id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17089 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020954c840 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.mlp._mlp (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-13 11:07:36.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.1 (24D70)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""69343086-CCD4-4610-BBE2-1E2B74C8EC06""} { ""uptime"" : 330000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,7"", ""coalitionID"" : 1298, ""osVersion"" : { ""train"" : ""macOS 15.3.1"", ""build"" : ""24D70"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-13 11:07:31.8171 -0500"", ""codeSigningMonitor"" : 1, ""incident"" : ""69343086-CCD4-4610-BBE2-1E2B74C8EC06"", ""pid"" : 78433, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-12 22:17:53.1384 -0500"", ""procStartAbsTime"" : 7880780866538, ""procExitAbsTime"" : 8128691747725, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""039446C8-56F1-54A1-9531-85BD2E8F600D"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""3C03AB57-DF91-6538-731F-87145E7E925C"", ""lowPowerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""740CAC07-7A35-4E6E-9C78-D586F3D0754E"", ""wakeTime"" : 5426, ""sleepWakeUUID"" : ""697FDE6D-1F24-405B-95E5-1AE0A368F3C2"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x168 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" opened ChimeraX session > select #23-26 /A :151,153,155,223,220,147 170 atoms, 159 bonds, 24 residues, 4 models selected > ui tool show Contacts > contacts sel restrict both ignoreHiddenModels 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: True 12 contacts atom1 atom2 overlap distance 1uol #25/A TYR 220 CD2 1uol #25/A PRO 151 CG 0.038 3.602 1uol #25/A TYR 220 CE2 1uol #25/A PRO 151 CG 0.035 3.605 1uol #25/A PRO 151 CD 1uol #25/A TYR 220 CE2 0.026 3.614 1uol #25/A THR 155 OG1 1uol #25/A PRO 151 CB -0.144 3.484 1uol #25/A TYR 220 CB 1uol #25/A THR 155 O -0.159 3.459 1uol #25/A THR 155 CG2 1uol #25/A PRO 151 CB -0.190 3.950 1uol #25/A TYR 220 OH 1uol #25/A VAL 147 CG2 -0.199 3.539 1uol #25/A PRO 151 CG 1uol #25/A THR 155 CG2 -0.208 3.968 1uol #25/A TYR 220 N 1uol #25/A THR 155 O -0.225 2.885 1uol #25/A PRO 223 CD 1uol #25/A TYR 220 OH -0.294 3.634 1uol #25/A TYR 220 CB 1uol #25/A THR 155 CG2 -0.295 4.055 1uol #25/A THR 155 CB 1uol #25/A PRO 151 CB -0.322 4.082 12 contacts > ui mousemode right select > select clear > select #25/A:151@CD 1 atom, 1 residue, 1 model selected > select #25/A:220@OH 1 atom, 1 residue, 1 model selected > select add #25/A:151@CD 2 atoms, 2 residues, 2 models selected > ui tool show Contacts > contacts sel restrict both ignoreHiddenModels 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: True 0 contacts atom1 atom2 overlap distance No contacts > select #23-26 /A :151,153,155,223,220,147 170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 5 models selected > color (#!25 & sel) byelement > style sel & #!25 ball Changed 47 atom styles > select clear > hide #!25 atoms > show #!25 atoms > hide #!25 atoms > select up 12 pseudobonds, 1 model selected > select up 130556 atoms, 124515 bonds, 12 pseudobonds, 24333 residues, 27 models selected > select #23-26 /A :151,153,155,223,220,147 170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 5 models selected > show sel & #!25 atoms > hide sel & #!25 cartoons > show sel & #!25 cartoons > hide sel & #!25 cartoons > ui mousemode right distance > distance #25/A:153@CD #25/A:220@O Distance between 1uol #25/A PRO 153 CD and TYR 220 O: 8.203Å > distance #25/A:153@CA #25/A:220@O Distance between 1uol #25/A PRO 153 CA and TYR 220 O: 6.286Å > distance #25/A:153@CB #25/A:220@O Distance between 1uol #25/A PRO 153 CB and TYR 220 O: 7.164Å > hide #25.4 models > select subtract #25.4 170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 9 models selected > select add #25.4 170 atoms, 159 bonds, 12 pseudobonds, 24 residues, 9 models selected > show #25.4 models > distance #25/A:223@CD #25/A:220@OH Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å > close #25.4 > open ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" opened ChimeraX session > style sel & #!25 ball Changed 47 atom styles > color (#!25 & sel) byelement > distance #25/A:153@CA #25/A:220@CD2 Distance between 1uol #25/A PRO 153 CA and TYR 220 CD2: 6.945Å > close #27 > hide sel & #!25 cartoons > distance #25/A:223@CD #25/A:220@OH Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å > distance #25/A:147@CG2 #25/A:220@OH Distance between 1uol #25/A VAL 147 CG2 and TYR 220 OH: 3.539Å > distance #25/A:151@CD #25/A:220@OH Distance between 1uol #25/A PRO 151 CD and TYR 220 OH: 4.277Å > distance #25/A:155@O #25/A:220@N Distance between 1uol #25/A THR 155 O and TYR 220 N: 2.885Å > ui mousemode right select > select #25/A:153@CA 1 atom, 1 residue, 1 model selected > select #23-26 /A :153 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 cartoons > hide sel & #!25 atoms > color (#!25 & sel) dark gray > select clear > select #23-26 /A :155 28 atoms, 24 bonds, 4 residues, 4 models selected > select #23-26 /A :222 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > style sel & #!25 ball Changed 7 atom styles > color (#!25 & sel) byelement > hide #27.1 models > show #27.1 models > select #23-26 /A :22 Nothing selected > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style (#!25 & sel) ringFill thick Changed 1 residue ring style > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style (#!25 & sel) ringFill thin Changed 1 residue ring style > select clear > select #23-26 /A :222, 153 56 atoms, 56 bonds, 8 residues, 4 models selected > select #23-26 /A :222, 151 56 atoms, 56 bonds, 8 residues, 4 models selected > style (#!25 & sel) ringFill thin Changed 2 residue ring styles > color (#!25 & sel) black > color (#!25 & sel) byelement > select clear > select #23-26 /A :156-146 Nothing selected > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!25 cartoons > show sel & #!25 atoms > hide (#!25 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!25 & sel-residues) > show (#!25 & sel-residues & backbone) target ab > select #23-26 /A :219-224 179 atoms, 188 bonds, 1 pseudobond, 24 residues, 5 models selected > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!25 cartoons > show sel & #!25 atoms > hide (#!25 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!25 & sel-residues) > show (#!25 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147 142 atoms, 131 bonds, 4 pseudobonds, 20 residues, 5 models selected > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected > show (#!25 & sel-residues & sidechain) target ab > select clear > select #25/A:145 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #25/A:230@C 1 atom, 1 residue, 1 model selected > select #25/A:230@CA 1 atom, 1 residue, 1 model selected > select #25/A:230@CA 1 atom, 1 residue, 1 model selected > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style sel & #!25 sphere Changed 12 atom styles > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style sel & #!25 ball Changed 12 atom styles > select clear > hide #27.1 models > hide #!27 models > show #!26 models > hide #!25 models > show #!25 models > show #!24 models > hide #!25 models > hide #!26 models > show #!25 models > hide #!25 models > show #!23 models > hide #!23 models > hide #!24 models > show #!24 models > show #!26 models > hide #!26 models > show #!25 models > show #!23 models > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected > style sel & #!23-25 ball Changed 129 atom styles > show sel & #!23-25 atoms > color (#!23-25 & sel) byelement > style (#!23-25 & sel) ringFill thin Changed 18 residue ring styles > hide #!25 models > hide #!24 models > show #!24 models > hide #!23 models > show #!23 models > hide #!24 models > show #!25 models > hide #!23 models > show #!27 models > select clear > ui tool show ""Side View"" > save ""/Users/kompa012/Desktop/P53/1uol Y220 .png"" width 3000 height 2320 > supersample 3 transparentBackground true > hide #!25 models > show #!24 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > select #23-26 /A :220,155 58 atoms, 51 bonds, 1 pseudobond, 8 residues, 5 models selected > hide sel & #!24 cartoons > ui mousemode right distance > distance #24/A:220@N #24/A:155@O Distance between 2j1x #24/A CYS 220 N and THR 155 O: 2.911Å > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!24 cartoons > hide sel & #!24 atoms > show sel & #!24 atoms > hide sel & #!24 cartoons > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > select up 707 atoms, 732 bonds, 1 pseudobond, 92 residues, 9 models selected > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > hide sel & #!24 cartoons > show sel & #!24 atoms > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > show (#!24 & sel-residues & sidechain) target ab > ui mousemode right select > select clear > select #23-26 /A :151,223,222 84 atoms, 88 bonds, 12 residues, 4 models selected > color (#!24 & sel) black > color (#!24 & sel) byelement > select clear > show #!23 models > hide #!24 models > select #23-26 /A :151,223,222 84 atoms, 88 bonds, 12 residues, 4 models selected > color (#!23 & sel) black > color (#!23 & sel) byelement > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!23 cartoons > show sel & #!23 atoms > hide (#!23 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!23 & sel-residues) > show (#!23 & sel-residues & backbone) target ab > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!23 cartoons > show sel & #!23 atoms > hide (#!23 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!23 & sel-residues) > show (#!23 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > show (#!23 & sel-residues & sidechain) target ab > show #!24 models > select clear > save ""/Users/kompa012/Desktop/P53/6shz_2j1x C220.png"" width 3000 height 2320 > supersample 3 transparentBackground