/B:114

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:114-134

163 atoms, 172 bonds, 21 residues, 1 model selected  

> hide sel cartoons

> select #3/A:56-57

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3/A:56-57

14 atoms, 13 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 interModel false angleSlop 30.0
> twoColors true slopColor #f7bb22 intraMol false intraRes false select true
> reveal true retainCurrent true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 30 degrees
    Models used:
    	3 PWL2_HIPP43_12-11-2020-final.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    PWL2_HIPP43_12-11-2020-final.pdb #3/A THR 57 OG1             PWL2_HIPP43_12-11-2020-final.pdb #3/B GLU 48 O  no hydrogen  2.846  N/A
    PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 N               PWL2_HIPP43_12-11-2020-final.pdb #3/A THR 57 O  no hydrogen  2.834  N/A
    PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 NE (alt loc B)  PWL2_HIPP43_12-11-2020-final.pdb #3/A VAL 56 O  no hydrogen  3.289  N/A
    

  
3 hydrogen bonds found  
2 strict hydrogen bonds found  

> show #5 models

> select #5/B:410-411

37 atoms, 37 bonds, 2 residues, 1 model selected  

> select #5/B:410-411

37 atoms, 37 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> ~displace HC

Unknown command: ~displace HC  

> ~display HC

> select #3/B:48

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:48-98

407 atoms, 420 bonds, 51 residues, 1 model selected  

> select #3/B:48

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:48

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #5 models

> show #5 models

> select #5/B:410

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #5/B:410-411

37 atoms, 37 bonds, 2 residues, 1 model selected  

> ui tool show Matchmaker

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 interModel false angleSlop 30.0
> twoColors true slopColor #f7bb22 intraMol false intraRes false select true
> reveal true retainCurrent true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 30 degrees
    Models used:
    	5 MLA3
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    MLA3 #5/A ARG 23 N   MLA3 #5/B TYR 411 O  MLA3 #5/A ARG 23 H   2.889  1.906
    MLA3 #5/A ARG 23 NE  MLA3 #5/B VAL 410 O  MLA3 #5/A ARG 23 HE  2.851  2.304
    

  
2 hydrogen bonds found  
1 strict hydrogen bonds found  

> ~display HC

> select #1/A:23 #5/A:23 #6/A:23 #7/A:23

96 atoms, 92 bonds, 4 residues, 4 models selected  

> select #1/A:23 #5/A:23 #6/A:23 #7/A:23

96 atoms, 92 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [23] RMSD: 20.134  
  

> ~display HC

> ~display H

> undo

> color sel & #!5 byhetero

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> display HC

> color sel byhetero

> undo

> select #3/B:23

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

> select #3/B:23-101

630 atoms, 648 bonds, 79 residues, 1 model selected  

> hide sel surfaces

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select #3/B:44display HC

Expected a keyword  

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> display HC

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> addH

Unknown command: addH  

> select #3/B:44

11 atoms, 10 bonds, 1 residue, 1 model selected  

> addh #3/B:44

Summary of feedback from adding hydrogens to PWL2_HIPP43_12-11-2020-final.pdb
#3  
---  
notes | No usable SEQRES records for PWL2_HIPP43_12-11-2020-final.pdb (#3) chain A; guessing termini instead  
No usable SEQRES records for PWL2_HIPP43_12-11-2020-final.pdb (#3) chain B;
guessing termini instead  
Chain-initial residues that are actual N termini:
PWL2_HIPP43_12-11-2020-final.pdb #3/A ARG 26, PWL2_HIPP43_12-11-2020-final.pdb
#3/B GLY 23  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:
PWL2_HIPP43_12-11-2020-final.pdb #3/A MET 100,
PWL2_HIPP43_12-11-2020-final.pdb #3/B HIS 134  
661 hydrogen bonds  
PWL2_HIPP43_12-11-2020-final.pdb #3/A MET 100 is not terminus, removing H atom
from 'C'  
PWL2_HIPP43_12-11-2020-final.pdb #3/B HIS 134 is not terminus, removing H atom
from 'C'  
1725 hydrogens added  
  

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A #5/A #6/A #7/A

7331 atoms, 7459 bonds, 496 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-124] RMSD: 25.974  
  

