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Changes between Initial Version and Version 1 of Ticket #18674

Timestamp:: Sep 2, 2025, 10:22:03 AM (7 weeks ago)
Author:: pett
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #18674
- Property Component Unassigned → Window Toolkit
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

Ticket #18674 – Description

-              initial
+              v1
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+    "name" : "ast.cpython-311-darwin.so"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64",
+    "base" : 13308329984,
+    "size" : 81920,
+    "uuid" : "6f70cad3-dcb4-30f4-a886-666d124ed77f",
+    "path" : "\/Applications\/ChimeraX-1.10.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
+    "name" : "_chem_group.cpython-311-darwin.so"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64",
+    "base" : 13319241728,
+    "size" : 16384,
+    "uuid" : "b73c9868-d7da-309a-8d4a-1e5f333d7879",
+    "path" : "\/Applications\/ChimeraX-1.10.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mlp\/_mlp.cpython-311-darwin.so",
+    "name" : "_mlp.cpython-311-darwin.so"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64",
+    "base" : 13415530496,
+    "size" : 114688,
+    "uuid" : "eeed9345-c6ca-3901-838d-b142fec81992",
+    "path" : "\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/_pyKVFinder.cpython-311-darwin.so",
+    "name" : "_pyKVFinder.cpython-311-darwin.so"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64",
+    "base" : 14660927488,
+    "size" : 491520,
+    "uuid" : "c84ec7aa-d6a2-300c-b853-271379d59690",
+    "path" : "\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/libomp.dylib",
+    "name" : "libomp.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6579965952,
+    "size" : 243284,
+    "uuid" : "6e4a96ad-04b8-3e8a-b91d-087e62306246",
+    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
+    "name" : "libsystem_kernel.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6580211712,
+    "size" : 51784,
+    "uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
+    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
+    "name" : "libsystem_pthread.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6578733056,
+    "size" : 528964,
+    "uuid" : "dfea8794-80ce-37c3-8f6a-108aa1d0b1b0",
+    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
+    "name" : "libsystem_c.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6580461568,
+    "size" : 32268,
+    "uuid" : "fd19a599-8750-31f9-924f-c2810c938371",
+    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
+    "name" : "libsystem_platform.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6647164928,
+    "CFBundleShortVersionString" : "6.9",
+    "CFBundleIdentifier" : "com.apple.AppKit",
+    "size" : 21564992,
+    "uuid" : "860c164c-d04c-30ff-8c6f-e672b74caf11",
+    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
+    "name" : "AppKit",
+    "CFBundleVersion" : "2575.70.52"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6681145344,
+    "CFBundleShortVersionString" : "1.600.0",
+    "CFBundleIdentifier" : "com.apple.SkyLight",
+    "size" : 5398624,
+    "uuid" : "4e052846-80c2-38af-85bf-1482e070a32b",
+    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
+    "name" : "SkyLight"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6578429952,
+    "size" : 288608,
+    "uuid" : "24ce0d89-4114-30c2-a81a-3db1f5931cff",
+    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
+    "name" : "libdispatch.dylib"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6580690944,
+    "CFBundleShortVersionString" : "6.9",
+    "CFBundleIdentifier" : "com.apple.CoreFoundation",
+    "size" : 5500928,
+    "uuid" : "8d45baee-6cc0-3b89-93fd-ea1c8e15c6d7",
+    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
+    "name" : "CoreFoundation",
+    "CFBundleVersion" : "3603"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6776094720,
+    "CFBundleShortVersionString" : "2.1.1",
+    "CFBundleIdentifier" : "com.apple.HIToolbox",
+    "size" : 3174368,
+    "uuid" : "1a037942-11e0-3fc8-aad2-20b11e7ae1a4",
+    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
+    "name" : "HIToolbox"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6576406528,
+    "size" : 636280,
+    "uuid" : "3247e185-ced2-36ff-9e29-47a77c23e004",
+    "path" : "\/usr\/lib\/dyld",
+    "name" : "dyld"
+  },
+  {
+    "size" : 0,
+    "source" : "A",
+    "base" : 0,
+    "uuid" : "00000000-0000-0000-0000-000000000000"
+  },
+  {
+    "source" : "P",
+    "arch" : "arm64e",
+    "base" : 6603698176,
+    "CFBundleShortVersionString" : "6.9",
+    "CFBundleIdentifier" : "com.apple.Foundation",
+    "size" : 14587296,
+    "uuid" : "b9a92060-f21e-3ecf-9ded-94a65c68a6f4",
+    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
+    "name" : "Foundation",
+    "CFBundleVersion" : "3603"
+  }
+[deleted to fit within ticket limits]
 ],
   "sharedCache" : {
 …
 > ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.95306,-0.23881,-0.18612,55.377,0.066915,0.4334,-0.89871,42.854,0.29528,-0.86899,-0.39708,32.966
+> view matrix models
+> #2,-0.95139,0.064309,-0.30119,55.993,0.3073,0.26314,-0.91451,37.267,0.020443,-0.96261,-0.27011,38.734
+> view matrix models
+> #2,-0.9238,0.27869,-0.26252,48.177,0.34,0.28194,-0.89717,34.491,-0.17602,-0.91806,-0.35522,51.067
+> view matrix models
+> #2,-0.95121,0.25091,-0.17957,44.939,0.26484,0.36532,-0.89241,35.635,-0.15831,-0.89643,-0.41395,53.39
+> volume #1 level 0.0347
+> volume #1 level 0.1003
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.93909,0.24057,-0.24544,48.57,0.32404,0.38183,-0.86557,31.238,-0.11451,-0.89237,-0.43653,52.832
+> volume #1 level 0.1162
+> select clear
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/BIO-
+> SAXS_data/EPN_24196/reduced_data/standard_mode_reduction/1E4_12mgml_2565fa7c_E12k4_D750/DENSS_20_slow/A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_refine_aligned.mrc
+Opened A_S_SM_1E4_12mgml_2565fa7c_E12k4_D750_refine_aligned.mrc as #3, grid
+size 64,64,64, pixel 2.58, shown at level 0.00127, step 1, values float32
+> volume #3 level 0.05394
+> select add #3
+models selected
+> view matrix models
+> #3,0.90439,-0.32834,0.27253,0.55824,0.30016,0.03557,-0.95322,1.122,0.30329,0.94389,0.13073,-1.6301
+> view matrix models
+> #3,0.90114,-0.28883,0.3233,0.53428,0.34884,0.0403,-0.93632,1.1979,0.25741,0.95653,0.13707,-1.7097
+> view matrix models
+> #3,0.90998,-0.25742,0.32508,0.50189,0.36592,0.12972,-0.92156,1.1016,0.19506,0.95755,0.21223,-1.7428
+> volume #3 level 0.01005
+> view matrix models
+> #3,0.85452,-0.29737,0.42588,0.71244,0.4528,0.024725,-0.89127,1.7863,0.2545,0.95444,0.15578,-1.6904
+> view matrix models
+> #3,0.82766,-0.42728,0.36389,0.72372,0.4185,0.037858,-0.90743,1.571,0.37395,0.90333,0.21015,-0.93365
+> view matrix models
+> #3,0.82868,-0.44662,0.33737,0.68869,0.4024,0.056409,-0.91373,1.444,0.38905,0.89295,0.22646,-0.79796
+> ui mousemode right "translate selected models"
+> view matrix models
+> #3,0.82868,-0.44662,0.33737,2.7517,0.4024,0.056409,-0.91373,0.90906,0.38905,0.89295,0.22646,2.1876
+> volume #3 level 0.02761
+> volume #3 style mesh
+> select clear
+> hide #!1 models
+> color #3 black models
+> color #3 #942193ff models
+> color #3 #0433ffff models
+> color #3 #9437ffff models
+> color #3 #ff2600ff models
+> color #3 #d6d6d6ff models
+> color #3 #919191ff models
+> color #3 #797979ff models
+> color #3 silver models
+> color #3 darkgrey models
+> show #!1 models
+> hide #!3 models
+> show #!3 models
+> volume #3 level -0.007502
+> hide #!3 models
+> ui mousemode right "rotate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.93051,0.25996,-0.25802,48.569,0.35574,0.47383,-0.80556,24.471,-0.087155,-0.84137,-0.53338,56.427
+> view matrix models
+> #2,-0.65984,0.74305,-0.1117,18.76,0.46661,0.28868,-0.83602,25.446,-0.58896,-0.60377,-0.5372,72.682
+> view matrix models
+> #2,-0.65535,0.74253,-0.13843,20.177,0.50482,0.29426,-0.81152,22.284,-0.56185,-0.60171,-0.56769,73.329
+> view matrix models
+> #2,-0.81072,0.54348,-0.21764,35.41,0.43735,0.31511,-0.84228,26.497,-0.38917,-0.77803,-0.49316,65.298
+> hide #2 models
+> show #2 models
+> select subtract #2
+Nothing selected
+> select clear
+> volume #1 level 0.09437
+> ui mousemode right "translate selected models"
+> hide #2 models
+> show #2 models
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.81072,0.54348,-0.21764,35.713,0.43735,0.31511,-0.84228,24.938,-0.38917,-0.77803,-0.49316,64.981
+> hide #2 models
+> show #2 models
+> select subtract #2
+Nothing selected
+> color #2 #919191ff
+> color #2 #008f00ff
+> color #2 #919191ff
+> color #2 #797979ff
+> color #2 #919191ff
+> color #2 darkgrey
+> color #2 silver
+> color #2 #919191ff
+> color #2 #929292ff
+> color #1 #797979ff models
+> color #1 #919191ff models
+> color #1 #797979ff models
+> color #1 #5e5e5eff models
+> color #1 #797979ff models
+> color #1 #919191ff models
+> select clear
+> volume #1 level 0.1123
+> volume #1 level 0.1819
+> volume #1 level 0.1262
+> volume #1 level 0.08243
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.81072,0.54348,-0.21764,35.569,0.43735,0.31511,-0.84228,25.584,-0.38917,-0.77803,-0.49316,65.236
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.076082,0.97165,0.22384,-30.001,0.62727,0.22114,-0.74674,13.908,-0.77507,0.083593,-0.62632,71.673
+> select subtract #2
+Nothing selected
+> select clear
+> volume #1 level 0.168
+> select clear
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.084348,0.96935,0.23075,-30.022,0.64497,0.22963,-0.72889,11.936,-0.75954,0.087344,-0.64457,72.039
+> view matrix models
+> #2,-0.095717,0.89863,0.42813,-39.871,0.61133,0.3925,-0.68718,7.5333,-0.78557,0.19595,-0.58693,67.475
+> view matrix models
+> #2,-0.16416,0.91475,0.36916,-33.84,0.60904,0.38838,-0.69154,7.9715,-0.77596,0.11132,-0.62088,70.822
+> view matrix models
+> #2,-0.17183,0.91089,0.37518,-33.801,0.62501,0.39518,-0.67319,6.0759,-0.76147,0.11882,-0.63722,71.04
+> view matrix models
+> #2,-0.53276,0.84625,0.0055281,4.5488,-0.58212,-0.3712,0.72342,-11.353,0.61425,0.38219,0.69038,-70.633
+> view matrix models
+> #2,-0.47611,0.8724,-0.11061,8.5821,-0.5465,-0.19499,0.81444,-21.845,0.68895,0.44822,0.56961,-67.886
+> view matrix models
+> #2,-0.47923,0.87645,-0.046643,4.8173,-0.5294,-0.24626,0.81185,-21.358,0.70006,0.41376,0.582,-68.385
+> view matrix models
+> #2,-0.45136,0.88961,-0.069751,4.7676,-0.54197,-0.2112,0.81343,-21.643,0.7089,0.40495,0.57747,-68.303
+> view matrix models
+> #2,-0.42339,0.90019,-0.10199,5.3101,-0.68646,-0.24532,0.68454,-7.2606,0.59119,0.35984,0.72181,-71.091
+> view matrix models
+> #2,-0.42612,0.89919,-0.099372,5.2879,-0.67465,-0.24267,0.69711,-8.5548,0.60272,0.36409,0.71005,-70.956
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.42612,0.89919,-0.099372,5.4026,-0.67465,-0.24267,0.69711,-9.7406,0.60272,0.36409,0.71005,-71.422
+> select subtract #2
+Nothing selected
+> select clear
+> ui mousemode right "rotate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.43109,0.89722,-0.095713,5.4316,-0.65373,-0.23745,0.71851,-11.992,0.62193,0.37231,0.6889,-71.128
+> select subtract #2
+Nothing selected
+> ui mousemode right "translate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.43109,0.89722,-0.095713,5.3511,-0.65373,-0.23745,0.71851,-12.464,0.62193,0.37231,0.6889,-70.662
+> hide #!3 models
+> volume #1 level 0.1859
+> select clear
+> volume #1 level 0.286
+> volume #1 level 0.186
+> color #1 #008f00ff models
+> color #1 #fffb00ff models
+> color #1 darkgrey models
+> color #2 #fffb00ff
+> color #2 #fffc79ff
+> color #2 #ffd479ff
+> color #2 #fffc79ff
+> color #2 #d4fb79ff
+> color #2 #ebebebff
+> color #2 #d6d6d6ff
+> color #2 silver
+> color #2 darkgrey
+> color #2 #929292ff
+> color #2 darkgrey
+> color #1 black models
+> color #1 #424242ff models
+> color #1 #797979ff models
+> color #1 #929292ff models
+> select clear
+> volume #1 level 0.176
+> volume #1 level 0.196
+> volume #1 level 0.199
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.44073,0.89306,-0.090513,5.5266,-0.62073,-0.23038,0.74941,-15.821,0.64842,0.38647,0.65589,-70.085
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.44073,0.89306,-0.090513,5.3586,-0.62073,-0.23038,0.74941,-14.772,0.64842,0.38647,0.65589,-69.805