true > hide #!24 models > hide #!23 models > show #!26 models > show #!25 models > hide #!25 models > select add #26 3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected > select solvent 19518 atoms, 19518 residues, 51 models selected > hide sel & #!26 atoms > select clear > show #!24 models > hide #!24 models > hide #!26 models > show #!26 models > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!26 cartoons > show sel & #!26 cartoons > style sel & #!26 ball Changed 79 atom styles > hide (#!26 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!26 & sel-residues) > show (#!26 & sel-residues & backbone) target ab > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!26 cartoons > show sel & #!26 atoms > style sel & #!26 ball Changed 85 atom styles > hide (#!26 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!26 & sel-residues) > show (#!26 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > color (#!26 & sel) black > style (#!26 & sel) ringFill thin Changed 6 residue ring styles > show (#!26 & sel-residues & sidechain) target ab > color (#!26 & sel) byelement > select add #26.3 1690 atoms, 163 bonds, 5 pseudobonds, 223 residues, 9 models selected > select subtract #26.2 1649 atoms, 124 bonds, 5 pseudobonds, 217 residues, 10 models selected > select add #26.1 1649 atoms, 124 bonds, 13 pseudobonds, 217 residues, 10 models selected > select add #26 3660 atoms, 3283 bonds, 13 pseudobonds, 860 residues, 10 models selected > show sel & #!26 surfaces > hide sel & #!26 surfaces > select ligand 274 atoms, 218 bonds, 60 residues, 16 models selected > style sel & #!26 ball Changed 48 atom styles > color (#!26 & sel) byelement > style sel & #!26 stick Changed 48 atom styles > ui mousemode right distance > distance #26/A:220@N #26/A:155@O Distance between 8a32 #26/A CYS 220 N and THR 155 O: 2.934Å > style (#!26 & sel) ringFill thin Changed 4 residue ring styles > color (#!26 & sel) black > color (#!26 & sel) byelement > distance #26/A:401@O #26/A:151@CD Distance between 8a32 #26/A KVA 401 O and PRO 151 CD: 6.205Å > distance #26/A:401@O1 #26/A:147@CG2 Distance between 8a32 #26/A KVA 401 O1 and VAL 147 CG2: 5.072Å > show #27.1 models > hide #27.1 models > show #27.1 models > hide #27.1 models > distance #26/A:401@O2 #26/A:147@CG2 Distance between 8a32 #26/A KVA 401 O2 and VAL 147 CG2: 3.735Å > show #27.1 models > hide #27.1 models > ui mousemode right select > hide #!26 atoms > undo > hide #!27 models > show #!27 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > ui mousemode right ""delete markers"" > ui mousemode right distance > ~distance #26/A:401@O #26/A:151@CD > ~distance #26/A:401@O1 #26/A:147@CG2 > save ""/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769.png"" width 3000 > height 2320 supersample 3 transparentBackground true > save ""/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"" > hide #!26 models > show #!25 models > show #!26 models > show #!24 models > show #!23 models > hide #!23 models > hide #!24 models > hide #!25 models > hide #!26 models > show #!25 models > hide #!27 models > transparency #25 70 > select add #25 3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected > show sel surfaces > select add #25.3 3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 6 models selected > select subtract #25.3 1929 atoms, 1572 bonds, 8 pseudobonds, 588 residues, 5 models selected > select subtract #25.2 393 atoms, 393 residues, 2 models selected > select add #25.3 1929 atoms, 588 residues, 2 models selected > hide sel surfaces > select add #25 3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 5 models selected > select subtract #25.3 1929 atoms, 1572 bonds, 8 pseudobonds, 588 residues, 5 models selected > hide #!25.3 models > transparency (#!25 & sel) 90 > ui mousemode right select > select clear > select add #25.2 1536 atoms, 195 residues, 1 model selected > mlp sel Map values for surface ""1uol_A SES surface"": minimum -28.72, mean -5.719, maximum 23.04 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!25 & sel) 80 > ui mousemode right ""color key"" > transparency (#!25 & sel) 0 > hide sel surfaces > key pos 0.855729,0.814485 size 0,0 > ui mousemode right select > select clear > ui mousemode right select > select clear > ui tool show ""Side View"" > select add #25.2 1536 atoms, 195 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide #!25 models > show #!24 models > select add #24 4995 atoms, 3133 bonds, 9 pseudobonds, 981 residues, 5 models selected > select subtract #24.3 3462 atoms, 1565 bonds, 5 pseudobonds, 786 residues, 7 models selected > mlp sel & #!24 Map values for surface ""2j1x_A SES surface"": minimum -27.43, mean -5.658, maximum 22.9 To also show corresponding color key, enter the above mlp command and add key true > show #!25 models > hide #!25 models > show #!26 models > hide #!24 models > select add #26 6993 atoms, 4724 bonds, 15 pseudobonds, 1628 residues, 8 models selected > select subtract #26.3 5473 atoms, 3169 bonds, 11 pseudobonds, 1429 residues, 10 models selected > mlp sel & #!26 Map values for surface ""8a32_A SES surface"": minimum -30.19, mean -5.652, maximum 22.73 To also show corresponding color key, enter the above mlp command and add key true > select clear > hide #!26 models > show #!25 models > save ""/Users/kompa012/Desktop/P53/1uol Y220 surface.png"" width 3000 height > 2320 supersample 3 transparentBackground true > hide #!25 models > show #!25 models > hide #!25 models > show #!24 models > show #!23 models > hide #!23 models > save ""/Users/kompa012/Desktop/P53/2j1x Y220 surface.png"" width 3000 height > 2320 supersample 3 transparentBackground true > show #!26 models > hide #!24 models > save ""/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769 surface.png"" width > 3000 height 2320 supersample 3 transparentBackground true > hide #!26 models > hide #28 models > show #!25 models > transparency #25.1-2#!25 90 > save ""/Users/kompa012/Desktop/P53/Transparrent surface 1uol.png"" width 3000 > height 2320 supersample 3 transparentBackground true > ui mousemode right ""color key"" > key lipophilicity :min : :max > show #!26 models > show #!24 models > show #!23 models > hide #!26 models > hide #!23 models > key lipophilicity :min : :max > help help:user/tools/colorkey.html > ui mousemode right select > select add #24 3459 atoms, 3133 bonds, 9 pseudobonds, 786 residues, 3 models selected > select subtract #24 2 models selected > select add #25 3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected > ui mousemode right ""color key"" > key lipophilicity :min : :max > ui mousemode right select > show #28 models > select clear > ui mousemode right ""move label"" > ui mousemode right ""color key"" > key labelSide left/top > select add #28 1 model selected > ui mousemode right ""move label"" > ui mousemode right ""color key"" > key pos 0.70206,0.0744216 > ui mousemode right ""move label"" > select subtract #28 Nothing selected > ui mousemode right ""move label"" > ui mousemode right clip > ui mousemode right ""move label"" > ui mousemode right ""color key"" > key pos 0.474902,0.105324 size 0.267526,0.0631905 > hide #!25 models > show #!26 models > hide #!24 models > key pos 0.339284,0.0601194 size 0.39171,0.0330387 > ui mousemode right ""move label"" > save ""/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769 surface.png"" width > 3000 height 2282 supersample 3 transparentBackground true > show #!25 models > hide #!26 models > show #!24 models > hide #!25 models > save ""/Users/kompa012/Desktop/P53/2j1x Y220 surface.png"" width 3000 height > 2282 supersample 3 transparentBackground true > show #!25 models > hide #!24 models > transparency #28#25.1-2#!25 0 > save ""/Users/kompa012/Desktop/P53/1uol Y220 surface.png"" width 3000 height > 2282 supersample 3 transparentBackground true > hide #28 models > transparency #25.1-2#!25 80 > select add #25 3465 atoms, 3144 bonds, 12 pseudobonds, 783 residues, 3 models selected > ui mousemode right select > select clear > transparency #25.1-2#!25 90 > save ""/Users/kompa012/Desktop/P53/Transparrent surface 1uol.png"" width 3000 > height 2282 supersample 3 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"" Log from Thu Mar 13 10:36:24 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" Log from Wed Mar 12 17:13:32 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" Log from Wed Mar 12 16:42:08 2025 Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kompa012/Desktop/New Folder/Experiment6.mrc"" format mrc Opened Experiment6.mrc as #1, grid size 336,336,336, pixel 0.66, shown at level 1.18, step 2, values float32 > close > toolshed show > ui tool show Rotamers Populating font family aliases took 164 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > open 1TUP fromDatabase pdb format mmcif Summary of feedback from opening 1TUP fetched from pdb --- note | Fetching compressed mmCIF 1tup from http://files.rcsb.org/download/1tup.cif 1tup title: Tumor suppressor P53 complexed with DNA [more info...] Chain information for 1tup #1 --- Chain | Description | UniProt A B C | PROTEIN (P53 TUMOR SUPPRESSOR ) | P53_HUMAN 94-312 E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') | F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') | Non-standard residues in 1tup #1 --- ZN — zinc ion > open 1TSR fromDatabase pdb format mmcif Summary of feedback from opening 1TSR fetched from pdb --- note | Fetching compressed mmCIF 1tsr from http://files.rcsb.org/download/1tsr.cif 1tsr title: P53 core domain In complex with DNA [more info...] Chain information for 1tsr #2 --- Chain | Description | UniProt A B C | PROTEIN (P53 TUMOR SUPPRESSOR) | P53_HUMAN 94-312 E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') | F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') | Non-standard residues in 1tsr #2 --- ZN — zinc ion > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select add #2 