> color (#!5 & sel) #79d9ddff

> undo

> select #1/A:1-2 #5/A:1-2 #6/A:1-2 #7/A:1-2

64 atoms, 60 bonds, 8 residues, 4 models selected  

> select #1/A #5/A #6/A #7/A

7331 atoms, 7459 bonds, 496 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-124] RMSD: 25.974  
  

> color (#!5 & sel) #79d9ddff

> ~display HC

> select #1/A:23 #5/A:23 #6/A:23 #7/A:23

96 atoms, 92 bonds, 4 residues, 4 models selected  

> select #1/A:23 #5/A:23 #6/A:23 #7/A:23

96 atoms, 92 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [23] RMSD: 20.134  
  

> color sel & #!5 byhetero

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> ~display HC

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A

1193 atoms, 1202 bonds, 75 residues, 1 model selected  

> color (#!3 & sel) #a3ec9eff

> select #3/B:23

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:23-101

1199 atoms, 1217 bonds, 79 residues, 1 model selected  

> hide #!5 models

> select #3/B:23-24

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/B:23-113

1360 atoms, 1382 bonds, 91 residues, 1 model selected  

> show sel surfaces

> transparency (#!3 & sel) 60

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select #3/B:113

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/B:113

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/B:114-115

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #3/B:114-117

38 atoms, 38 bonds, 4 residues, 1 model selected  

> select #3/B:69-117

700 atoms, 712 bonds, 49 residues, 1 model selected  

> select #3/B:69-115

686 atoms, 698 bonds, 47 residues, 1 model selected  

> select #3/B:111-112

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #3/B:111-115

66 atoms, 67 bonds, 5 residues, 1 model selected  

> show sel surfaces

> undo

> select #3/B:111

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/B:111-121

140 atoms, 143 bonds, 11 residues, 1 model selected  

> select #3/B:114-115

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #3/B:114-121

98 atoms, 100 bonds, 8 residues, 1 model selected  

> hide sel surfaces

> select #3/A:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:56-57

30 atoms, 29 bonds, 2 residues, 1 model selected  

> view sel

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> ~display HC

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:57

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel atoms

> ~display HC

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 3 models selected  

> select subtract #3

2 models selected  

> select #3/B:23

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:23-113

1360 atoms, 1382 bonds, 91 residues, 1 model selected  

> transparency (#!3 & sel) 50

> transparency (#!3 & sel) 70

> view sel

> select #3/A:56-57

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select #3/A:56-57

30 atoms, 29 bonds, 2 residues, 1 model selected  

> view

> view sel

> select #3/A:67

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3/A:67-73

107 atoms, 107 bonds, 7 residues, 1 model selected  

> select #3/A:67

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3/A:67-75

138 atoms, 138 bonds, 9 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #3/A:83

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:83-85

49 atoms, 48 bonds, 3 residues, 1 model selected  

> select #3/A:76-77

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:76-78

43 atoms, 42 bonds, 3 residues, 1 model selected  

> select #3/A:76

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #3/A:76-81

93 atoms, 92 bonds, 6 residues, 1 model selected  

> show #6 models

> select #6/B:408-409

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select #6/B:408-409

36 atoms, 36 bonds, 2 residues, 1 model selected  

> show sel atoms

> ~display HC

> color sel byhetero

> show #!5 models

> show #7 models

> hide #!5 models

> hide #6 models

> select #7/B:407

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #7/B:407-408

31 atoms, 32 bonds, 2 residues, 1 model selected  

> select #7/B:410-411

41 atoms, 41 bonds, 2 residues, 1 model selected  

> select #7/B:410-411

41 atoms, 41 bonds, 2 residues, 1 model selected  

> show sel atoms

> ~display HC

> color sel byhetero

> ~display HC

> select #7/B:410

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #7/B:410

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #7/B:411

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #7/B:411

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show #1 models

> hide #7 models

> select #1/B:410-411

31 atoms, 32 bonds, 2 residues, 1 model selected  

> select #1/B:410-411

31 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> ~display HC

> color sel byhetero

> hide #1 models

> select #3/A:67

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3/A:67-75

138 atoms, 138 bonds, 9 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #3/A:26-27