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.43095,0.89704,-0.097985,5.3165,-0.6493,-0.23285,0.72401,-12.02,0.62665,0.37564,0.6828,-70.283
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.43095,0.89704,-0.097985,5.6796,-0.6493,-0.23285,0.72401,-12.965,0.62665,0.37564,0.6828,-71.117
+> view matrix models
+> #2,-0.43095,0.89704,-0.097985,5.4149,-0.6493,-0.23285,0.72401,-12.877,0.62665,0.37564,0.6828,-70.315
+> view matrix models
+> #2,-0.43095,0.89704,-0.097985,5.4984,-0.6493,-0.23285,0.72401,-12.89,0.62665,0.37564,0.6828,-70.577
+> view matrix models
+> #2,-0.43095,0.89704,-0.097985,5.4888,-0.6493,-0.23285,0.72401,-12.815,0.62665,0.37564,0.6828,-70.588
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.42984,0.89753,-0.098356,5.4545,-0.65201,-0.23319,0.72146,-12.543,0.6246,0.37424,0.68544,-70.632
+> view matrix models
+> #2,0.72897,0.67465,0.11595,-50.959,-0.28779,0.14835,0.94613,-48.843,0.62111,-0.72307,0.3023,-25.316
+> view matrix models
+> #2,-0.36726,0.88871,-0.27443,13.524,-0.68642,-0.059863,0.72474,-14.837,0.62766,0.45454,0.63201,-69.211
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.36726,0.88871,-0.27443,13.257,-0.68642,-0.059863,0.72474,-14.235,0.62766,0.45454,0.63201,-68.693
+> select clear
+> ui mousemode right "rotate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.35924,0.89032,-0.27979,13.21,-0.7067,-0.063715,0.70464,-12.115,0.60952,0.45086,0.65208,-69.06
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.35924,0.89032,-0.27979,13.406,-0.7067,-0.063715,0.70464,-11.986,0.60952,0.45086,0.65208,-69.65
+> select subtract #2
+Nothing selected
+> ui mousemode right "rotate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,-0.38281,0.70266,-0.59978,37.274,-0.84038,-0.5345,-0.089808,50.497,-0.38369,0.46966,0.79511,-37.26
+> view matrix models
+> #2,-0.26922,0.56303,-0.78135,46.214,-0.82765,0.27958,0.48664,-0.95674,0.49245,0.77771,0.39073,-55.863
+> view matrix models
+> #2,-0.41461,-0.73281,-0.53952,64.232,-0.65936,-0.16669,0.73311,-13.555,-0.62717,0.65969,-0.41408,41.049
+> view matrix models
+> #2,0.57268,-0.81626,0.07588,-11.79,-0.3511,-0.16058,0.92246,-37.78,-0.74079,-0.55492,-0.37855,68.386
+> view matrix models
+> #2,0.5712,-0.81739,0.0749,-11.647,-0.35131,-0.16099,0.92231,-37.754,-0.74183,-0.55314,-0.37911,68.426
+> view matrix models
+> #2,0.26197,-0.9629,-0.064823,12.498,-0.1515,-0.10737,0.98261,-50.746,-0.95311,-0.2476,-0.17401,58.768
+> view matrix models
+> #2,0.28078,-0.95711,-0.071408,11.991,-0.22437,-0.1378,0.96471,-46.03,-0.93318,-0.25485,-0.25344,62.82
+> view matrix models
+> #2,0.28266,-0.95661,-0.070694,11.86,-0.22403,-0.1375,0.96483,-46.058,-0.93269,-0.25688,-0.25317,62.826
+> select clear
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,0.27601,-0.95878,-0.067489,11.99,-0.18811,-0.12274,0.97445,-48.425,-0.94257,-0.25626,-0.21423,60.903
+> select clear
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.27601,-0.95878,-0.067489,12.105,-0.18811,-0.12274,0.97445,-49.331,-0.94257,-0.25626,-0.21423,60.712
+> select subtract #2
+Nothing selected
+> volume #1 level 0.1354
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,0.27601,-0.95878,-0.067489,11.743,-0.18811,-0.12274,0.97445,-45.93,-0.94257,-0.25626,-0.21423,61.16
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.26169,-0.96512,-0.0071889,8.8737,-0.27926,-0.082848,0.95663,-41.891,-0.92387,-0.24834,-0.2912,64.807
+> view matrix models
+> #2,-0.035977,-0.9571,-0.28751,37.791,-0.050686,-0.28557,0.95702,-47.29,-0.99807,0.049004,-0.038238,46.765
+> view matrix models
+> #2,0.35137,-0.93581,0.028388,2.4282,-0.25569,-0.066748,0.96445,-43.665,-0.90064,-0.34614,-0.26273,64.136
+> view matrix models
+> #2,0.39555,-0.91755,-0.040398,4.3186,-0.20352,-0.13046,0.97034,-44.888,-0.89561,-0.3756,-0.23834,63.074
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.39555,-0.91755,-0.040398,5.0464,-0.20352,-0.13046,0.97034,-47.195,-0.89561,-0.3756,-0.23834,63.401
+> view matrix models
+> #2,0.39555,-0.91755,-0.040398,4.9786,-0.20352,-0.13046,0.97034,-47.153,-0.89561,-0.3756,-0.23834,63.196
+> select clear
+> volume #1 level 0.145
+> volume #1 level 0.155
+> graphics silhouettes true
+> graphics silhouettes width 0.5
+> graphics silhouettes width 0.6
+> graphics silhouettes width 0.7
+> graphics silhouettes width 0.8
+> select clear
+> lighting flat
+> lighting soft
+> lighting simple
+> lighting full
+> lighting flat
+> lighting shadows true intensity 0.5
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting soft
+> ui mousemode right "rotate selected models"
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,0.40195,-0.91481,-0.039464,4.601,-0.25621,-0.15374,0.95432,-43.534,-0.87909,-0.37348,-0.29618,65.912
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.40195,-0.91481,-0.039464,4.4932,-0.25621,-0.15374,0.95432,-42.647,-0.87909,-0.37348,-0.29618,65.627
+> view matrix models
+> #2,0.40195,-0.91481,-0.039464,4.451,-0.25621,-0.15374,0.95432,-42.319,-0.87909,-0.37348,-0.29618,65.366
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.57486,-0.81089,0.10955,-13.734,-0.28538,-0.073207,0.95562,-42.824,-0.76688,-0.58061,-0.27349,63.566
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.57486,-0.81089,0.10955,-13.705,-0.28538,-0.073207,0.95562,-42.949,-0.76688,-0.58061,-0.27349,64.475
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.57073,-0.81388,0.10894,-13.436,-0.25194,-0.047294,0.96659,-45.521,-0.78153,-0.57911,-0.23204,62.584
+> view matrix models
+> #2,0.57664,-0.80321,0.14948,-16.314,-0.27198,-0.016199,0.96217,-45.057,-0.7704,-0.59548,-0.2278,62.202
+> view matrix models
+> #2,0.58355,-0.80984,0.060278,-11.151,-0.22137,-0.087221,0.97128,-46.259,-0.78132,-0.58013,-0.23017,62.485
+> view matrix models
+> #2,0.58355,-0.80986,0.06001,-11.135,-0.22078,-0.087106,0.97143,-46.294,-0.78149,-0.58012,-0.22963,62.46
+> view matrix models
+> #2,0.47365,-0.87566,0.094267,-7.2668,-0.26187,-0.03783,0.96436,-45.168,-0.84088,-0.48145,-0.24723,63.968
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.47365,-0.87566,0.094267,-7.0143,-0.26187,-0.03783,0.96436,-45.913,-0.84088,-0.48145,-0.24723,63.068
+> select clear
+> volume #1 level 0.165
+> volume #1 level 0.175
+> volume #1 level 0.185
+> volume #1 level 0.195
+> color #2 #f6f6f6ff
+> color #2 #942193ff
+> color #2 #941751ff
+> select /A
+atoms, 902 bonds, 68 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel slate gray
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel light gray target c
+> color sel silver target c
+> select clear
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel gray target c
+> color sel light gray target c
+> color sel silver target c
+> color sel gainsboro target c
+> color sel silver target c
+> select clear
+> color #1 black models
+> color #1 #212121ff models
+> color #1 #424242ff models
+> color #1 #5e5e5eff models
+> color #1 #797979ff models
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> view matrix models
+> #2,0.47365,-0.87566,0.094267,-6.1759,-0.26187,-0.03783,0.96436,-45.88,-0.84088,-0.48145,-0.24723,62.917
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.50678,-0.86127,0.037171,-4.4442,-0.18467,-0.066345,0.98056,-49.475,-0.84206,-0.5038,-0.19268,60.17
+> select clear
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel black target c
+> color sel light slate gray target c
+> color sel slate gray target c
+> color sel gray target c
+> color sel gainsboro target c
+> color sel light gray target c
+> select clear
+> lighting soft
+> lighting flat
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel gray target c
+> color sel silver target c
+> color sel light gray target c
+> color sel silver target c
+> select clear
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel dark gray target c
+> select clear
+> volume #1 level 0.205
+> save /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/BIO-SAXS_data/1E4_DENSS_model.cxs
+> save /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-SAXS-
+> model.png width 867 height 739 supersample 4 transparentBackground true
+> hide #!1 models
+> select clear
+> show atoms
+> ui tool show Contacts
+> contacts saveFile /Users/u6290062/Downloads/1E4-contacts ignoreHiddenModels
+> true select true reveal true
+contacts
+> close #1
+> close #3
+> close #2.1
+> select clear
+> ui tool show Contacts
+> select /A
+atoms, 902 bonds, 68 residues, 1 model selected
+> select add #2
+atoms, 1798 bonds, 189 residues, 1 model selected
+> contacts sel restrict both intraModel false intraMol false
+> ignoreHiddenModels true select true reveal true log true
+    Allowed overlap: -0.4
+    H-bond overlap reduction: 0.4
+    Ignore contacts between atoms separated by 4 bonds or less
+    Detect intra-residue contacts: False
+    Detect intra-molecule contacts: False
+contacts
+    atom1  atom2  overlap  distance
+No contacts
+> select clear
+> hide atoms
+> select /A-B:40
+atoms, 34 bonds, 2 residues, 1 model selected
+> select /A-B:40
+atoms, 34 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:40
+atoms, 34 bonds, 2 residues, 1 model selected
+> select /A-B:40-41
+atoms, 62 bonds, 4 residues, 1 model selected
+> select /A-B:40-41
+atoms, 62 bonds, 4 residues, 1 model selected
+> select /A-B:40-41
+atoms, 62 bonds, 4 residues, 1 model selected
+> select clear
+> select /A-B:40-41
+atoms, 62 bonds, 4 residues, 1 model selected
+> select /A-B:40-41
+atoms, 62 bonds, 4 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:46-47
+atoms, 74 bonds, 4 residues, 1 model selected
+> select /A-B:46-50
+atoms, 172 bonds, 10 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:60-61
+atoms, 64 bonds, 4 residues, 1 model selected
+> select /A-B:60-62
+atoms, 102 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A
+atoms, 902 bonds, 68 residues, 1 model selected
+> select /B
+atoms, 896 bonds, 66 residues, 1 model selected
+> color sel silver target c
+> color sel light gray target c
+> color sel silver target ac
+> color sel dim gray target ac
+> color sel gray target ac
+> color sel dark gray target ac
+> select clear
+> color byhetero
+> select clear
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting soft
+> lighting shadows true intensity 0.5
+> lighting soft
+> graphics silhouettes width 1
+> select clear
+> select ::name="HOH"
+atoms, 55 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:60
+atoms, 32 bonds, 2 residues, 1 model selected
+> select /A-B:60-62
+atoms, 102 bonds, 6 residues, 1 model selected
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select clear
+> show surfaces
+> select clear
+> hide surfaces
+> select clear
+> hide atoms
+> select clear
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select /A-B:50
+atoms, 40 bonds, 2 residues, 1 model selected
+> select /A-B:50
+atoms, 40 bonds, 2 residues, 1 model selected
+> select /A-B:50,61-62
+atoms, 108 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select clear
+> show cartoons
+> select clear
+> hide atoms
+> select add /B:21
+atoms, 10 bonds, 1 residue, 1 model selected
+> setattr #2:19-21 res ss_type )
+Assigning ss_type attribute to 8 items
+Cannot set attribute 'ss_type' to ')'
+> setattr #2:19-21 res ss_type 0
+Assigning ss_type attribute to 8 items
+> select clear
+> show surfaces
+> select clear
+> transparency 50
+> select clear
+> transparency 70
+> select clear
+> save
+> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
+> crescent.png width 791 height 739 supersample 4 transparentBackground true
+> select clear
+> transparency 0
+> select clear
+> transparency 70
+> select clear
+> save
+> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
+> core.png width 791 height 739 supersample 4 transparentBackground true
+> select clear
+> transparency 0
+> transparency 50
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select clear
+> transparency 70
+> select clear
+> save
+> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
+> hydrophobic.png width 791 height 739 supersample 4 transparentBackground
+> true
+> select clear
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:35,41
+atoms, 58 bonds, 4 residues, 1 model selected
+> select /A-B:35,41
+atoms, 58 bonds, 4 residues, 1 model selected
+> select clear
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> ui tool show Distances
+> select /B:41@CG2
+atom, 1 residue, 1 model selected
+> select clear
+> hide surfaces
+> select /B:41@OG1
+atom, 1 residue, 1 model selected