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > hide sel atoms > show sel cartoons > select subtract #2 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select subtract #1 Nothing selected > select add #2 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #2 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #2 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #2 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select add #2 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > select add #1 11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected > select subtract #1 5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected > close #2 > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select subtract #1 Nothing selected > open 2ac0 fromDatabase pdb format mmcif Summary of feedback from opening 2ac0 fetched from pdb --- note | Fetching compressed mmCIF 2ac0 from http://files.rcsb.org/download/2ac0.cif 2ac0 title: Structural Basis of DNA Recognition by p53 Tetramers (complex I) [more info...] Chain information for 2ac0 #2 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F G H | 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3' | Non-standard residues in 2ac0 #2 --- ZN — zinc ion 37 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!1 models > open 2ady fromDatabase pdb format mmcif Summary of feedback from opening 2ady fetched from pdb --- note | Fetching compressed mmCIF 2ady from http://files.rcsb.org/download/2ady.cif 2ady title: Structural Basis of DNA Recognition by p53 Tetramers (complex IV) [more info...] Chain information for 2ady #3 --- Chain | Description | UniProt A B | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' | Non-standard residues in 2ady #3 --- ZN — zinc ion 2ady mmCIF Assemblies --- 1| author_defined_assembly 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2ahi fromDatabase pdb format mmcif Summary of feedback from opening 2ahi fetched from pdb --- note | Fetching compressed mmCIF 2ahi from http://files.rcsb.org/download/2ahi.cif 2ahi title: Structural Basis of DNA Recognition by p53 Tetramers (complex III) [more info...] Chain information for 2ahi #4 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F G H | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' | Non-standard residues in 2ahi #4 --- ZN — zinc ion 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2ata fromDatabase pdb format mmcif Summary of feedback from opening 2ata fetched from pdb --- note | Fetching compressed mmCIF 2ata from http://files.rcsb.org/download/2ata.cif 2ata title: Structural Basis of DNA Recognition by p53 Tetramers (complex II) [more info...] Chain information for 2ata #5 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F G H | 5'-D(*AP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*T)-3' | Non-standard residues in 2ata #5 --- ZN — zinc ion 9 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > select subtract #2 Nothing selected > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > select add #4 16245 atoms, 14689 bonds, 152 pseudobonds, 3729 residues, 6 models selected > select add #3 20034 atoms, 18391 bonds, 189 pseudobonds, 4364 residues, 9 models selected > select add #5 27815 atoms, 25698 bonds, 259 pseudobonds, 5919 residues, 12 models selected > hide sel atoms > show sel cartoons > hide #!2 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!3 models > show #!3 models > show #!4 models > show #!2 models > ui tool show Matchmaker > matchmaker #!3 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 2ac0, chain D (#2) with 2ady, chain A (#3), sequence alignment score = 1041 RMSD between 194 pruned atom pairs is 0.457 angstroms; (across all 196 pairs: 0.530) > hide #!5 models > hide #!4 models > hide #!2 models > show #!2 models > show #!4 models > show #!5 models > style sel sphere Changed 27815 atom styles > show sel atoms > hide sel cartoons > style sel stick Changed 27815 atom styles > hide #!4 models > hide #!5 models > hide #!2 models > nucleotides sel & #!3 atoms > style nucleic & sel & #!3 stick Changed 486 atom styles > show #!4 models > show #!2 models > show #!5 models > show sel surfaces > hide sel surfaces > select subtract #2 19605 atoms, 18290 bonds, 181 pseudobonds, 4023 residues, 37 models selected > select subtract #3 15816 atoms, 14588 bonds, 144 pseudobonds, 3388 residues, 26 models selected > select subtract #4 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 19 models selected > select subtract #5 8 models selected > show #!1 models > matchmaker #!1 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 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment score = 1024.8 RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs: 1.132) > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > show sel atoms > style sel stick Changed 5828 atom styles > hide sel cartoons > select subtract #1 Nothing selected > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.33546,-0.80914,-0.48246,77.205,0.20225,-0.43834,0.87576,-68.732,-0.92009,-0.39136,0.016605,93.096 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.33546,-0.80914,-0.48246,75.538,0.20225,-0.43834,0.87576,-81.654,-0.92009,-0.39136,0.016605,70.995 > select subtract #1 Nothing selected > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > select add #1 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 14 models selected > show sel cartoons > hide sel atoms > select subtract #2 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 11 models selected > view matrix models > #1,0.33546,-0.80914,-0.48246,83.959,0.20225,-0.43834,0.87576,-27.201,-0.92009,-0.39136,0.016605,56.212 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.47854,-0.70175,0.52777,0.92818,-0.3715,0.3828,0.84584,-5.1579,-0.7956,-0.60084,-0.077517,59.209 > view matrix models > #1,0.66211,-0.70583,0.25184,10.847,0.14066,-0.21303,-0.96687,106.96,0.73609,0.67559,-0.04177,-47.372 > view matrix models > #1,-0.22202,0.86187,0.45595,22.171,0.41802,-0.33833,0.84308,-38.3,0.88089,0.37778,-0.28516,-33.349 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.22202,0.86187,0.45595,17.518,0.41802,-0.33833,0.84308,-75.138,0.88089,0.37778,-0.28516,-18.673 > view matrix models > #1,-0.22202,0.86187,0.45595,-30.27,0.41802,-0.33833,0.84308,-66.789,0.88089,0.37778,-0.28516,-17.681 > view matrix models > #1,-0.22202,0.86187,0.45595,-32.908,0.41802,-0.33833,0.84308,-66.426,0.88089,0.37778,-0.28516,-19.539 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.58924,-0.80159,-0.10128,-13.083,0.17546,0.24931,-0.9524,69.057,0.78868,0.54342,0.28755,-58.505 > view matrix models > #1,0.080048,-0.6908,0.7186,-46.019,-0.56887,0.56032,0.60202,-7.1708,-0.81852,-0.45698,-0.34813,91.867 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.080048,-0.6908,0.7186,-15.014,-0.56887,0.56032,0.60202,-25.742,-0.81852,-0.45698,-0.34813,109 > matchmaker #!1 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 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment score = 1024.8 RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs: 1.132) > matchmaker #1/E to #2/E pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment score = 23.5 RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs: 3.330) > matchmaker #1/F to #2/F pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/F to 2ac0 #2/F Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain F (#2) with 1tup, chain F (#1), sequence alignment score = 23.5 RMSD between 9 pruned atom pairs is 1.079 angstroms; (across all 12 pairs: 2.836) > show #!3 models > show #!4 models > show #!5 models > hide #!1 models > matchmaker #1/E to #2/E pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment score = 23.5 RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs: 3.330) > show #!1 models > hide #!3 models > hide #!4 models > hide #!5 models > matchmaker #1/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 1tup, chain B (#1), sequence alignment score = 1007.4 RMSD between 191 pruned atom pairs is 0.597 angstroms; (across all 194 pairs: 0.710) > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > show #!3 models > show #!4 models > hide #!4 models > select add #3 9617 atoms, 9351 bonds, 92 pseudobonds, 1649 residues, 6 models selected > select subtract #1 3789 atoms, 3702 bonds, 37 pseudobonds, 635 residues, 7 models selected > close #3 > show #!4 models > show #!5 models > hide #!1 models > hide #!5 models > hide #!4 models > open 5lgy fromDatabase pdb format mmcif Summary of feedback from opening 5lgy fetched from pdb --- note | Fetching compressed mmCIF 5lgy from http://files.rcsb.org/download/5lgy.cif 5lgy title: Lysine 120-acetylated P53 DNA binding domain in a complex with the BAX response element. [more info...] Chain information for 5lgy #3 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') | F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') | Non-standard residues in 5lgy #3 --- ALY — N(6)-acetyllysine ZN — zinc ion 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 5bua fromDatabase pdb format mmcif Summary of feedback from opening 5bua fetched from pdb --- note | Fetching compressed mmCIF 5bua from http://files.rcsb.org/download/5bua.cif 5bua title: Lysine 120-acetylated P53 DNA binding domain in a complex with DNA. [more info...] Chain information for 5bua #6 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 94-293 B | DNA (5'-D(P*GP*GP*AP*CP*AP*TP*GP*TP*CP*C)-3') | Non-standard residues in 5bua #6 --- ALY — N(6)-acetyllysine ZN — zinc ion 5bua mmCIF Assemblies --- 1| author_and_software_defined_assembly 58 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!2 models > show #!2 models > hide #!3 models > hide #!6 models > show #!3 models > show #!6 models > matchmaker #6/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 5bua, chain A (#6), sequence alignment score = 1001.4 RMSD between 187 pruned atom pairs is 0.507 angstroms; (across