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select #3/A

1193 atoms, 1202 bonds, 75 residues, 1 model selected  

> show sel cartoons

> hide #!3 models

> show #!3 models

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 3 models selected  

> select subtract #3

2 models selected  

> select #3/B:23

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:23-113

1360 atoms, 1382 bonds, 91 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> select #3/B:111-112

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #3/B:111-113

42 atoms, 42 bonds, 3 residues, 1 model selected  

> hide sel surfaces

> select #3/A:47-48

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #3/A:47-48

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #3/A:47

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/A:47

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/A:51

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/A:51

22 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/B:23-24

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/B

1647 atoms, 1679 bonds, 112 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 4 models selected  

> select subtract #3

2 models selected  

> lighting soft

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> lighting full

[Repeated 1 time(s)]

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

[Repeated 1 time(s)]

> select #3/B:44

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3/B:44-116

1067 atoms, 1086 bonds, 73 residues, 1 model selected  

> select #3/B:23-24

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/B:23-113

1360 atoms, 1382 bonds, 91 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #3.2:
minimum, -18.40, mean -1.40, maximum 13.14  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency (#!3 & sel) 70

> hide sel surfaces

> select #3/B:23-24

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/B

1647 atoms, 1679 bonds, 112 residues, 1 model selected  

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 4 models selected  

> select subtract #3

2 models selected  

> show #1 models

> hide #!3 models

> show #!5 models

> hide #1 models

> show #!3 models

> show #1 models

> show #6 models

> show #7 models

> hide #1 models

> hide #!3 models

> hide #6 models

> hide #7 models

> show #1 models

> hide #1 models

> show #6 models

> select #6/B:409

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #6/B:409

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #6/B:409 #1/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> select #6/B:409 #1/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> select #6/B:409, #1/A:23

Expected an objects specifier or a keyword  

> select #6/B:409 #1/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> select #6/B:409 #1/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> select #6/B:409 #5/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.4 angstroms and 30 degrees
    Models used:
    	5 MLA3
    	6 MLA6
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  
0 strict hydrogen bonds found  

> select #6/B:409 #5/A:23

43 atoms, 41 bonds, 2 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.8 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.8 angstroms and 30 degrees
    Models used:
    	5 MLA3
    	6 MLA6
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hide #6 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP_VT.png" width 3000 height 2208
> supersample 3 transparentBackground true

> hide #!3 models

> show #!5 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #5/B:411 #5/A:23

45 atoms, 44 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select #5/B:410,411 #3/B:44

61 atoms, 60 bonds, 3 residues, 2 models selected  

> hide #5.1 models

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.8 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.8 angstroms and 30 degrees
    Models used:
    	3 PWL2_HIPP43_12-11-2020-final.pdb
    	5 MLA3
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 N (alt loc B)  MLA3 #5/B TYR 411 O  PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 H (alt loc B)  3.649  2.754
    

  
1 hydrogen bonds found  
0 strict hydrogen bonds found  

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A #5/A #6/A #7/A

7331 atoms, 7459 bonds, 496 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-124] RMSD: 25.974  
  

> hide sel & #!5 surfaces

> hide sel & #!5 cartoons

> show sel & #!5 cartoons

> hide sel & #!5 cartoons

> select#3/B:44

Unknown command: select#3/B:44  

> hide sel & #!5 atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A

1193 atoms, 1202 bonds, 75 residues, 1 model selected  

> hide #!5 models

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 3 models selected  

> select subtract #3

2 models selected  

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP_VT_v1.png" width 3000 height
> 2208 supersample 3 transparentBackground true

> select #3/A:26-87

978 atoms, 981 bonds, 62 residues, 1 model selected  

> select #3/A

1193 atoms, 1202 bonds, 75 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!5 models

> show #5.1 models

> select#3/B:44

Unknown command: select#3/B:44  

> select #3/B:44

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3/B:44 #5/B:410,411

61 atoms, 60 bonds, 1 pseudobond, 3 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.8 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.8 angstroms and 30 degrees
    Models used:
    	3 PWL2_HIPP43_12-11-2020-final.pdb
    	5 MLA3
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 N (alt loc B)  MLA3 #5/B TYR 411 O  PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 H (alt loc B)  3.649  2.754
    