+> select add /B:47@NE2
+atoms, 2 residues, 2 models selected
+> distance /B:41@OG1 /B:47@NE2
+Distance between /B THR 41 OG1 and GLN 47 NE2: 4.764Å
+> select clear
+> hide #1.1 models
+> select clear
+> select /B:47@OE1
+atom, 1 residue, 1 model selected
+> select add /B:41@HG1
+atoms, 2 residues, 2 models selected
+> distance /B:47@OE1 /B:41@HG1
+Distance between /B GLN 47 OE1 and THR 41 HG1: 5.427Å
+> select clear
+> select /A:41@OG1
+atom, 1 residue, 1 model selected
+Drag select of 1 atoms
+> select /A:41@OG1
+atom, 1 residue, 1 model selected
+> select add /A:47@NE2
+atoms, 2 residues, 2 models selected
+> distance /A:41@OG1 /A:47@NE2
+Distance between /A THR 41 OG1 and GLN 47 NE2: 4.772Å
+> select clear
+> hide #!1 models
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> select /A-B:28-33,36-41,56-60,64-68
+atoms, 608 bonds, 44 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> hbonds sel reveal true
+hydrogen bonds found
+> select add /A:48
+atoms, 46 bonds, 3 residues, 3 models selected
+> show sel atoms
+> select clear
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> select /A-B:47
+atoms, 32 bonds, 2 residues, 1 model selected
+> hbonds sel reveal true
+hydrogen bonds found
+> select /A:27
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> select /A-B:41
+atoms, 26 bonds, 2 residues, 1 model selected
+> hbonds sel reveal true
+hydrogen bonds found
+> select clear
+> select /A:48
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> hide atoms
+> show atoms
+> select clear
+> hide atoms
+> select clear
+> ~hbonds
+> select clear
+> select /A-B:46-47
+atoms, 74 bonds, 4 residues, 1 model selected
+> select /A-B:46-48
+atoms, 116 bonds, 6 residues, 1 model selected
+> select /A-B:44-45
+atoms, 48 bonds, 4 residues, 1 model selected
+> select /A-B:44-48
+atoms, 166 bonds, 10 residues, 1 model selected
+> show sel cartoons
+> select clear
+> show surfaces
+> select clear
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> select /A-B:61-62
+atoms, 68 bonds, 4 residues, 1 model selected
+> show sel atoms
+> select clear
+> select /A-B:50
+atoms, 40 bonds, 2 residues, 1 model selected
+> select /A-B:50
+atoms, 40 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> transparency #2 70
+> transparency #2 90
+> transparency #2 80
+> select clear
+> save
+> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/1E4-dimer-
+> hydrophobic.png width 791 height 739 supersample 4 transparentBackground
+> true
+> save
+> /Users/u6290062/Documents/PhD/Manuscripts/01_Stb6-AvrStb6/Data/Fig_4_poses.cxs
+> includeMaps true
+> close #2
+> close
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6.pdb
+Chain information for stb6.pdb #1
+---
+Chain | Description
+A | No description available
+> select ::name="MAN"
+atoms, 11 bonds, 1 residue, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select ::name="NAG"
+atoms, 57 bonds, 4 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select clear
+> save /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb displayedOnly
+> true relModel #1
+> save /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb displayedOnly
+> true
+> close
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/BIO-
+> SAXS_data/AvrStb6_dimer_refine_027.pdb format pdb
+Chain information for AvrStb6_dimer_refine_027.pdb #1
+---
+Chain | Description
+A B | No description available
+Computing secondary structure
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/BIO-
+> SAXS_data/AvrStb6_monomer_refine_029.pdb
+Chain information for AvrStb6_monomer_refine_029.pdb #2
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> select clear
+> lighting soft
+> 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 AvrStb6_dimer_refine_027.pdb, chain A (#1) with
+AvrStb6_monomer_refine_029.pdb, chain A (#2), sequence alignment score = 363.9
+RMSD between 57 pruned atom pairs is 0.767 angstroms; (across all 64 pairs:
+.655)
+> select clear
+> hide atoms
+> select clear
+> select #1/B
+atoms, 896 bonds, 66 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #1/A:19
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #2/A:14
+atoms, 12 bonds, 2 residues, 2 models selected
+Alignment identifier is 1/A
+Alignment identifier is 2/A
+> select clear
+> select #1/A:19
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #1/A:21
+atoms, 16 bonds, 2 residues, 1 model selected
+> select clear
+> setattr #2:19-21 res ss_type 0
+Assigning ss_type attribute to 3 items
+> setattr #2:19-21 res ss_type 0
+Assigning ss_type attribute to 3 items
+> setattr #1:19-21 res ss_type 0
+Assigning ss_type attribute to 8 items
+> setattr #2:14-16 res ss_type 0
+Assigning ss_type attribute to 4 items
+> select clear
+> select #1/A:32
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #1/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #1/A:36
+atoms, 32 bonds, 2 residues, 1 model selected
+> select clear
+> select #1/A:37
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #1/A:36
+atoms, 35 bonds, 2 residues, 1 model selected
+> select add #1/A:35
+atoms, 51 bonds, 3 residues, 1 model selected
+> select add #1/A:34
+atoms, 57 bonds, 4 residues, 1 model selected
+> select add #1/A:33
+atoms, 68 bonds, 5 residues, 1 model selected
+> select add #1/A:32
+atoms, 84 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select clear
+> select add #2/A:32
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #2/A:31
+atoms, 35 bonds, 2 residues, 1 model selected
+> select add #2/A:30
+atoms, 51 bonds, 3 residues, 1 model selected
+> select add #2/A:29
+atoms, 57 bonds, 4 residues, 1 model selected
+> select add #2/A:28
+atoms, 68 bonds, 5 residues, 1 model selected
+> select add #2/A:27
+atoms, 84 bonds, 6 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #2/A:32
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/A:32
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/A:32-36
+atoms, 80 bonds, 5 residues, 1 model selected
+> select #2/A:28-29
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #2/A:28-32
+atoms, 72 bonds, 5 residues, 1 model selected
+> select #2/A:23-27,32-36,51-55,59-63
+atoms, 270 bonds, 20 residues, 1 model selected
+> select #2/A:28-29
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #2/A:28-33
+atoms, 96 bonds, 6 residues, 1 model selected
+> select clear
+> select #1/A:26
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #1/A:26-29
+atoms, 47 bonds, 4 residues, 1 model selected
+> select add #2/A:32
+atoms, 61 bonds, 5 residues, 2 models selected
+> select clear
+> select #1/A:20-21
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #1/A:20-26
+atoms, 93 bonds, 7 residues, 1 model selected
+> select clear
+> select #1/A:26-27
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #1/A:26-29
+atoms, 47 bonds, 4 residues, 1 model selected
+> select clear
+> select #1/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1/A:26
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #1/A:26-33
+atoms, 107 bonds, 8 residues, 1 model selected
+> select clear
+> select #1/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1/A:33-37
+atoms, 72 bonds, 5 residues, 1 model selected
+> select clear
+> select #1/A:38-39
+atoms, 33 bonds, 2 residues, 1 model selected
+> select #1/A:38-39
+atoms, 33 bonds, 2 residues, 1 model selected
+> select clear
+> select #1/A:28
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #1/A:28
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> select #1/A:32
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #1/A:32
+atoms, 16 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #2/A:27
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/A:27
+atoms, 16 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #1/A:32-33
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #1/A:32-37
+atoms, 89 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #2/A:27-28
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #2/A:27-32
+atoms, 89 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #1/A:37
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #1/A:37
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/A:33
+atoms, 23 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select add #1/A:38
+atoms, 46 bonds, 2 residues, 2 models selected
+> show sel atoms
+> hide sel cartoons
+> select clear
+> show cartoons
+> hide atoms
+> select clear
+> select #1/B
+atoms, 896 bonds, 66 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select ::name="CYS"
+atoms, 339 bonds, 36 residues, 2 models selected
+> show sel atoms
+> select clear
+> select #1/B
+atoms, 896 bonds, 66 residues, 1 model selected
+> hide sel cartoons
+> hide sel atoms
+> select clear
+> select add #1/A:38
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #1/A:37
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #1/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1/A:33-42
+atoms, 148 bonds, 10 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #2/A:28
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/A:28-37
+atoms, 148 bonds, 10 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #1/A:31
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #1/A:31-32
+atoms, 37 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #2/A:26-27
+atoms, 37 bonds, 2 residues, 1 model selected
+> select #2/A:26-27
+atoms, 37 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> hide atoms
+> close #1
+> close
+> open
+> /Users/u6290062/Downloads/ZmWAKLYecto_58d61_0/ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> lighting soft
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6.pdb
+Chain information for stb6.pdb #2
+---
+Chain | Description
+A | No description available
+> close #2
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb
+Summary of feedback from opening
+/Users/u6290062/Library/CloudStorage/OneDrive-
+AustralianNationalUniversity/Documents/Figures/stb6-NG.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 80 LEU A 85 1 6
+End residue of secondary structure not found: HELIX 2 2 GLU A 126 LEU A 134 1
+Start residue of secondary structure not found: SHEET 1 1 1 PHE A 22 LEU A 24
+Start residue of secondary structure not found: SHEET 2 2 1 PHE A 41 LEU A 43
+Start residue of secondary structure not found: SHEET 3 3 1 THR A 44 TYR A 46
+Start residue of secondary structure not found: SHEET 4 4 1 TYR A 50 LEU A 53
+Start residue of secondary structure not found: SHEET 5 5 1 PHE A 63 SER A 69
+messages similar to the above omitted
+Cannot find LINK/SSBOND residue CYS (9 )
+Cannot find LINK/SSBOND residue CYS (13 )
+Cannot find LINK/SSBOND residue CYS (96 )
+Cannot find LINK/SSBOND residue CYS (124 )
+Chain information for stb6-NG.pdb #2
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> close #2
+> open /Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/stb6.pdb
+Chain information for stb6.pdb #2
+---
+Chain | Description
+A | No description available
+> select clear
+> hide cartoons
+> show cartoons
+> hide atoms
+> select clear
+> 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
+ZmWAKLYecto_58d61_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#1) with stb6.pdb, chain A (#2), sequence alignment score = 193.8
+RMSD between 50 pruned atom pairs is 1.179 angstroms; (across all 172 pairs:
+.786)
+> select add #1/A:35
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #1/A:36
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #1/A:37
+atoms, 25 bonds, 3 residues, 1 model selected
+> setattr #1:35-36 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select clear
+Alignment identifier is 1/A
+Alignment identifier is 2/A
+> select #2/A:43
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/A:42
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #2/A:41
+atoms, 26 bonds, 3 residues, 1 model selected
+> select clear
+> select #1/A:37-38
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #1/A:37-39
+atoms, 29 bonds, 3 residues, 1 model selected
+> setattr #1:37-39 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select #1/A:36
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #1/A:36
+atoms, 5 bonds, 1 residue, 1 model selected
+> setattr #1:36-39 res ss_type 2
+Assigning ss_type attribute to 4 items
+> select clear
+> setattr #1:36-39 res ss_type 2
+Assigning ss_type attribute to 4 items
+> setattr #1:35-39 res ss_type 2
+Assigning ss_type attribute to 5 items
+> select add #1/A:23
