id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15864 ChimeraX bug report submission chimerax-bug-report@… "{{{ 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) {""app_name"":""ChimeraX"",""timestamp"":""2024-09-02 12:03:41.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""04958DED-A103-4253-8DB2-67569B735966""} { ""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"" }, ""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. 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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 }}} " defect new normal Unassigned