  
1 hydrogen bonds found  
0 strict hydrogen bonds found  

> select #3/B:44 #5/B:410,411

61 atoms, 60 bonds, 1 pseudobond, 3 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 1.0 angleSlop 35.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 1 angstroms and 35 degrees
    Models used:
    	3 PWL2_HIPP43_12-11-2020-final.pdb
    	5 MLA3
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 N (alt loc B)  MLA3 #5/B TYR 411 O  PWL2_HIPP43_12-11-2020-final.pdb #3/B ARG 44 H (alt loc B)  3.649  2.754
    

  
1 hydrogen bonds found  
0 strict hydrogen bonds found  

> hide #!3 models

> select #1/A:1-2 #5/A:1-2 #6/A:1-2 #7/A:1-2

64 atoms, 60 bonds, 8 residues, 4 models selected  

> select #1/A:1-91 #5/A:1-91 #6/A:1-91 #7/A:1-91

5412 atoms, 5500 bonds, 364 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-91] RMSD: 23.040  
  

> show sel & #!5 cartoons

> select #1/A:92 #5/A:92 #6/A:92 #7/A:92

56 atoms, 52 bonds, 4 residues, 4 models selected  

> select #1/A:92-124 #5/A:92-124 #6/A:92-124 #7/A:92-124

1919 atoms, 1955 bonds, 132 residues, 4 models selected  
1 [ID: 1] region 4 chains [92-124] RMSD: 32.728  
  

> select #1/A:87 #5/A:87 #6/A:87 #7/A:87

56 atoms, 56 bonds, 4 residues, 4 models selected  

> select #1/A:87-110 #5/A:87-110 #6/A:87-110 #7/A:87-110

1276 atoms, 1312 bonds, 96 residues, 4 models selected  
1 [ID: 1] region 4 chains [87-110] RMSD: 30.175  
  

> select #1/A:88 #5/A:88 #6/A:88 #7/A:88

40 atoms, 36 bonds, 4 residues, 4 models selected  

> select #1/A:88-102 #5/A:88-102 #6/A:88-102 #7/A:88-102

772 atoms, 788 bonds, 60 residues, 4 models selected  
1 [ID: 1] region 4 chains [88-102] RMSD: 32.296  
  

> show sel & #!5 cartoons

[Repeated 1 time(s)]

> select #5/A:23 #5/B:410,411

61 atoms, 60 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> show sel atoms

> ~display HC

> select add #5

8732 atoms, 8823 bonds, 2 pseudobonds, 561 residues, 2 models selected  

> select subtract #5

Nothing selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA3_VY.png" width 3000 height 2208
> supersample 3 transparentBackground true

> select #1/A:51 #5/A:51 #6/A:51 #7/A:51

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select #1/A:50-51 #5/A:50-51 #6/A:50-51 #7/A:50-51

84 atoms, 80 bonds, 8 residues, 4 models selected  
1 [ID: 1] region 4 chains [50-51] RMSD: 18.227  
  

> select #1/A:53 #5/A:53 #6/A:53 #7/A:53

76 atoms, 72 bonds, 4 residues, 4 models selected  

> select #1/A:53 #5/A:53 #6/A:53 #7/A:53

76 atoms, 72 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [53] RMSD: 9.779  
  

> select #1/A:51 #5/A:51 #6/A:51 #7/A:51

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select #1/A:51-55 #5/A:51-55 #6/A:51-55 #7/A:51-55

284 atoms, 280 bonds, 20 residues, 4 models selected  
1 [ID: 1] region 4 chains [51-55] RMSD: 12.590  
  

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A:1-3 #5/A:1-3 #6/A:1-3 #7/A:1-3

92 atoms, 88 bonds, 12 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-3] RMSD: 28.861  
  

> select #1/A:1 #5/A:1 #6/A:1 #7/A:1

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #1/A:1-2 #5/A:1-2 #6/A:1-2 #7/A:1-2

64 atoms, 60 bonds, 8 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-2] RMSD: 29.833  
  

> hide sel & #!5 cartoons

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA3_VY_v1.png" width 3000 height
> 2208 supersample 3 transparentBackground true