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #1/A:26
+atoms, 19 bonds, 2 residues, 1 model selected
+> select clear
+> setattr #1:23-26 res ss_type 2
+Assigning ss_type attribute to 4 items
+> select #1/A:3
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:1-3
+atoms, 32 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select ::name="CYS"
+atoms, 84 bonds, 16 residues, 2 models selected
+> show sel atoms
+> select clear
+> bond sel
+Must specify two or more atoms
+> select clear
+> select add #1/A:7@SG
+atom, 1 residue, 1 model selected
+> select add #1/A:32@SG
+atoms, 1 bond, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #1/A:13@SG
+atom, 1 residue, 1 model selected
+> select add #1/A:41@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #1/A:120@SG
+atom, 1 residue, 1 model selected
+> select add #1/A:162@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #1/A:80@SG
+atoms, 3 residues, 1 model selected
+> select add #1/A:135@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> hide #2 models
+> select #1/A:206
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #1/A:205
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #1/A:204
+atoms, 20 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #1/A:203
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #1/A:172
+atoms, 6 bonds, 2 residues, 1 model selected
+> select #1/A:172
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #1/A:172-202
+atoms, 242 bonds, 31 residues, 1 model selected
+> select #1/A:205
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:205-206
+atoms, 14 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select
+> #1/A:23-26,35-41,46-50,53-61,66-71,113-120,130-132,141-148,162-170,194-197
+atoms, 543 bonds, 63 residues, 1 model selected
+> select #1/A:205
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:205-206
+atoms, 14 bonds, 2 residues, 1 model selected
+> select clear
+> select add #1/A:203
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #1/A:202
+atoms, 10 bonds, 2 residues, 1 model selected
+> select #1/A:185-186
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #1/A:185-206
+atoms, 171 bonds, 22 residues, 1 model selected
+> select add #1/A:171
+atoms, 174 bonds, 23 residues, 1 model selected
+> select subtract #1/A:171
+atoms, 171 bonds, 22 residues, 1 model selected
+> select add #1/A:172
+atoms, 174 bonds, 23 residues, 1 model selected
+> select #1/A:173-174
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #1/A:173-186
+atoms, 108 bonds, 14 residues, 1 model selected
+> select #1/A:172-173
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #1/A:172-206
+atoms, 269 bonds, 35 residues, 1 model selected
+> color sel forest green target c
+> select clear
+> select #1/A:154
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #1/A:155
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #1/A:156
+atoms, 19 bonds, 3 residues, 1 model selected
+> setattr #1:154-156 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #1/A:71
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/A:1-2
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #1/A:1-71
+atoms, 581 bonds, 71 residues, 1 model selected
+> color sel dark sea green target ac
+> color sel light green target ac
+> color sel dark sea green target ac
+> select clear
+> select add #1/A:113
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #1/A:110
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #1/A:112
+atoms, 19 bonds, 3 residues, 1 model selected
+> select add #1/A:111
+atoms, 26 bonds, 4 residues, 1 model selected
+> select subtract #1/A:113
+atoms, 19 bonds, 3 residues, 1 model selected
+> select #1/A:72-73
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #1/A:73-112
+atoms, 357 bonds, 40 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #1/A:72
+atoms, 4 bonds, 1 residue, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #1/A:171
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #1/A:113
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/A:113-171
+atoms, 479 bonds, 59 residues, 1 model selected
+> color sel burly wood target ac
+> color sel wheat target ac
+> color sel goldenrod target ac
+> color sel dark khaki target ac
+> select clear
+> select add #1/A:122
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #1/A:123
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #1/A:124
+atoms, 22 bonds, 3 residues, 1 model selected
+> select add #1/A:125
+atoms, 30 bonds, 4 residues, 1 model selected
+> select add #1/A:126
+atoms, 37 bonds, 5 residues, 1 model selected
+> select add #1/A:127
+atoms, 44 bonds, 6 residues, 1 model selected
+> select add #1/A:121
+atoms, 49 bonds, 7 residues, 1 model selected
+> setattr #1:121-127 res ss_type 1
+Assigning ss_type attribute to 7 items
+> select clear
+> setattr #1:121-127 res ss_type 0
+Assigning ss_type attribute to 7 items
+> select ::name="CYS"
+atoms, 88 bonds, 16 residues, 2 models selected
+> color (#1 & sel) byhetero
+> select clear
+> select #1/A:4-5
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #1/A:4-5
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #1/A:5
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:5-6
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #1/A:4
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:4-6
+atoms, 28 bonds, 3 residues, 1 model selected
+> select #1/A:5
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/A:4-5
+atoms, 21 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> lighting soft
+> select ::name="ASN"
+atoms, 149 bonds, 21 residues, 2 models selected
+> select clear
+> select add #1/A:138
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #1/A:119
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #1/A:95
+atoms, 21 bonds, 3 residues, 1 model selected
+> show sel atoms
+> color sel byhetero
+> select clear
+> select #1/A:72
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #1/A:111
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #1/A:112
+atoms, 16 bonds, 3 residues, 1 model selected
+> select #1/A:72-73
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #1/A:73-113
+atoms, 365 bonds, 41 residues, 1 model selected
+> select #1/A:112
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #1/A:111-112
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #1/A:72
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #1/A:72-112
+atoms, 362 bonds, 41 residues, 1 model selected
+> color sel honeydew target ac
+> color sel white smoke target ac
+> select clear
+> select #1/A:72
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #1/A:72-112
+atoms, 362 bonds, 41 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select ::name="ASN"
+atoms, 149 bonds, 21 residues, 2 models selected
+> color (#1 & sel) byhetero
+> select clear
+> select add #1/A:80
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel byhetero
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAKL-Y.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> hide #1 models
+> open
+> /Users/u6290062/Downloads/ZmWAK_b7dcf/ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+Chain information for
+ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> select clear
+> ui tool show Matchmaker
+> matchmaker #2 to #3
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker ZmWAK_b7dcf_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#3) with stb6.pdb, chain A (#2), sequence alignment score = 106.7
+RMSD between 44 pruned atom pairs is 1.034 angstroms; (across all 159 pairs:
+.006)
+> show #2 models
+Alignment identifier is 1/A
+Destroying pre-existing alignment with identifier 2/A
+Alignment identifier is 2/A
+Alignment identifier is 3/A
+> select #2/A:41
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #2/A:41-46
+atoms, 54 bonds, 6 residues, 1 model selected
+> select clear
+Drag select of 3 residues
+> select clear
+> select add #3/A:19
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #3/A:21
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #3/A:19
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #3/A:19-21
+atoms, 22 bonds, 3 residues, 1 model selected
+> setattr #3:19-21 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:29
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #2/A:41
+atoms, 14 bonds, 2 residues, 2 models selected
+> select subtract #2/A:41
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #3/A:30
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #3/A:31
+atoms, 24 bonds, 3 residues, 1 model selected
+> select add #3/A:28
+atoms, 32 bonds, 4 residues, 1 model selected
+> setattr #3:28-31 res ss_type 2
+Assigning ss_type attribute to 4 items
+> setattr #3:28-30 res ss_type 2
+Assigning ss_type attribute to 3 items
+> setattr #3:28-30 res ss_type 0
+Assigning ss_type attribute to 3 items
+> setattr #3:28-30 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #2 models
+> select clear
+> select ::name="CYS"
+atoms, 209 bonds, 40 residues, 3 models selected
+> color (#3 & sel) byhetero
+> show sel & #3 atoms
+> select clear
+> select add #3/A:5
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #3/A:1-4
+atoms, 25 bonds, 4 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #3/A:6@SG
+atom, 1 residue, 1 model selected
+> select add #3/A:25@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #3/A:10@SG
+atom, 1 residue, 1 model selected
+> select add #3/A:34@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:324@SG
+atoms, 3 residues, 1 model selected
+> select add #3/A:333@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:322@SG
+atoms, 5 residues, 1 model selected
+> select add #3/A:307@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:313@SG
+atoms, 7 residues, 1 model selected
+> select add #3/A:299@SG
+atoms, 8 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:293@SG
+atoms, 9 residues, 1 model selected
+> select add #3/A:277@SG
+atoms, 10 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:257@SG
+atoms, 11 residues, 1 model selected
+> select add #3/A:275@SG
+atoms, 12 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:264@SG
+atoms, 13 residues, 1 model selected
+> select add #3/A:246@SG
+atoms, 14 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:189@SG
+atoms, 15 residues, 1 model selected
+> select add #3/A:115@SG
+atoms, 16 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:156@SG
+atoms, 17 residues, 1 model selected
+> select add #3/A:161@SG
+atoms, 18 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #3/A:162@SG
+atoms, 19 residues, 1 model selected
+> select add #3/A:141@SG
+atoms, 20 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #3/A:78@SG
+atom, 1 residue, 1 model selected
+> select add #3/A:191@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #3/A:251
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:250
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #3/A:249
+atoms, 18 bonds, 3 residues, 1 model selected
+> setattr #3/A:249-251 res ss_type 2
+Assigning ss_type attribute to 3 items
+> setattr #3/A:249-251 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:300
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #3/A:299
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #3/A:298
+atoms, 21 bonds, 3 residues, 1 model selected
+> setattr #3/A:298-300 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:209
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:208
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #3/A:207
+atoms, 19 bonds, 3 residues, 1 model selected
+> select add #3/A:206
+atoms, 23 bonds, 4 residues, 1 model selected
+> setattr #3/A:206-209 res ss_type 0
+Assigning ss_type attribute to 4 items
+> select clear
+> select add #3/A:302
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:303
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #3/A:304
+atoms, 20 bonds, 3 residues, 1 model selected
+> setattr #3/A:302-304 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:219
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:220
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #3/A:221
+atoms, 21 bonds, 3 residues, 1 model selected
+> setattr #3/A:219-221 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:214
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:204
+atoms, 18 bonds, 2 residues, 1 model selected
+> setattr #3/A:204-214 res ss_type 1
+Assigning ss_type attribute to 11 items
+> select clear