all 198 pairs: 1.246) > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!6 models > show #!6 models > hide #!6 models > show #!3 models > hide #!2 models > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected > hide sel atoms > style sel stick Changed 7093 atom styles > show sel atoms > show sel cartoons > hide sel atoms > show #!2 models > matchmaker #3/C to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 5lgy, chain C (#3), sequence alignment score = 1018.3 RMSD between 196 pruned atom pairs is 0.474 angstroms; (across all 197 pairs: 0.534) > matchmaker #3/D to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 5lgy, chain D (#3), sequence alignment score = 1015.3 RMSD between 194 pruned atom pairs is 0.536 angstroms; (across all 197 pairs: 0.673) > open 4mzr fromDatabase pdb format mmcif Summary of feedback from opening 4mzr fetched from pdb --- note | Fetching compressed mmCIF 4mzr from http://files.rcsb.org/download/4mzr.cif 4mzr title: Crystal structure of a polypeptide p53 mutant bound to DNA [more info...] Chain information for 4mzr #7 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-358 K | consensus DNA sense strand | L | consensus DNA anti-sense strand | Non-standard residues in 4mzr #7 --- ZN — zinc ion > matchmaker #7/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment score = 948.8 RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs: 2.117) > select add #7 15686 atoms, 16125 bonds, 130 pseudobonds, 1916 residues, 6 models selected > select subtract #3 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected > style sel stick Changed 8593 atom styles > show sel cartoons > hide sel atoms > matchmaker #7/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment score = 843.2 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs: 1.070) > hide #!2 models > hide #!3 models > show #!2 models > matchmaker #7/C to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment score = 933.2 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs: 0.889) > matchmaker #7/D to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment score = 948.8 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs: 2.118) > matchmaker #7/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment score = 948.8 RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs: 2.117) > select subtract #7 Nothing selected > matchmaker #7/C to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment score = 933.2 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs: 0.889) > matchmaker #7/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment score = 843.2 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs: 1.070) > matchmaker #7/D to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment score = 948.8 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs: 2.118) > open 4ibu fromDatabase pdb format mmcif Summary of feedback from opening 4ibu fetched from pdb --- note | Fetching compressed mmCIF 4ibu from http://files.rcsb.org/download/4ibu.cif 4ibu title: Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation T284R in sequence-specific complex with DNA [more info...] Chain information for 4ibu #8 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F G H | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | Non-standard residues in 4ibu #8 --- ACT — acetate ion EDO — 1,2-ethanediol (ethylene glycol) ZN — zinc ion 382 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 4ibv fromDatabase pdb format mmcif Summary of feedback from opening 4ibv fetched from pdb --- note | Fetching compressed mmCIF 4ibv from http://files.rcsb.org/download/4ibv.cif 4ibv title: Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R in sequence-specific complex with DNA [more info...] Chain information for 4ibv #9 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 94-293 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | Non-standard residues in 4ibv #9 --- EDO — 1,2-ethanediol (ethylene glycol) ZN — zinc ion 4ibv mmCIF Assemblies --- 1| author_and_software_defined_assembly 98 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 4ibw fromDatabase pdb format mmcif Summary of feedback from opening 4ibw fetched from pdb --- note | Fetching compressed mmCIF 4ibw from http://files.rcsb.org/download/4ibw.cif 4ibw title: Human p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R in sequence-specific complex with DNA [more info...] Chain information for 4ibw #10 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 94-293 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | Non-standard residues in 4ibw #10 --- EDO — 1,2-ethanediol (ethylene glycol) ZN — zinc ion 4ibw mmCIF Assemblies --- 1| author_defined_assembly 140 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 4hje fromDatabase pdb format mmcif Summary of feedback from opening 4hje fetched from pdb --- note | Fetching compressed mmCIF 4hje from http://files.rcsb.org/download/4hje.cif 4hje title: Crystal structure of p53 core domain in complex with DNA [more info...] Chain information for 4hje #11 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') | F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') | Non-standard residues in 4hje #11 --- ZN — zinc ion > select add #11 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected > select add #10 10147 atoms, 9266 bonds, 68 pseudobonds, 2240 residues, 6 models selected > select add #9 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected > select add #8 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected > select add #7 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected > style sel stick Changed 28777 atom styles > hide sel atoms > show sel cartoons > ui mousemode right select > select clear > matchmaker #11/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment score = 1018.3 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs: 0.530) > matchmaker #10/B to #2/B pairing ss Match chain (4ibw (#10) chain B) not compatible with BLOSUM-62 similarity matrix > hide #!11 models > hide #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > show #!2 models > matchmaker #10/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4ibw, chain A (#10), sequence alignment score = 1011.7 RMSD between 188 pruned atom pairs is 0.497 angstroms; (across all 195 pairs: 0.717) > show #!1 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > matchmaker #9/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4ibv, chain A (#9), sequence alignment score = 1000.1 RMSD between 185 pruned atom pairs is 0.508 angstroms; (across all 195 pairs: 1.235) > show #!9 models > show #!8 models > hide #!9 models > show #!9 models > matchmaker #8/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4ibu, chain B (#8), sequence alignment score = 1018 RMSD between 196 pruned atom pairs is 0.320 angstroms; (across all 198 pairs: 0.451) > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select subtract #1 Nothing selected > select add #10 2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected > select add #9 4121 atoms, 3717 bonds, 10 pseudobonds, 942 residues, 6 models selected > show #!11 models > matchmaker #11/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment score = 1018.3 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs: 0.530) > matchmaker #11/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4hje, chain A (#11), sequence alignment score = 1018.3 RMSD between 196 pruned atom pairs is 0.344 angstroms; (across all 198 pairs: 0.482) > select add #11 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected > select add #8 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected > select add #7 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected > select add #6 30709 atoms, 29107 bonds, 231 pseudobonds, 5860 residues, 17 models selected > select add #5 38490 atoms, 36414 bonds, 301 pseudobonds, 7415 residues, 20 models selected > select add #4 46525 atoms, 43695 bonds, 375 pseudobonds, 9248 residues, 31 models selected > select add #3 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected > select add #2 61828 atoms, 58416 bonds, 510 pseudobonds, 11999 residues, 45 models selected > select add #1 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected > style sel stick Changed 67656 atom styles > hide sel atoms > show sel cartoons > select clear > select O 18203 atoms, 12968 residues, 11 models selected > show sel atoms > select clear > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select add #2 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected > select add #3 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected > select add #5 28912 atoms, 27677 bonds, 260 pseudobonds, 5320 residues, 20 models selected > select add #4 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected > select add #6 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected > select add #7 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected > select add #8 55560 atoms, 52962 bonds, 492 pseudobonds, 10393 residues, 47 models selected > select add #9 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected > select add #10 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected > select add #11 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected > hide sel atoms > show sel atoms > hide sel cartoons > select H Nothing selected > show atoms > select hydroxyl 1506 atoms, 1466 residues, 11 models selected > show sel atoms > select add #1 7211 atoms, 5649 bonds, 55 pseudobonds, 2357 residues, 37 models selected > select subtract #1 1383 atoms, 1343 residues, 34 models selected > select clear > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select add #2 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected > select add #3 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected > select add #4 29166 atoms, 27651 bonds, 264 pseudobonds, 5598 residues, 20 