> show #1 models

> select #5/B:1-2

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #5/B

6900 atoms, 6959 bonds, 437 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA23_HP.png" width 3000 height 2208
> supersample 3 transparentBackground true

> hide #1 models

> show #6 models

> select #5/A:23 #6/B:409

43 atoms, 41 bonds, 2 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 1.0 angleSlop 35.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 1 angstroms and 35 degrees
    Models used:
    	5 MLA3
    	6 MLA6
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  
0 strict hydrogen bonds found  

> show #1 models

> hide #1 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA6_HL.png" width 3000 height 2208
> supersample 3 transparentBackground true

> hide #6 models

> show #7 models

> ~display HC

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA28_HR.png" width 3000 height 2208
> supersample 3 transparentBackground true

> set bgColor white

> set bgColor gray

> set bgColor black

> set bgColor white

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> set bgColor black

> show #!3 models

> hide #7 models

> show #7 models

> hide #7 models

> hide #!5 models

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A

1193 atoms, 1202 bonds, 75 residues, 1 model selected  

> show sel cartoons

> select #3/A:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:56-57

30 atoms, 29 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> ~display HC

> set bgColor white

> show #!5 models

> hide #!5 models

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 3 models selected  

> select subtract #3

2 models selected  

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> graphics silhouettes false

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP_VT_v2.png" width 3000 height
> 2092 supersample 3 transparentBackground true

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP_VT_v3.png" width 1000 height 712
> supersample 3 transparentBackground true

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP_VT_v3.png" width 3000 height
> 2137 supersample 3 transparentBackground true

> show #!5 models

> hide #!3 models

> select #5/B:301

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #5/B:301-437

2105 atoms, 2125 bonds, 137 residues, 1 model selected  

> show sel cartoons

> select #5/B:410

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #5/B:410-411

37 atoms, 37 bonds, 2 residues, 1 model selected  

> show sel atoms

> ~display HC

> select add #5

8732 atoms, 8823 bonds, 2 pseudobonds, 561 residues, 2 models selected  

> select subtract #5

Nothing selected  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA3_VY_v2.png" width 3000 height
> 2137 supersample 3 transparentBackground true

> show #!3 models

> hide #!3 models

> select #5/B:301-302

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #5/B:301-437

2105 atoms, 2125 bonds, 137 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #6 models

> show #1 models

> hide #6 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA23_HP_V1.png" width 3000 height
> 2137 supersample 3 transparentBackground true

> hide #1 models

> show #6 models

> hide #!5 models

> show #!5 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA6_HL_V1.png" width 3000 height
> 2137 supersample 3 transparentBackground true

> hide #6 models

> show #7 models

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLA28_HR_V1.png" width 3000 height
> 2137 supersample 3 transparentBackground true

> show #!3 models

> hide #!3 models

> show #!3 models

Destroying pre-existing alignment with identifier 5/B  
Alignment identifier is 5/B  

> select add #3

5470 atoms, 5356 bonds, 3 pseudobonds, 499 residues, 3 models selected  
Alignment identifier is 3/A  
Alignment identifier is 3/B  
Destroying pre-existing alignment with identifier 5/B  
Alignment identifier is 5/B  

> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/mimicry.cxs"

——— End of log from Mon May 20 11:49:05 2024 ———

opened ChimeraX session  

> show #2 models

> hide #2 models

> hide #!3 models

> hide #!5 models

> close #6,7

> hide #8 models

> close #1

> show #2 models

> show #!3 models

> hide #2 models

> select add #3

5470 atoms, 5356 bonds, 3 pseudobonds, 499 residues, 3 models selected  

> select subtract #3

2105 atoms, 2125 bonds, 137 residues, 1 model selected  

> select add #5

8732 atoms, 8823 bonds, 2 pseudobonds, 561 residues, 2 models selected  

> select subtract #5

Nothing selected  

> show #!4 models

> show #!5 models

> ui tool show "Side View"