+> select add #3/A:204
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #3/A:205
+atoms, 19 bonds, 2 residues, 1 model selected
+> setattr #3/A:sel res ss_type 1
+Assigning ss_type attribute to 0 items
+> select clear
+> select add #3/A:204
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #3/A:205
+atoms, 19 bonds, 2 residues, 1 model selected
+> setattr #3/A:204-205 res ss_type 1
+Assigning ss_type attribute to 2 items
+> setattr #3/A:204-205 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select clear
+> select add #3/A:214
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:213
+atoms, 13 bonds, 2 residues, 1 model selected
+> setattr #3/A:213-214 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select clear
+> select add #3/A:236
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:237
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #3/A:238
+atoms, 17 bonds, 3 residues, 1 model selected
+> select clear
+> select add #3/A:199
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #3/A:200
+atoms, 11 bonds, 2 residues, 1 model selected
+> select subtract #3/A:199
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add #3/A:232
+atoms, 7 bonds, 2 residues, 1 model selected
+> select #3/A:200
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #3/A:200-233
+atoms, 296 bonds, 34 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select #3/A:234
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:234-339
+atoms, 825 bonds, 106 residues, 1 model selected
+> color sel pink target ac
+> color sel dark turquoise target ac
+> color sel light sea green target ac
+> color sel teal target ac
+> color sel yellow green target ac
+> color sel sandy brown target ac
+> color sel royal blue target ac
+> select clear
+> select #3/A:73
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:74
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:75
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #3/A:74
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:73
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #3/A:1-73
+atoms, 556 bonds, 73 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select add #3/A:199
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #3/A:74
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #3/A:74-75
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #3/A:74-199
+atoms, 1000 bonds, 126 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select add #3/A:234
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:234
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #3/A:234-339
+atoms, 825 bonds, 106 residues, 1 model selected
+> color sel dim gray target ac
+> color sel lavender target ac
+> color sel pale goldenrod target ac
+> color sel khaki target ac
+> color sel wheat target ac
+> color sel light steel blue target ac
+> color sel powder blue target ac
+> color sel light blue target ac
+> color sel light steel blue target ac
+> select clear
+> select ::name="CYS"
+atoms, 221 bonds, 40 residues, 3 models selected
+> color (#3 & sel) byhetero
+> select clear
+> select add #3/A:334
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:334
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #3/A:334-339
+atoms, 47 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #3/A:74
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #3/A:108
+atoms, 13 bonds, 2 residues, 1 model selected
+> select subtract #3/A:108
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #3/A:107
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #3/A:74
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #3/A:74-107
+atoms, 262 bonds, 34 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select ::name="CYS"
+atoms, 221 bonds, 40 residues, 3 models selected
+> color (#3 & sel) byhetero
+> select clear
+> select add #3/A:208
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #3/A:207
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #3/A:209
+atoms, 19 bonds, 3 residues, 1 model selected
+> setattr #3/A:207-209 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #3/A:212
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #3/A:211
+atoms, 15 bonds, 2 residues, 1 model selected
+> select add #3/A:213
+atoms, 21 bonds, 3 residues, 1 model selected
+> select add #3/A:210
+atoms, 27 bonds, 4 residues, 1 model selected
+> setattr #3/A:210-213 res ss_type 0
+Assigning ss_type attribute to 4 items
+> select clear
+> select ::name="ASN"
+atoms, 311 bonds, 44 residues, 3 models selected
+> select clear
+> show #1 models
+> hide #1 models
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAK.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> hide #3 models
+> open
+> /Users/u6290062/Downloads/Xa4_7f217/Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #4
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+Alignment identifier is 1/A
+Destroying pre-existing alignment with identifier 2/A
+Alignment identifier is 2/A
+Destroying pre-existing alignment with identifier 3/A
+Alignment identifier is 3/A
+Alignment identifier is 4/A
+> select #4/A:26
+atoms, 7 bonds, 1 residue, 1 model selected
+Drag select of 4 residues
+> select clear
+> select add #4/A:27
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #4/A:25
+atoms, 12 bonds, 2 residues, 1 model selected
+> setattr #3/A:25-27 res ss_type 0
+Assigning ss_type attribute to 3 items
+> setattr #4/A:25-27 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> show #2 models
+> ui tool show Matchmaker
+> matchmaker #2 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 Xa4_7f217_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#4) with stb6.pdb, chain A (#2), sequence alignment score = 103.2
+RMSD between 47 pruned atom pairs is 0.921 angstroms; (across all 161 pairs:
+.144)
+> select add #4/A:34
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #4/A:37
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #4/A:35
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #4/A:35-37
+atoms, 26 bonds, 3 residues, 1 model selected
+> setattr #4/A:35-37 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #4/A:22
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #4/A:24
+atoms, 17 bonds, 2 residues, 1 model selected
+> select add #4/A:25
+atoms, 24 bonds, 3 residues, 1 model selected
+> setattr #4/A:22-25 res ss_type 2
+Assigning ss_type attribute to 4 items
+> select clear
+> hide #2 models
+> select clear
+> select ::name="CYS"
+atoms, 342 bonds, 64 residues, 4 models selected
+> show sel & #4 atoms
+> select clear
+> select add #4/A:9@SG
+atom, 1 residue, 1 model selected
+> select add #4/A:27@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #4/A:13@SG
+atom, 1 residue, 1 model selected
+> select add #4/A:39@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select #4/A:180@SG
+atom, 1 residue, 1 model selected
+> select add #4/A:71@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #4/A:131@SG
+atom, 1 residue, 1 model selected
+> select add #4/A:109@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:150@SG
+atoms, 3 residues, 1 model selected
+> select add #4/A:127@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:144@SG
+atoms, 5 residues, 1 model selected
+> select add #4/A:149@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #4/A:245@SG
+atom, 1 residue, 1 model selected
+> select add #4/A:228@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:256@SG
+atoms, 3 residues, 1 model selected
+> select add #4/A:238@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:258@SG
+atoms, 5 residues, 1 model selected
+> select add #4/A:272@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:291@SG
+atoms, 7 residues, 1 model selected
+> select add #4/A:278@SG
+atoms, 8 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:300@SG
+atoms, 9 residues, 1 model selected
+> select add #4/A:285@SG
+atoms, 10 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #4/A:320@SG
+atoms, 11 residues, 1 model selected
+> select add #4/A:302@SG
+atoms, 12 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #4/A:8
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/A:6
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/A:1-6
+atoms, 44 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #4/A:325
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #4/A:322
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #4/A:321
+atoms, 22 bonds, 3 residues, 1 model selected
+> select #4/A:321-322
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/A:321-326
+atoms, 45 bonds, 6 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #4/A:135
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #4/A:136
+atoms, 10 bonds, 2 residues, 1 model selected
+> select add #4/A:134
+atoms, 17 bonds, 3 residues, 1 model selected
+> setattr #4:134-136 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #4/A:198
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #4/A:195
+atoms, 21 bonds, 2 residues, 1 model selected
+> setattr #4:195-198 res ss_type 0
+Assigning ss_type attribute to 4 items
+> select clear
+> select add #4/A:188
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #4/A:189
+atoms, 18 bonds, 2 residues, 1 model selected
+> select subtract #4/A:188
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #4/A:221
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #4/A:189
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/A:189-221
+atoms, 304 bonds, 33 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #4/A:222
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/A:222-224
+atoms, 27 bonds, 3 residues, 1 model selected
+> select #4/A:222-326
+atoms, 796 bonds, 105 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #4/A:67
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #4/A:101
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #4/A:67-68
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #4/A:67-101
+atoms, 281 bonds, 35 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #4/A:66
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #4/A:1-66
+atoms, 524 bonds, 66 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select add #4/A:102
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #4/A:188
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #4/A:102
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #4/A:102-188
+atoms, 644 bonds, 87 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select ::name="CYS"
+atoms, 354 bonds, 64 residues, 4 models selected
+> color (#4 & sel) byhetero
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Xa4.png" width
+> 900 height 739 supersample 4 transparentBackground true
+> hide #4 models
+> open
+> /Users/u6290062/Downloads/snn1_d97b8/snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #5
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> select clear
+> hide #5 models
+> show #4 models
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 1423 residues, atom bfactor range 32.5 to 191
+> select clear
+> hide #4 atoms
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Xa4-pLDDT.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> hide #4 models
+> show #3 models
+> hide #3 atoms
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAK-
+> pLDDT.png" width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> hide #3 models
+> show #1 models
+> select clear
+> hide #1 atoms
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/ZmWAKL-Y-
+> pLDDT.png" width 900 height 739 supersample 4 transparentBackground true
+> hide #1 models
+> show #5 models
+> color #5 #d4fb79ff
+> show #2 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 snn1_d97b8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#5) with stb6.pdb, chain A (#2), sequence alignment score = 78.7
+RMSD between 44 pruned atom pairs is 0.933 angstroms; (across all 166 pairs:
+.577)
+> color #5 #941751ff
+> color #5 #ff2f92ff
+> color #5 #ff8ad8ff
+> color #5 #ff85ffff
+> color #5 #73fcd6ff
+> color #5 #ff8ad8ff
+> select clear
+> color #2 #d6d6d6ff
+> select clear
+> select add #5/A:31
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 5/A
+> select #5/A:31
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #5/A:31-36
+atoms, 48 bonds, 6 residues, 1 model selected
+> setattr #5:31-36 res ss_type 2
+Assigning ss_type attribute to 6 items
+> select clear
+> setattr #5:30-36 res ss_type 2
+Assigning ss_type attribute to 7 items