models selected > select add #5 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected > select add #6 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected > select add #7 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected > select add #9 49421 atoms, 47442 bonds, 416 pseudobonds, 8960 residues, 47 models selected > select add #8 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected > select add #10 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected > select add #11 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected > show sel cartoons > hide sel atoms > open 3ts8 fromDatabase pdb format mmcif Summary of feedback from opening 3ts8 fetched from pdb --- note | Fetching compressed mmCIF 3ts8 from http://files.rcsb.org/download/3ts8.cif 3ts8 title: Crystal structure of a multidomain human p53 tetramer bound to the natural CDKN1A(p21) p53-response element [more info...] Chain information for 3ts8 #12 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 K | CDKN1A(p21) sense strand | L | CDKN1A(p21) anti-sense strand | Non-standard residues in 3ts8 #12 --- ZN — zinc ion > select clear > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected > style sel stick Changed 8621 atom styles > show sel cartoons > hide sel atoms > matchmaker #12/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment score = 893.7 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs: 1.399) > matchmaker #12/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment score = 947.1 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs: 2.430) > matchmaker #11/C to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 4hje, chain C (#11), sequence alignment score = 1018.3 RMSD between 196 pruned atom pairs is 0.349 angstroms; (across all 198 pairs: 0.485) > matchmaker #12/D to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment score = 950.1 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs: 2.431) > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!11 models > show #!2 models > hide #!11 models > matchmaker #12/A to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment score = 947.1 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs: 2.430) > matchmaker #12/B to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment score = 893.7 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs: 1.399) > matchmaker #12/C to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain C (#12), sequence alignment score = 939.3 RMSD between 192 pruned atom pairs is 0.573 angstroms; (across all 198 pairs: 0.928) > matchmaker #12/D to #2/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment score = 950.1 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs: 2.431) > hide #!12 models > show #!12 models > hide #!2 models > show #!2 models > matchmaker #12/L to #2/E pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment score = 23.5 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs: 3.750) > matchmaker #12/K to #2/E pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/K to 2ac0 #2/E Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain E (#2) with 3ts8, chain K (#12), sequence alignment score = 23.5 RMSD between 9 pruned atom pairs is 1.158 angstroms; (across all 12 pairs: 3.771) > matchmaker #12/L to #2/E pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment score = 23.5 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs: 3.750) > hide #!2 models > select clear > show #!11 models > matchmaker #11/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment score = 941.4 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs: 2.439) > matchmaker #11/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4hje, chain B (#11), sequence alignment score = 941.4 RMSD between 183 pruned atom pairs is 0.461 angstroms; (across all 198 pairs: 2.441) > matchmaker #11/C to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4hje, chain C (#11), sequence alignment score = 941.4 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs: 2.433) > matchmaker #11/D to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4hje, chain D (#11), sequence alignment score = 941.4 RMSD between 183 pruned atom pairs is 0.466 angstroms; (across all 198 pairs: 2.450) > matchmaker #11/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment score = 941.4 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs: 2.439) > hide #!11 models > show #!10 models > matchmaker #10/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibw, chain A (#10), sequence alignment score = 942.4 RMSD between 184 pruned atom pairs is 0.577 angstroms; (across all 197 pairs: 2.357) > hide #!10 models > show #!9 models > matchmaker #9/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibv, chain A (#9), sequence alignment score = 944 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs: 2.583) > hide #!9 models > show #!8 models > matchmaker #8/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment score = 928.3 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs: 2.491) > hide #!12 models > show #!12 models > matchmaker #8/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment score = 915.7 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs: 2.406) > matchmaker #8/D to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibu, chain D (#8), sequence alignment score = 910.9 RMSD between 187 pruned atom pairs is 0.556 angstroms; (across all 196 pairs: 2.334) > show #!9 models > hide #!9 models > matchmaker #8/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment score = 915.7 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs: 2.406) > matchmaker #8/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment score = 928.3 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs: 2.491) > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!8 models > show #!7 models > matchmaker #7/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4mzr, chain A (#7), sequence alignment score = 1190.7 RMSD between 226 pruned atom pairs is 0.355 angstroms; (across all 234 pairs: 0.747) > show #!6 models > hide #!7 models > matchmaker #6/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 5bua, chain A (#6), sequence alignment score = 951.9 RMSD between 184 pruned atom pairs is 0.599 angstroms; (across all 200 pairs: 2.577) > hide #!6 models > show #!5 models > matchmaker #5/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 2ata, chain A (#5), sequence alignment score = 945.3 RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 197 pairs: 2.459) > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!4 models > hide #!5 models > matchmaker #4/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 2ahi, chain A (#4), sequence alignment score = 947.7 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs: 2.473) > show #!5 models > hide #!5 models > hide #!4 models > show #!3 models > matchmaker #3/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 5lgy, chain A (#3), sequence alignment score = 944.4 RMSD between 185 pruned atom pairs is 0.528 angstroms; (across all 197 pairs: 2.320) > hide #!3 models > show #!2 models > matchmaker #2/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 2ac0, chain A (#2), sequence alignment score = 950.7 RMSD between 187 pruned atom pairs is 0.618 angstroms; (across all 198 pairs: 2.423) > hide #!2 models > show #!1 models > matchmaker #1/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1tup, chain A (#1), sequence alignment score = 931.1 RMSD between 184 pruned atom pairs is 0.596 angstroms; (across all 196 pairs: 2.426) > matchmaker #1/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment score = 919.1 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs: 2.414) > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select subtract #1 Nothing selected > show #!11 models > hide #!11 models > show #!11 models > hide #!1 models > hide #!12 models > hide #!11 models > show #!12 models > show #!11 models > hide #!11 models > show #!1 models > matchmaker #1/C to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1tup, chain C (#1), sequence alignment score = 913.7 RMSD between 182 pruned atom pairs is 0.634 angstroms; (across all 195 pairs: 2.442) > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!12 models > show #!12 models > matchmaker #1/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment score = 919.1 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs: 2.414) > hide #!1 models > show #!6 models > show #!3 models > hide #!12 models > show #!12 models > show #!11 models > show #!10 models > show #!9 models > show #!8 models > hide #!6 models > hide #!3 models > hide #!12 models > hide #!11 models > hide #!8 models > hide #!9 models > show #!9 models > show #!8 models > open /Users/kompa012/Desktop/P53/4ibv.pdb1 4ibv.pdb1 title: Human P53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R In sequence-specific complex with DNA [more info...] 98 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 4ibv.pdb1 --- Chain | Description 13.1/A | No description available 13.2/A | No description available 13.1/B | No description available 13.2/B | No description available 98 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!13 models > hide #!13.1 models > show #!13.1 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!13.2 models > show #!13.2 models > hide #!13.1 models > show #!13.1 models > hide #!13.2 models > show #!13.2 models > show #!12 models > matchmaker #13.1/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.1), sequence alignment score = 944 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs: 2.583) No reference and/or match structure/chain chosen > hide #!13 models > matchmaker #13.2/B to #12/B pairing ss Match chain (4ibv.pdb1 (#13.2) chain B) not compatible with BLOSUM-62 similarity matrix > show #!13 models > matchmaker #13.2/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.2), sequence