> view

> set bgColor black

> select #3/A:26

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3/A:26-28

59 atoms, 59 bonds, 3 residues, 1 model selected  

> select #3/A:89-90

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select #3/A:89-100

193 atoms, 198 bonds, 12 residues, 1 model selected  

> select #5/B:63

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #5/B:63-114

815 atoms, 819 bonds, 52 residues, 1 model selected  

> select #5/B:56

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #5/B:56-170

1827 atoms, 1837 bonds, 115 residues, 1 model selected  

> select add #4

5932 atoms, 6023 bonds, 636 residues, 2 models selected  

> select add #5

12837 atoms, 13009 bonds, 2 pseudobonds, 1082 residues, 4 models selected  

> select subtract #5

4105 atoms, 4186 bonds, 521 residues, 2 models selected  
Alignment identifier is 4/A  
Alignment identifier is 4/B  

> select subtract #4

1 model selected  

> select add #4

4105 atoms, 4186 bonds, 521 residues, 1 model selected  

> select subtract #4

1 model selected  

> select #4/B:257-258

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:257-310

427 atoms, 432 bonds, 54 residues, 1 model selected  

> select add #4

4105 atoms, 4186 bonds, 521 residues, 2 models selected  

> select subtract #4

1 model selected  

> select #4/B:382

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:382-384

20 atoms, 19 bonds, 3 residues, 1 model selected  

> select #4/B:345-346

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #4/B:345-349

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select #4/B:338-339

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #4/B:338-340

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select #4/B:339

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #4/B:339-343

43 atoms, 43 bonds, 5 residues, 1 model selected  

> select #3/A:31

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:31-32

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select #3/A:29-34,56-62,67-72,95-97

336 atoms, 334 bonds, 22 residues, 1 model selected  

> select #3/A:32

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #3/A:32-34

55 atoms, 54 bonds, 3 residues, 1 model selected  

> select #3/A:31

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:31-34

71 atoms, 70 bonds, 4 residues, 1 model selected  

> select #4/B:338

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

> select #4/B:338-344

52 atoms, 52 bonds, 7 residues, 1 model selected  

> select #3/A:29

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #3/A:29-34

102 atoms, 101 bonds, 6 residues, 1 model selected  

> select #4/B:212-263

428 atoms, 441 bonds, 52 residues, 1 model selected  

> select #4/B:212-263

428 atoms, 441 bonds, 52 residues, 1 model selected  

> select #4/B:337

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/B:336-337

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:29

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #3/A:29-88

941 atoms, 943 bonds, 60 residues, 1 model selected  

> select add #3

3365 atoms, 3231 bonds, 3 pseudobonds, 362 residues, 3 models selected  
Destroying pre-existing alignment with identifier 3/A  
Alignment identifier is 3/A  
Alignment identifier is 3/B  

> open
> /Users/gomezdd/Downloads/fold_mla3_lrr_866_hipp43_29_88/fold_mla3_lrr_866_hipp43_29_88_model_0.cif

Chain information for fold_mla3_lrr_866_hipp43_29_88_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #1 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
Pwl2delta_LRR_rec6_b0207_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#4) with fold_mla3_lrr_866_hipp43_29_88_model_0.cif, chain A (#1),
sequence alignment score = 1685.9  
RMSD between 324 pruned atom pairs is 0.594 angstroms; (across all 385 pairs:
5.836)  
  

> select subtract #3

2 models selected  

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!3 models

> hide #!4 models

> select
> #4/B:7-10,33-36,55-57,84-86,107-109,131-133,154-160,177-182,205-210,236-239,264-267,289-293,302-305,315-319,325-328,338-344,370-376,404-410

705 atoms, 702 bonds, 86 residues, 1 model selected  

> select add #1

3826 atoms, 3870 bonds, 483 residues, 3 models selected  
Destroying pre-existing alignment with identifier 4/B  
Alignment identifier is 4/B  
Alignment identifier is 1/A  

> select subtract #1

705 atoms, 702 bonds, 86 residues, 2 models selected  

> select #1/A:338-339

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:338-397

456 atoms, 457 bonds, 60 residues, 1 model selected  

> show #!4 models

> show #!3 models

> hide #1 models


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3B/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 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: 23 days, 23 hours, 55 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PL2492H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

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

comment:2 by Tom Goddard, 15 months ago

Resolution: → duplicate
Status: assigned → closed

Mac Qt bug, crashing in _NSViewHierarchyDidChangeBackingProperties, on connecting or disconnecting external display or waking from sleep.

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