+> setattr #5:29-36 res ss_type 2
+Assigning ss_type attribute to 8 items
+> setattr #5:29-36 res ss_type 0
+Assigning ss_type attribute to 8 items
+> setattr #5:30-36 res ss_type 2
+Assigning ss_type attribute to 7 items
+> select clear
+> select add #5/A:20
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #5/A:21
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/A:21-22
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #5/A:20
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #5/A:20-22
+atoms, 23 bonds, 3 residues, 1 model selected
+> setattr #5:20-22 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #2 models
+> select clear
+> select ::name="CYS"
+atoms, 465 bonds, 86 residues, 5 models selected
+> show sel & #5 atoms
+> color (#5 & sel) byhetero
+> select clear
+> select #5/A:7@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:26@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select #5/A:11@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:35@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #5/A:208@SG
+atoms, 3 residues, 1 model selected
+> select add #5/A:94@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #5/A:170@SG
+atoms, 5 residues, 1 model selected
+> select add #5/A:175@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #5/A:152@SG
+atoms, 7 residues, 1 model selected
+> select add #5/A:176@SG
+atoms, 8 residues, 1 model selected
+> select subtract #5/A:176@SG
+atoms, 7 residues, 1 model selected
+> select add #5/A:176@SG
+atoms, 8 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> bond sel
+Created 0 bonds
+> select clear
+> select add #5/A:152@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:176@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> select clear
+> select add #5/A:152@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:176@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> select clear
+> select add #5/A:210
+atoms, 12 bonds, 1 residue, 1 model selected
+> select clear
+> select add #5/A:176@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:152@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> select clear
+> select add #5/A:331@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:344@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #5/A:329@SG
+atoms, 3 residues, 1 model selected
+> select add #5/A:314@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #5/A:306@SG
+atoms, 5 residues, 1 model selected
+> select add #5/A:320@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #5/A:266@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:284@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #5/A:300@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:286@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #5/A:273@SG
+atom, 1 residue, 1 model selected
+> select add #5/A:253@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #5/A:6
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/A:1-4
+atoms, 31 bonds, 4 residues, 1 model selected
+> select #5/A:1
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/A:1-5
+atoms, 40 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #5/A:238
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #5/A:235
+atoms, 20 bonds, 2 residues, 1 model selected
+> setattr #4:235-238 res ss_type 2
+Assigning ss_type attribute to 4 items
+> setattr #5:235-238 res ss_type 1
+Assigning ss_type attribute to 4 items
+> select clear
+> select add #5/A:247
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #5/A:216
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #5/A:216
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/A:216-247
+atoms, 274 bonds, 32 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #5/A:73
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #5/A:71
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #5/A:72
+atoms, 20 bonds, 3 residues, 1 model selected
+> setattr #5:71-73 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #5/A:74
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #5/A:121
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #5/A:74
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/A:74-125
+atoms, 404 bonds, 52 residues, 1 model selected
+> select #5/A:120
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #5/A:120-121
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #5/A:120-121
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #5/A:74
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #5/A:74-121
+atoms, 373 bonds, 48 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #5/A:73
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #5/A:1-2
+atoms, 13 bonds, 2 residues, 1 model selected
+> select #5/A:1-73
+atoms, 582 bonds, 73 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select #5/A:248
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #5/A:249
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #5/A:249-346
+atoms, 741 bonds, 98 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #5/A:248
+atoms, 4 bonds, 1 residue, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #5/A:122
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #5/A:215
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #5/A:122-123
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #5/A:122-215
+atoms, 755 bonds, 94 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select ::name="CYS"
+atoms, 475 bonds, 86 residues, 5 models selected
+> show sel & #5 atoms
+> color (#5 & sel) byhetero
+> select clear
+> select add #5/A:225
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #5/A:226
+atoms, 14 bonds, 2 residues, 1 model selected
+> setattr #5:225-226 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select clear
+> select add #5/A:224
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #5/A:223
+atoms, 13 bonds, 2 residues, 1 model selected
+> setattr #5:223-224 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1.png" width
+> 900 height 739 supersample 4 transparentBackground true
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 1423 residues, atom bfactor range 32.5 to 191
+> select clear
+> hide #5 atoms
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Snn1-pLDDT.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> hide #5 models
+> open
+> /Users/u6290062/Downloads/rlm9_d87e1/rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #6
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/u6290062/Downloads/rlm4_42bc7/rlm4_42bc7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+rlm4_42bc7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #7
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/u6290062/Downloads/rlm7_404af/rlm7_404af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+rlm7_404af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #8
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #6 models
+> hide #7 models
+> hide #8 models
+> show #7 models
+> hide #7 models
+> show #6 models
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 2467 residues, atom bfactor range 32.5 to 191
+> hide #6 models
+> show #7 models
+> hide #7 models
+> show #8 models
+> hide #8 models
+> show #6 models
+> select clear
+> color #7 white
+> close #7
+> close #8
+> color #6 white
+> select clear
+> show #2 models
+> color #2 #00fdffff
+> select clear
+> ui tool show Matchmaker
+> matchmaker #2 to #6
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker rlm9_d87e1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
+chain A (#6) with stb6.pdb, chain A (#2), sequence alignment score = 83.2
+RMSD between 26 pruned atom pairs is 0.902 angstroms; (across all 150 pairs:
+.495)
+> select add #6/A:16
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #6/A:18
+atoms, 18 bonds, 2 residues, 1 model selected
+Alignment identifier is 6/A
+> select #6/A:16-17
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #6/A:16-18
+atoms, 23 bonds, 3 residues, 1 model selected
+> setattr #6:16-18 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #6/A:26
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #6/A:28
+atoms, 20 bonds, 2 residues, 1 model selected
+> setattr #6:26-28 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select #6/A:32
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #6/A:30
+atoms, 12 bonds, 2 residues, 1 model selected
+> select add #6/A:27
+atoms, 27 bonds, 3 residues, 1 model selected
+> setattr #6:27-30 res ss_type 2
+Assigning ss_type attribute to 4 items
+> select clear
+> hide #2 models
+> select clear
+> select ::name="CYS"
+atoms, 596 bonds, 110 residues, 6 models selected
+> show sel & #6 atoms
+> color (#6 & sel) byhetero
+> select clear
+> select #6/A:3@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:22@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #6/A:7@SG
+atoms, 3 residues, 1 model selected
+> select add #6/A:32@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #6/A:213@SG
+atoms, 5 residues, 1 model selected
+> select add #6/A:88@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #6/A:139@SG
+atoms, 7 residues, 1 model selected
+> select add #6/A:119@SG
+atoms, 8 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #6/A:140
+atoms, 7 bonds, 9 residues, 1 model selected
+> select add #6/A:187@SG
+atoms, 7 bonds, 10 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> select clear
+> select add #6/A:135@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:187@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:186@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:181@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #6/A:170@SG
+atoms, 3 residues, 1 model selected
+> select clear
+> select add #6/A:170@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:156@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:288@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:300@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:316@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:302@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:286@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:263@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:345@SG
+atom, 1 residue, 1 model selected
+> select clear
+> select add #6/A:345@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:331@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:336@SG
+atom, 1 residue, 1 model selected
+> select add #6/A:322@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #6/A:83
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #6/A:82
+atoms, 14 bonds, 2 residues, 1 model selected
+> select subtract #6/A:83
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #6/A:1
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #6/A:82
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:1-82
+atoms, 655 bonds, 82 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select add #6/A:247
+atoms, 15 bonds, 1 residue, 1 model selected
+> select add #6/A:248
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #6/A:220
+atoms, 33 bonds, 3 residues, 1 model selected
+> select #6/A:220
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:220-263
+atoms, 355 bonds, 44 residues, 1 model selected
+> select #6/A:248
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #6/A:248
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #6/A:248
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #6/A:220-248
+atoms, 236 bonds, 29 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #6/A:249
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:250
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #6/A:250-350
+atoms, 818 bonds, 101 residues, 1 model selected
+> select #6/A:249
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #6/A:249-350
+atoms, 826 bonds, 102 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #6/A:219
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #6/A:113
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #6/A:219
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #6/A:113-219
+atoms, 823 bonds, 107 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select ::name="CYS"
+atoms, 608 bonds, 110 residues, 6 models selected
+> color (#6 & sel) byhetero
+> select clear
+> select add #6/A:88
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel byhetero
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rlm9.png" width
+> 900 height 739 supersample 4 transparentBackground true