alignment score = 923.8 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs: 2.583) No reference and/or match structure/chain chosen > matchmaker #13.2/A to #12/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain B (#12) with 4ibv.pdb1, chain A (#13.2), sequence alignment score = 889.6 RMSD between 178 pruned atom pairs is 0.879 angstroms; (across all 197 pairs: 1.492) > hide #!12 models > close #13 > show #!12 models > show #!11 models > show #!8 models > hide #!8 models > hide #!11 models > show #!7 models > hide #!7 models > open 3kmd fromDatabase pdb format mmcif Summary of feedback from opening 3kmd fetched from pdb --- note | Fetching compressed mmCIF 3kmd from http://files.rcsb.org/download/3kmd.cif 3kmd title: Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer [more info...] Chain information for 3kmd #13 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 E F | 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' | Non-standard residues in 3kmd #13 --- ZN — zinc ion > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected > style sel sphere Changed 7587 atom styles > style sel stick Changed 7587 atom styles > show sel cartoons > hide sel atoms > select clear > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > matchmaker #13/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3kmd, chain A (#13), sequence alignment score = 938.4 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs: 2.352) > hide #!12 models > show #!12 models > hide #!13 models > open 3igk fromDatabase pdb format mmcif Summary of feedback from opening 3igk fetched from pdb --- note | Fetching compressed mmCIF 3igk from http://files.rcsb.org/download/3igk.cif 3igk title: Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 2) [more info...] Chain information for 3igk #14 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 94-293 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | Non-standard residues in 3igk #14 --- ZN — zinc ion 3igk mmCIF Assemblies --- 1| author_and_software_defined_assembly 57 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 3igl fromDatabase pdb format mmcif Summary of feedback from opening 3igl fetched from pdb --- note | Fetching compressed mmCIF 3igl from http://files.rcsb.org/download/3igl.cif 3igl title: Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 1) [more info...] Chain information for 3igl #15 --- Chain | Description | UniProt A | Cellular tumor antigen p53 | P53_HUMAN 94-293 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | Non-standard residues in 3igl #15 --- EDO — 1,2-ethanediol (ethylene glycol) ZN — zinc ion 3igl mmCIF Assemblies --- 1| author_and_software_defined_assembly 28 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 3kz8 fromDatabase pdb format mmcif Summary of feedback from opening 3kz8 fetched from pdb --- notes | Fetching compressed mmCIF 3kz8 from http://files.rcsb.org/download/3kz8.cif Fetching CCD IOD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif 3kz8 title: Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3) [more info...] Chain information for 3kz8 #16 --- Chain | Description | UniProt A B | Cellular tumor antigen p53 | P53_HUMAN 94-293 C | DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') | Non-standard residues in 3kz8 #16 --- IOD — iodide ion ZN — zinc ion 3kz8 mmCIF Assemblies --- 1| author_defined_assembly 87 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #14/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3igk, chain A (#14), sequence alignment score = 934.3 RMSD between 181 pruned atom pairs is 0.672 angstroms; (across all 197 pairs: 2.601) > matchmaker #15/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3igl, chain A (#15), sequence alignment score = 944.1 RMSD between 182 pruned atom pairs is 0.630 angstroms; (across all 197 pairs: 2.594) > matchmaker #16/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3kz8, chain A (#16), sequence alignment score = 948.3 RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs: 2.497) > hide #!14 models > hide #!15 models > hide #!12 models > show #!12 models > hide #!16 models > open 3q05 fromDatabase pdb format mmcif Summary of feedback from opening 3q05 fetched from pdb --- note | Fetching compressed mmCIF 3q05 from http://files.rcsb.org/download/3q05.cif 3q05 title: An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity [more info...] Chain information for 3q05 #17 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 K | DNA (26-MER) | L | DNA (26-MER) | Non-standard residues in 3q05 #17 --- ZN — zinc ion > open 3q06 fromDatabase pdb format mmcif Summary of feedback from opening 3q06 fetched from pdb --- note | Fetching compressed mmCIF 3q06 from http://files.rcsb.org/download/3q06.cif 3q06 title: An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity [more info...] Chain information for 3q06 #18 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 96-292 321-354 K | DNA (26-MER) | L | DNA (26-MER) | Non-standard residues in 3q06 #18 --- ZN — zinc ion > select add #17 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected > select add #18 17133 atoms, 17540 bonds, 136 pseudobonds, 2133 residues, 6 models selected > style sel stick Changed 17133 atom styles > hide sel atoms > show sel cartoons > matchmaker #17/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3q05, chain A (#17), sequence alignment score = 1171 RMSD between 223 pruned atom pairs is 0.512 angstroms; (across all 234 pairs: 1.303) > matchmaker #18/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3q06, chain A (#18), sequence alignment score = 1133.5 RMSD between 221 pruned atom pairs is 0.602 angstroms; (across all 230 pairs: 1.295) > select subtract #17 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected > select subtract #18 Nothing selected > hide #!17 models > hide #!18 models > open 3d0a fromDatabase pdb format mmcif Summary of feedback from opening 3d0a fetched from pdb --- warnings | Atom P has no neighbors to form bonds with according to residue template for DG /F:3 Atom CE has no neighbors to form bonds with according to residue template for MET /B:243 note | Fetching compressed mmCIF 3d0a from http://files.rcsb.org/download/3d0a.cif 3d0a title: Human p53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA [more info...] Chain information for 3d0a #19 --- Chain | Description | UniProt A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 E F G H | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') | Non-standard residues in 3d0a #19 --- ZN — zinc ion 3d0a mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 224 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected > style sel stick Changed 7633 atom styles > hide sel atoms > show sel cartoons > matchmaker #19/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3d0a, chain A (#19), sequence alignment score = 917.5 RMSD between 185 pruned atom pairs is 0.571 angstroms; (across all 196 pairs: 2.397) > hide #!12 models > show #!12 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!13 models > show #!14 models > show #!16 models > show #!15 models > show #!17 models > show #!18 models > select clear > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > select subtract #1 Nothing selected > hide #!3 models > hide #!2 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > show #!12 models > hide #!12 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B Alignment identifier is 1/B > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected > show sel surfaces Cell requested for row 12 is out of bounds for table with 21 rows! Resizing table model. > hide sel surfaces > select subtract #1.4 4306 atoms, 4092 bonds, 51 pseudobonds, 820 residues, 8 models selected > select subtract #1.7 3871 atoms, 3602 bonds, 8 pseudobonds, 799 residues, 6 models selected > select subtract #1.6 3451 atoms, 3134 bonds, 8 pseudobonds, 778 residues, 5 models selected > hide sel cartoons > select add #1 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 5 models selected > select subtract #1 5 models selected > select add #1.7 435 atoms, 21 residues, 1 model selected > select add #1.6 855 atoms, 42 residues, 2 models selected > select add #1.4 2377 atoms, 236 residues, 3 models selected > hide sel cartoons > show sel atoms > select clear > select > #1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274 530 atoms, 532 bonds, 64 residues, 1 model selected > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > save ""/Users/kompa012/Desktop/P53/Before mutation.cxs"" > ui tool show Rotamers > swapaa interactive sel SER rotLib Dunbrack 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > swapaa interactive sel SER rotLib Dynameomics 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > hide sel atoms > show sel atoms > style sel stick Changed 12 atom styles > style sel stick Changed 12 atom styles > style sel ball Changed 12 atom styles > style sel stick Changed 12 atom styles > style (#!1 & sel) ringFill thin Changed 1 residue ring style > style (#!1 & sel) stick Changed 12 atom styles > style (#!1 & sel) ringFill off Changed 1 residue ring style > color (#!1 & sel) byhetero > select add #1.8 24 atoms, 21 bonds, 4 residues, 6 models selected > select subtract #1.4 12 atoms, 9 bonds, 3 residues, 5 models selected > select add #1.9 24 atoms, 18 bonds, 6 residues, 8 models selected > close #1.8-9 > select #1/B:220@CA 1 atom, 1 residue, 1 model selected > select #1/B:220@CA 1 atom, 1 residue, 1 model selected > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > swapaa interactive sel SER rotLib Richardson.common 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > hide sel atoms > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > swapaa interactive sel TYR rotLib Richardson.common 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans Changed 40 bond radii > select add #1.9 