+> select clear
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 1773 residues, atom bfactor range 32.5 to 191
+> select clear
+> hide #6 atoms
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Rlm9-pLDDT.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> hide #6 models
+> open
+> /Users/u6290062/Downloads/Htn1_00234/Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #7
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> color #7 white
+> select clear
+> select #7/A:20
+atoms, 7 bonds, 1 residue, 1 model selected
+Alignment identifier is 7/A
+> select #7/A:20
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:1-20
+atoms, 156 bonds, 20 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> color #2 #8efa00ff
+> show #2 models
+> select clear
+> ui tool show Matchmaker
+> matchmaker #2 to #7
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Htn1_00234_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#7) with stb6.pdb, chain A (#2), sequence alignment score = 103.3
+RMSD between 69 pruned atom pairs is 0.971 angstroms; (across all 182 pairs:
+.215)
+> select add #7/A:64
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #7/A:63
+atoms, 14 bonds, 2 residues, 1 model selected
+> select add #7/A:62
+atoms, 20 bonds, 3 residues, 1 model selected
+> setattr #7:62-64 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #7/A:45
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #7/A:43
+atoms, 18 bonds, 2 residues, 1 model selected
+> setattr #7:43-45 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #2 models
+> select ::name="CYS"
+atoms, 678 bonds, 124 residues, 7 models selected
+> show sel & #7 atoms
+> color (#7 & sel) byhetero
+> select clear
+> select add #7/A:281@SG
+atom, 1 residue, 1 model selected
+> select add #7/A:271@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #7/A:269@SG
+atoms, 3 residues, 1 model selected
+> select add #7/A:249@SG
+atoms, 4 residues, 1 model selected
+> select add #7/A:258@SG
+atoms, 5 residues, 1 model selected
+> select add #7/A:246@SG
+atoms, 6 residues, 1 model selected
+> select add #7/A:29@SG
+atoms, 7 residues, 1 model selected
+> select add #7/A:59@SG
+atoms, 8 residues, 1 model selected
+> bond sel
+Created 3 bonds
+> select clear
+> select add #7/A:34@SG
+atom, 1 residue, 1 model selected
+> select add #7/A:68@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #7/A:281
+atoms, 5 bonds, 3 residues, 1 model selected
+> select #7/A:31
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/A:1-31
+atoms, 235 bonds, 31 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #7/A:31
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/A:1-31
+atoms, 235 bonds, 31 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select add #7/A:26
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #7/A:27
+atoms, 9 bonds, 2 residues, 1 model selected
+> select add #7/A:28
+atoms, 16 bonds, 3 residues, 1 model selected
+> select add #7/A:29
+atoms, 21 bonds, 4 residues, 1 model selected
+> select clear
+> select add #7/A:199@SG
+atom, 1 residue, 1 model selected
+> select add #7/A:148@SG
+atoms, 2 residues, 1 model selected
+> select add #7/A:117@SG
+atoms, 1 bond, 3 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select #7/A:117@SG
+atom, 1 residue, 1 model selected
+> select add #7/A:166@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #7/A:26
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #7/A:28
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #7/A:29
+atoms, 16 bonds, 3 residues, 1 model selected
+> setattr #2/A:26-29 res ss_type 0
+Assigning ss_type attribute to 4 items
+> setattr #7:26-29 res ss_type 0
+Assigning ss_type attribute to 4 items
+> select clear
+> select add #7/A:1
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #7/A:27
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #7/A:27
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #7/A:1-27
+atoms, 209 bonds, 27 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #7/A:282
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #7/A:291
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #7/A:282-283
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #7/A:282-291
+atoms, 81 bonds, 10 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #7/A:86
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #7/A:86
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #7/A:1-86
+atoms, 682 bonds, 86 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select add #7/A:208
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #7/A:238
+atoms, 25 bonds, 2 residues, 1 model selected
+> select #7/A:208
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #7/A:208-238
+atoms, 260 bonds, 31 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #7/A:239
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:239
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #7/A:239-291
+atoms, 400 bonds, 53 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #7/A:208
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #7/A:139
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #7/A:139-140
+atoms, 19 bonds, 2 residues, 1 model selected
+> select #7/A:139-208
+atoms, 577 bonds, 70 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select ::name="CYS"
+atoms, 685 bonds, 124 residues, 7 models selected
+> color (#7 & sel) byhetero
+> select clear
+> select ::name="ASN"
+atoms, 881 bonds, 125 residues, 7 models selected
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1.png" width
+> 900 height 739 supersample 4 transparentBackground true
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 2064 residues, atom bfactor range 32.5 to 191
+> select clear
+> hide #7 atoms
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Htn1-pLDDT.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> hide #7 models
+> open
+> /Users/u6290062/Downloads/ghwak7A_70d62/ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+ghwak7A_70d62_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #8
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/u6290062/Downloads/SlWAK1_f88fd/SlWAK1_f88fd_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+SlWAK1_f88fd_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #9
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #8 models
+> hide #9 models
+> open
+> /Users/u6290062/Downloads/rfo1_1159a_0/rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+rfo1_1159a_0_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #10
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #10 models
+> open
+> /Users/u6290062/Downloads/BrWAK1_96657/BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #11
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #11 models
+> open
+> /Users/u6290062/Downloads/AtWAK1_f4e1e/AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+Chain information for
+AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #12
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #12 models
+> open
+> /Users/u6290062/Downloads/OsWAK1_3328c/OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #13
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #13 models
+> open
+> /Users/u6290062/Downloads/OsDEES1_24a01/OsDEES1_24a01_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+OsDEES1_24a01_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #14
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/Immunity-
+> WAKs.cxs" includeMaps true
+> hide #14 models
+> show #2 models
+> select add #2/A:79
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/A:80
+atoms, 14 bonds, 2 residues, 1 model selected
+> select subtract #2/A:79
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/A:201
+atoms, 10 bonds, 2 residues, 1 model selected
+> select #2/A:80-81
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #2/A:80-201
+atoms, 969 bonds, 122 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> hide #2 atoms
+> select clear
+> select #2/A:6-7
+atoms, 11 bonds, 2 residues, 1 model selected
+> select #2/A:6-79
+atoms, 577 bonds, 74 residues, 1 model selected
+> select #2/A:6-79,202-206
+atoms, 629 bonds, 79 residues, 1 model selected
+> show sel atoms
+> select subtract #2/A:23
+atoms, 612 bonds, 78 residues, 1 model selected
+> select add #2/A:23
+atoms, 627 bonds, 79 residues, 1 model selected
+> select subtract #2/A:22
+atoms, 615 bonds, 78 residues, 1 model selected
+> select subtract #2/A:43
+atoms, 606 bonds, 77 residues, 1 model selected
+> select subtract #2/A:52
+atoms, 597 bonds, 76 residues, 1 model selected
+> select add #2/A:52
+atoms, 604 bonds, 77 residues, 1 model selected
+> select subtract #2/A:53
+atoms, 596 bonds, 76 residues, 1 model selected
+> select add #2/A:53
+atoms, 603 bonds, 77 residues, 1 model selected
+> select subtract #2/A:75
+atoms, 594 bonds, 76 residues, 1 model selected
+> select subtract #2/A:206@CB
+atoms, 592 bonds, 76 residues, 1 model selected
+> select add #2/A:206@CB
+atoms, 592 bonds, 76 residues, 1 model selected
+> select subtract #2/A:18
+atoms, 584 bonds, 75 residues, 1 model selected
+> select add #2/A:18
+atoms, 591 bonds, 76 residues, 1 model selected
+> select clear
+> select add #2/A:22
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #2/A:206
+atoms, 26 bonds, 2 residues, 1 model selected
+> select add #2/A:42
+atoms, 34 bonds, 3 residues, 1 model selected
+> select add #2/A:41
+atoms, 45 bonds, 4 residues, 1 model selected
+> select add #2/A:43
+atoms, 52 bonds, 5 residues, 1 model selected
+> select subtract #2/A:42@CB
+atoms, 50 bonds, 5 residues, 1 model selected
+> select subtract #2/A:42@OE1
+atoms, 48 bonds, 5 residues, 1 model selected
+> select subtract #2/A:42@OE2
+atoms, 47 bonds, 5 residues, 1 model selected
+> select add #2/A:52
+atoms, 54 bonds, 6 residues, 1 model selected
+> select subtract #2/A:52
+atoms, 47 bonds, 5 residues, 1 model selected
+> select add #2/A:53
+atoms, 54 bonds, 6 residues, 1 model selected
+> select add #2/A:65
+atoms, 61 bonds, 7 residues, 1 model selected
+> select add #2/A:75
+atoms, 68 bonds, 8 residues, 1 model selected
+> select add #2/A:68
+atoms, 75 bonds, 9 residues, 1 model selected
+> select add #2/A:18
+atoms, 82 bonds, 10 residues, 1 model selected
+> select add #2/A:51
+atoms, 89 bonds, 11 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 1580 bonds, 196 residues, 1 model selected
+> hide sel atoms
+> select clear
+> color #2 byhetero
+> select clear
+> show #2 cartoons
+> select clear
+> show #2 atoms
+> hide #2 atoms
+> color #2 #ebebebff
+> select clear
+> show #2 surfaces
+> hide #!2 surfaces
+> select clear
+> show #10 models
+> hide #10 models
+> show #11 models
+> hide #11 models
+> show #8 models
+> hide #8 models
+> show #9 models
+> hide #9 models
+> show #10 models
+> hide #10 models
+> show #13 models
+> show #14 models
+> hide #14 models
+> select clear
+> ui tool show Matchmaker
+> matchmaker #13 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 stb6.pdb, chain A (#2) with
+OsWAK1_3328c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A
+(#13), sequence alignment score = 203.4
+RMSD between 88 pruned atom pairs is 1.029 angstroms; (across all 174 pairs:
+.037)
+> select clear
+> select add #13/A:41
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #13/A:42
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #13/A:43
+atoms, 22 bonds, 3 residues, 1 model selected
+> setattr #13:41-43 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #!2 models
+> select clear
+> select add #13/A:77
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #13/A:76
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #13/A:77
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #13/A:77
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #13/A:76
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #13/A:96
+atoms, 15 bonds, 2 residues, 1 model selected
+> setattr #13:76-96 res ss_type 0
+Assigning ss_type attribute to 21 items
+> select clear
+> select add #13/A:175
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #13/A:174
+atoms, 11 bonds, 2 residues, 1 model selected
+> select add #13/A:173
+atoms, 18 bonds, 3 residues, 1 model selected
+> setattr #13:173-175 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select ::name="GLN"
+atoms, 853 bonds, 106 residues, 14 models selected
+> select ::name="CYS"
+atoms, 1440 bonds, 274 residues, 14 models selected
+> show sel & #13 atoms
+> select clear
+> select add #13/A:86@SG
+atom, 1 residue, 1 model selected
+> select add #13/A:135@SG
+atoms, 2 residues, 1 model selected
+> select add #13/A:160@SG
+atoms, 3 residues, 1 model selected
+> select add #13/A:116@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 2 bonds
+> select clear
+> select add #13/A:47@SG
+atom, 1 residue, 1 model selected
+> select add #13/A:7@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #13/A:2@SG
+atoms, 3 residues, 1 model selected
+> select add #13/A:38@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #13/A:236@SG
+atom, 1 residue, 1 model selected
+> select add #13/A:226@SG
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #13/A:205@SG
+atoms, 3 residues, 1 model selected
+> select add #13/A:224@SG
+atoms, 4 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select add #13/A:202@SG
+atoms, 5 residues, 1 model selected
+> select subtract #13/A:202@SG
+atoms, 4 residues, 1 model selected
+> select add #13/A:202@SG
+atoms, 5 residues, 1 model selected
+> select add #13/A:212@SG
+atoms, 6 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> select add #13/A:194
+atoms, 15 bonds, 1 residue, 1 model selected
+> select add #13/A:168
+atoms, 22 bonds, 2 residues, 1 model selected
+Alignment identifier is 13/A
+> select #13/A:168
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #13/A:168-194
+atoms, 227 bonds, 27 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #13/A:75
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #13/A:76
+atoms, 18 bonds, 2 residues, 1 model selected
+> select subtract #13/A:75
+atoms, 8 bonds, 1 residue, 1 model selected
+> select add #13/A:107
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #13/A:76
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #13/A:76-107
+atoms, 232 bonds, 32 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #13/A:108
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #13/A:166
+atoms, 17 bonds, 2 residues, 1 model selected
+> select subtract #13/A:166
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #13/A:167
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #13/A:108
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #13/A:108-167
+atoms, 466 bonds, 60 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select add #13/A:195
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #13/A:195
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #13/A:195-243
+atoms, 354 bonds, 49 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select add #13/A:75
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #13/A:74-75
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #13/A:1-75
+atoms, 573 bonds, 75 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select ::name="CYS"
+atoms, 1447 bonds, 274 residues, 14 models selected
+> color (#13 & sel) byhetero
+> select clear
+> select #13/A:195
+atoms, 8 bonds, 1 residue, 1 model selected
+> color sel forest green target ac
+> select clear
+> select ::name="ASN"
+atoms, 2057 bonds, 292 residues, 14 models selected
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/OsWAK1.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 4250 residues, 1 surfaces, atom bfactor range 28.5 to 191
+> hide #13 atoms
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity
+> WAKs/OsWAK1-pLDDT.png" width 900 height 739 supersample 4
+> transparentBackground true
+> hide #13 models
+> show #14 models
+> close #14
+> select clear
+> show #11 models
+> color #11 darkgrey
+> select clear
+> show #!2 models
+> color #2 #00fdffff
+> select clear
+> ui tool show Matchmaker
+> matchmaker #!2 to #11
+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
+BrWAK1_96657_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain A
+(#11) with stb6.pdb, chain A (#2), sequence alignment score = 102.1
+RMSD between 31 pruned atom pairs is 0.917 angstroms; (across all 168 pairs:
+.481)
+> select clear
+> select add #11/A:43
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:45
+atoms, 18 bonds, 2 residues, 1 model selected
+> setattr #11:43-45 res ss_type 0
+Assigning ss_type attribute to 3 items
+> setattr #11:43-45 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #11/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #11/A:31
+atoms, 18 bonds, 2 residues, 1 model selected
+> setattr #11:31-33 res ss_type 0
+Assigning ss_type attribute to 3 items
+> select clear
+> select #11/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+Alignment identifier is 11/A
+> select #11/A:34
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:34-35
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #11/A:33-34
+atoms, 19 bonds, 2 residues, 1 model selected
+> select #11/A:33-35
+atoms, 27 bonds, 3 residues, 1 model selected
+> select #2/A:194
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #2/A:194-195
+atoms, 21 bonds, 2 residues, 1 model selected
+> select clear
+> select #11/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:33-35
+atoms, 27 bonds, 3 residues, 1 model selected
+> select add #11/A:38
+atoms, 34 bonds, 4 residues, 1 model selected
+> select #11/A:33-34
+atoms, 19 bonds, 2 residues, 1 model selected
+> select #11/A:33-40
+atoms, 68 bonds, 8 residues, 1 model selected
+> setattr #11:33-40 res ss_type 2
+Assigning ss_type attribute to 8 items
+> select clear
+> setattr #11:33-40 res ss_type 0
+Assigning ss_type attribute to 8 items
+> select add #11/A:36
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #11/A:38
+atoms, 13 bonds, 2 residues, 1 model selected
+> setattr #11:36-38 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select #11/A:35
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:32
+atoms, 12 bonds, 2 residues, 1 model selected
+> setattr #11:32-35 res ss_type 2
+Assigning ss_type attribute to 4 items
+> setattr #11:32-35 res ss_type 0
+Assigning ss_type attribute to 4 items
+> setattr #11:36-38 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #11/A:32
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #11/A:34
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #11/A:33
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:33-35
+atoms, 27 bonds, 3 residues, 1 model selected
+> setattr #11:32-34 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> setattr #11:31-34 res ss_type 2
+Assigning ss_type attribute to 4 items
+> select clear
+> select add #11/A:19
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #11/A:21
+atoms, 17 bonds, 2 residues, 1 model selected
+> setattr #11:19-21 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #!2 models
+> select clear
+> select add #11/A:305
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #11/A:305
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #11/A:305-311
+atoms, 60 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select ::name="CYS"
+atoms, 1336 bonds, 252 residues, 13 models selected
+> show sel & #11 atoms
+> color (#11 & sel) byelement
+> select clear
+> select add #11/A:10@SG
+atom, 1 residue, 1 model selected
+> select add #11/A:37@SG
+atoms, 2 residues, 1 model selected
+> select add #11/A:6@SG
+atoms, 3 residues, 1 model selected
+> select add #11/A:25@SG
+atoms, 4 residues, 1 model selected
+> select add #11/A:221@SG
+atoms, 5 residues, 1 model selected
+> select add #11/A:239@SG
+atoms, 6 residues, 1 model selected
+> select add #11/A:257@SG
+atoms, 7 residues, 1 model selected
+> select add #11/A:241@SG
+atoms, 8 residues, 1 model selected
+> select add #11/A:212@SG
+atoms, 9 residues, 1 model selected
+> select add #11/A:228@SG
+atoms, 10 residues, 1 model selected
+> select add #11/A:278@SG
+atoms, 11 residues, 1 model selected
+> select add #11/A:263@SG
+atoms, 12 residues, 1 model selected
+> select clear
+> select S
+atoms, 68 bonds, 288 residues, 13 models selected
+> bond sel
+Created 55 bonds
+> select clear
+> select add #11/A:206
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #11/A:179
+atoms, 12 bonds, 2 residues, 1 model selected
+> color sel forest green target ac
+> select #11/A:179
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:179-206
+atoms, 239 bonds, 28 residues, 1 model selected
+> color sel forest green target ac
+> select clear
+> select add #11/A:94
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:93
+atoms, 14 bonds, 2 residues, 1 model selected
+> select subtract #11/A:94
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:64
+atoms, 14 bonds, 2 residues, 1 model selected
+> select subtract #11/A:64
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:65
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #11/A:93
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:65-93
+atoms, 223 bonds, 29 residues, 1 model selected
+> color sel light gray target ac
+> select clear
+> select add #11/A:64
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:64
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:1-64
+atoms, 527 bonds, 64 residues, 1 model selected
+> color sel dark sea green target ac
+> select clear
+> select add #11/A:94
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #11/A:178
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #11/A:94
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:94-178
+atoms, 641 bonds, 85 residues, 1 model selected
+> color sel dark khaki target ac
+> select clear
+> select add #11/A:207
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:207
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:207-311
+atoms, 819 bonds, 105 residues, 1 model selected
+> color sel light steel blue target ac
+> select clear
+> select ::name="CYS"
+atoms, 1391 bonds, 252 residues, 13 models selected
+> color (#11 & sel) byhetero
+> select clear
+> select #11/A:3
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #11/A:1-3
+atoms, 27 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity WAKs/BrWAK1.png"
+> width 900 height 739 supersample 4 transparentBackground true
+> select clear
+> color bfactor palette
+> 0,darkorange:49.99,darkorange:50,yellow:69.99,yellow:70,lightskyblue:89.99,lightskyblue:90,blue:100,blue
+atoms, 3887 residues, 1 surfaces, atom bfactor range 28.5 to 191
+> select clear
+> save "/Users/u6290062/Library/CloudStorage/OneDrive-
+> AustralianNationalUniversity/Documents/Figures/Immunity
+> WAKs/BrWAK1-pLDDT.png" width 900 height 739 supersample 4
+> transparentBackground true
+> select clear
+> hide #11 models
+> show #12 models
+> color #12 #008f00ff
+> select clear
+> show #!2 models
+> color #2 #ebebebff
+> select clear
+> ui tool show "Render/Select by Attribute"
+> ui tool show Matchmaker
+> matchmaker #12 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 stb6.pdb, chain A (#2) with
+AtWAK1_f4e1e_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
+(#12), sequence alignment score = 130.5
+RMSD between 34 pruned atom pairs is 0.976 angstroms; (across all 170 pairs:
+.148)
+> select add #12/A:34
+atoms, 5 bonds, 1 residue, 1 model selected
+Alignment identifier is 12/A
+> select clear
+> select add #12/A:34
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #12/A:35
+atoms, 16 bonds, 2 residues, 1 model selected
+> setattr #12:34-35 res ss_type 0
+Assigning ss_type attribute to 2 items
+> select #12/A:35
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #12/A:35-37
+atoms, 25 bonds, 3 residues, 1 model selected
+> setattr #12:35-37 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> select add #12/A:21
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #12/A:23
+atoms, 18 bonds, 2 residues, 1 model selected
+> setattr #12:21-23 res ss_type 2
+Assigning ss_type attribute to 3 items
+> select clear
+> hide #!2 models
+> select ::name="CYS"
+atoms, 1391 bonds, 252 residues, 13 models selected
+> show sel & #12 atoms
+> color (#12 & sel) byhetero
+> select clear
+> select add #12/A:7
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #12/A:6
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/A:5-6
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #12/A:1
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/A:1-5
+atoms, 40 bonds, 5 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select add #12/A:306
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/A:306
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #12/A:306-312
+atoms, 64 bonds, 7 residues, 1 model selected
+> hide sel cartoons
+> select clear
+[deleted to fit within ticket limits]
 > select add #12/A:67