52 atoms, 52 bonds, 5 residues, 7 models selected > select add #1.8 64 atoms, 61 bonds, 8 residues, 11 models selected > close #1.8-9 > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > swapaa interactive sel TYR rotLib Richardson.mode 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans Changed 40 bond radii > close #1.8 > swapaa interactive sel SER rotLib Richardson.mode 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > hide #1.8.3 models > hide #1.8.2 models > close #1.8 > swapaa interactive sel SER rotLib Dunbrack 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > show sel atoms > hide sel atoms > show sel atoms > hide #1.8.3 models > hide #1.8.2 models > hide sel atoms [Repeated 1 time(s)] > show sel atoms > hide sel atoms [Repeated 1 time(s)] > select #!1/B:220@CD2 1 atom, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > select #!1/B:220@CG 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/B:220@CZ 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/B:220@CE2 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/B:220@OH 1 atom, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > select #!1/B:220@CE1 1 atom, 1 residue, 1 model selected > hide sel atoms > select #!1/B:220@CD1 1 atom, 1 residue, 1 model selected > hide sel atoms > style sel ball Changed 0 atom styles > style sel ball Changed 0 atom styles > style sel sphere Changed 0 atom styles > style sel sphere Changed 0 atom styles > select add #1.8.1 4 atoms, 3 bonds, 1 residue, 1 model selected > style sel sphere Changed 4 atom styles > style sel ball Changed 4 atom styles > style sel stick Changed 4 atom styles > select clear > select add #1.8.1 4 atoms, 3 bonds, 1 residue, 1 model selected > style sel sphere Changed 4 atom styles > select subtract #1.8.1 Nothing selected > select add #1.8.1 4 atoms, 3 bonds, 1 residue, 1 model selected > show #1.8.2 models > select add #1.8.2 8 atoms, 6 bonds, 2 residues, 2 models selected > style sel stick Changed 8 atom styles > show #1.8.3 models > select add #1.8 12 atoms, 9 bonds, 3 residues, 4 models selected > select subtract #1.8 Nothing selected > hide #!1.8 models > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) byhetero > select #1/B:280-281 19 atoms, 18 bonds, 2 residues, 1 model selected > select #1/B:280-284 48 atoms, 47 bonds, 5 residues, 1 model selected > select subtract #1.4 1 model selected > select add #1.3 1535 atoms, 196 residues, 1 model selected > show sel cartoons > select #1/A:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select subtract #1.3 1 model selected > select add #1.3 1535 atoms, 196 residues, 1 model selected > hide sel cartoons > select add #1.5 3064 atoms, 391 residues, 2 models selected > show sel cartoons > select subtract #1.5 1535 atoms, 196 residues, 3 models selected > hide sel cartoons > select #1/C:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select subtract #1.5 1 model selected > select add #1.5 1529 atoms, 195 residues, 1 model selected > hide sel cartoons > select add #1.3 3064 atoms, 391 residues, 2 models selected > select subtract #1.3 1529 atoms, 195 residues, 3 models selected > select add #1.4 3051 atoms, 389 residues, 2 models selected > select subtract #1.5 1522 atoms, 194 residues, 3 models selected > show sel cartoons > select clear > select #1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > swapaa interactive sel GLN rotLib Dunbrack 1tup #1/B ARG 282: phi -80.7, psi -38.2 trans Changed 648 bond radii > select add #1.8.108 18 atoms, 16 bonds, 2 residues, 3 models selected > select add #1.8.107 25 atoms, 22 bonds, 3 residues, 4 models selected > select add #1.8.106 32 atoms, 28 bonds, 4 residues, 5 models selected > select add #1.8.105 39 atoms, 34 bonds, 5 residues, 6 models selected > select add #1.8.104 46 atoms, 40 bonds, 6 residues, 7 models selected > select add #1.8.103 53 atoms, 46 bonds, 7 residues, 8 models selected > select add #1.8.102 60 atoms, 52 bonds, 8 residues, 9 models selected > select add #1.8.101 67 atoms, 58 bonds, 9 residues, 10 models selected > select add #1.8 767 atoms, 658 bonds, 109 residues, 111 models selected > select subtract #1.8 11 atoms, 10 bonds, 1 residue, 2 models selected > select add #1.8 767 atoms, 658 bonds, 109 residues, 111 models selected > select subtract #1.8.39 760 atoms, 652 bonds, 108 residues, 110 models selected > select subtract #1.8.38 753 atoms, 646 bonds, 107 residues, 109 models selected > select add #1.8.38 760 atoms, 652 bonds, 108 residues, 110 models selected > select subtract #1.8.40 753 atoms, 646 bonds, 107 residues, 109 models selected > select add #1.8.40 760 atoms, 652 bonds, 108 residues, 110 models selected > hide sel atoms > select #!1/B:282-283 22 atoms, 21 bonds, 2 residues, 1 model selected > select #!1/B:282-283 22 atoms, 21 bonds, 2 residues, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select add #1.8.40 18 atoms, 16 bonds, 2 residues, 3 models selected > show sel atoms > select add #1.8.41 25 atoms, 22 bonds, 3 residues, 4 models selected > show sel atoms > select subtract #1.8.40 18 atoms, 16 bonds, 2 residues, 3 models selected > select add #1.8.40 25 atoms, 22 bonds, 3 residues, 4 models selected > select subtract #1.8.41 18 atoms, 16 bonds, 2 residues, 3 models selected > hide sel atoms > select add #1.8 767 atoms, 658 bonds, 109 residues, 111 models selected > hide sel atoms > select #!1/B:282-289 72 atoms, 71 bonds, 8 residues, 1 model selected > select #!1/B:282-289 72 atoms, 71 bonds, 8 residues, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > swapaa interactive sel CYS rotLib Dunbrack 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans Changed 9 bond radii > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected > select subtract #1 5 models selected > hide #!1 models > show #!1 models > show #!2 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > show sel atoms > select clear > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!12 models > show #!11 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected > select subtract #1 5 models selected > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected > select add #4 15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 6 models selected > select add #5 22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 17 models selected > select add #6 24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 27 models selected > select add #7 33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 30 models selected > select add #8 41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 33 models selected > select add #10 43694 atoms, 41785 bonds, 364 pseudobonds, 8045 residues, 36 models selected > select add #9 45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 39 models selected > select add #11 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected > select add #12 62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 45 models selected > select add #13 69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 48 models selected > select add #14 71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 51 models selected > select add #15 74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 54 models selected > select add #16 77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 57 models selected > select add #17 86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 60 models selected > select add #18 94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 63 models selected > select add #19 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 67 models selected > show sel atoms > select clear > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!12 models > show #!12 models > select add #12 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected > hide sel cartoons > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > ui mousemode right distance > distance #!1/B:248@NH2 #12/L:35@N2 Distance between 1tup #!1/B ARG 248 NH2 and 3ts8 #12/L DG 35 N2: 5.304Å > distance #12/A:248@NH2 #!1/F:1113@N2 Distance between 3ts8 #12/A ARG 248 NH2 and 1tup #!1/F DG 1113 N2: 5.414Å > hide #!12 models > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected > select O 30159 atoms, 21045 residues, 127 models selected > show (#1.8.1-108#!1 & sel) target ab > ui mousemode right select > select clear > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!12 models > hide #!1 models > select #12/A:248@CB 1 atom, 1 residue, 1 model selected > select #12/A:248@CA 1 atom, 1 residue, 1 model selected > select #12/A:248@CA 1 atom, 1 residue, 1 model selected > show #!1 models > hide #!1 models > select #12/A:248@CA 1 atom, 1 residue, 1 model selected > select #12/A:248@CA 1 atom, 1 residue, 1 model selected > select #12/C:283@NH2 1 atom, 1 residue, 1 model selected Drag select of 1 atoms, 1 bonds > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A > select #12/A:248-249 22 atoms, 21 bonds, 2 residues, 1 model selected > select #12/A:248-249 22 atoms, 21 bonds, 2 residues, 1 model selected > select #12/A:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected > select clear > select O 30159 atoms, 21045 residues, 127 models selected > show (#!12 & sel) target ab > select clear > show #!1 models > select add #20 2 pseudobonds, 2 models selected > close #20 > select #12/A:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:248 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!12 models > show #!12 models > hide #!1 models > hide #!12 models > show #!1 models > show #!12 models > hide #!1 models > show #!1 models > hide #!12 models > show #!2 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!3 models > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!1 models > show #!1 models > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected > show sel cartoons > show #!2 models > show #!3 models > hide #!2 models > select clear > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!19 models > show #!18 models > hide #!1 models > hide #!18 models > hide #!19 models > show #!19 models > show #!18 models > show #!17 models > hide #!3 models > show #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > select add #16 3708 atoms, 3509 bonds, 10 pseudobonds, 726 residues, 5 models selected > style sel & #!16 stick Changed 3697 atom styles > hide sel & #!16 cartoons [Repeated 1 time(s)] > nucleotides sel & #!16 atoms > style nucleic & sel & #!16 stick Changed 410 atom styles > show #!15 models > hide #!16 models > select add #15 5817 atoms, 5336 bonds, 15 pseudobonds, 1277 residues, 8 models selected > select subtract #16 2120 atoms, 1837 bonds, 5 pseudobonds, 552 residues, 5 models selected > nucleotides sel & #!15 atoms > style nucleic & sel & #!15 stick Changed 225 atom styles > hide sel & #!15 cartoons > show #!16 models > show #!14 models > select add #14 4213 atoms, 3651 bonds, 10 pseudobonds, 1099 residues, 8 models selected > select subtract #15 2104 atoms, 1824 bonds, 5 pseudobonds, 548 residues, 5 models selected > nucleotides sel & #!14 atoms > style nucleic & sel & #!14 stick Changed 225 atom styles > hide sel & #!14 cartoons > show #!13 models > select subtract #14 11 atoms, 10 bonds, 1 residue, 2 models selected > select add #13 7598 atoms, 7308 bonds, 64 pseudobonds, 1366 residues, 5 models selected > hide sel & #!13 cartoons > hide #!14 models > hide #!15 models > hide #!16 models > show #!12 models > hide #!13 models > show #!11 models > show #!10 models > show #!9 models > show #!8 models > show #!7 models > show #!6 models > select add #12 16219 atoms, 16108 bonds, 135 pseudobonds, 2463 residues, 8 models selected > select subtract #13 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected > select add #11 16607 atoms, 16196 bonds, 134 pseudobonds, 2776 residues, 8 models selected > select add #10 18779 atoms, 18076 bonds, 139 pseudobonds, 3338 residues, 11 models selected > select add #9 20728 atoms, 19913 bonds, 144 pseudobonds, 3718 residues, 14 models selected > select add #8 28816 atoms, 27270 bonds, 225 pseudobonds, 5531 residues, 17 models selected > select add #6 30748 atoms, 29105 bonds, 229 pseudobonds, 5897 residues, 19 models selected > select add #7 39341 atoms, 37917 bonds, 302 pseudobonds, 6958 residues, 22 models selected > nucleotides sel & #!6-12 atoms > style nucleic & sel & #!6-12 stick Changed 4560 atom styles > hide sel & #!6-12 cartoons > hide #!6 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > select add #13 46928 atoms, 45215 bonds, 366 pseudobonds, 8323 residues, 25 models selected > select add #14 49021 atoms, 47029 bonds, 371 pseudobonds, 8870 residues, 28 models selected > select add #15 51130 atoms, 48856 bonds, 376 pseudobonds, 9421 residues, 31 models selected > select add #16 54827 atoms, 52355 bonds, 386 pseudobonds, 10146 residues, 34 models selected > select add #17 63504 atoms, 61155 bonds, 463 pseudobonds, 11299 residues, 37 models selected > select add #18 71960 atoms, 69895 bonds, 522 pseudobonds, 12279 residues, 40 models selected > select add #19 79593 atoms, 77007 bonds, 603 pseudobonds, 13857 residues, 44 models selected > hide sel & #!7-19 cartoons > nucleotides sel & #!7-19 atoms > style nucleic & sel & #!7-19 stick Changed 9010 atom styles > show #!6 models > select subtract #6 77661 atoms, 75172 bonds, 599 pseudobonds, 13491 residues, 42 models selected > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > select add #2 85871 atoms, 82580 bonds, 677 pseudobonds, 15387 residues, 45 models selected > select add #1 92456 atoms, 88876 bonds, 732 pseudobonds, 16511 residues, 168 models selected > select add #3 99549 atoms, 96189 bonds, 789 pseudobonds, 17366 residues, 175 models selected > select add #4 107584 atoms, 103470 bonds, 863 pseudobonds, 19199 residues, 178 models selected > select add #5 115365 atoms, 110777 bonds, 933 pseudobonds, 20754 residues, 189 models selected > select add #6 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models selected > select subtract #7 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models selected > select add #7 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models selected > hide #!7 models > select subtract #7 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models selected > hide #!8 models > show #!8 models > show #!7 models > select add #7 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models selected > hide sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 13700 atom styles > hide #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!10 models > hide #!10 models > hide #!1 models > hide #!4 models > hide #!11 models > hide #!5 models > hide #!7 models > hide #!17 models > hide #!9 models > hide #!12 models > show sel & #!2-3,6,13-16,18-19 surfaces > hide sel & #!2-3,6,13-16,18-19 surfaces > hide #!19 models > show #!19 models > hide #!19 models > hide #!18 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!6 models > hide #!3 models > select clear > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > select subtract #2.10 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected > select subtract #2.9 7724 atoms, 6864 bonds, 44 pseudobonds, 1872 residues, 10 models selected > select subtract #2.8 7481 atoms, 6592 bonds, 16 pseudobonds, 1860 residues, 8 models selected > select subtract #2.7 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected > select add #2.9 7481 atoms, 6320 bonds, 16 pseudobonds, 1860 residues, 6 models selected > select subtract #2.9 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected > select subtract #2.5 5709 atoms, 4756 bonds, 12 pseudobonds, 1653 residues, 6 models selected > select add #2.5 7238 atoms, 4756 bonds, 12 pseudobonds, 1848 residues, 5 models selected > select subtract #2.3 5686 atoms, 3169 bonds, 8 pseudobonds, 1649 residues, 6 models selected > hide sel atoms > select add #2.10 5929 atoms, 3169 bonds, 8 pseudobonds, 1661 residues, 5 models selected > select add #2.9 6172 atoms, 3169 bonds, 8 pseudobonds, 1673 residues, 6 models selected > select subtract #2.6 4618 atoms, 1580 bonds, 4 pseudobonds, 1475 residues, 7 models selected > select subtract #2.5 3089 atoms, 1580 bonds, 4 pseudobonds, 1280 residues, 6 models selected > select subtract #2.4 1544 atoms, 1082 residues, 4 models selected > hide sel atoms > select add #1 8140 atoms, 6306 bonds, 55 pseudobonds, 2207 residues, 119 models selected > select subtract #1 1544 atoms, 1082 residues, 8 models selected > show #!1 models > hide #!1 models > hide #!2 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected > select subtract #2 8 models selected > show #!3 models > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected > show #!1 models > hide #!1 models > select subtract #3.8 6666 atoms, 6835 bonds, 16 pseudobonds, 834 residues, 8 models selected > select subtract #3.7 6238 atoms, 6354 bonds, 16 pseudobonds, 813 residues, 7 models selected > select subtract #3.3 4686 atoms, 4767 bonds, 12 pseudobonds, 616 residues, 6 models selected > hide sel atoms > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected > select subtract #3 6 models selected Cell requested for row 3 is out of bounds for table with 27 rows! Resizing table model. > show #!4 models > select add #4 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 3 models selected > select subtract #4.10 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected > select add #4.10 8035 atoms, 7009 bonds, 42 pseudobonds, 1833 residues, 10 models selected > select subtract #4.10 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected > select subtract #4.9 7549 atoms, 6737 bonds, 42 pseudobonds, 1809 residues, 10 models selected > select subtract #4.8 7325 atoms, 6486 bonds, 16 pseudobonds, 1798 residues, 8 models selected > select subtract #4.7 7123 atoms, 6260 bonds, 16 pseudobonds, 1788 residues, 7 models selected > select subtract #4.3 5572 atoms, 4674 bonds, 12 pseudobonds, 1589 residues, 6 models selected > hide sel atoms > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > show #!3 models > select add #4 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 6 models selected > select subtract #4 8 models selected > select add #4.10 243 atoms, 12 residues, 1 model selected > select add #4.9 486 atoms, 24 residues, 2 models selected > hide sel atoms > select add #4 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected > select subtract #4 8 models selected > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!4 models > select add #5.10 223 atoms, 11 residues, 1 model selected > select add #5.9 466 atoms, 23 residues, 2 models selected > select add #5.6 2002 atoms, 221 residues, 3 models selected > select add #5.5 3537 atoms, 417 residues, 4 models selected > select add #5.4 5089 atoms, 616 residues, 5 models selected > hide sel atoms > show #!4 models > hide #!4 models > select add #5 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected > select subtract #5 8 models selected > show #!6 models > hide #!5 models > show #!7 models > hide #!6 models > select add #7 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #7 6 models selected > select add #7.8 535 atoms, 26 residues, 1 model selected > select add #7.7 1060 atoms, 52 residues, 2 models selected > select subtract #7.7 535 atoms, 26 residues, 3 models selected > select subtract #7.8 1 model selected > select add #7.6 1865 atoms, 234 residues, 1 model selected > select add #7.5 3730 atoms, 468 residues, 2 models selected > select add #7.4 5595 atoms, 702 residues, 3 models selected > hide sel atoms > show #!6 models > hide #!6 models > select add #7 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected > select subtract #7 6 models selected Cell requested for row 7 is out of bounds for table with 27 rows! Resizing table model. > show #!8 models > hide #!7 models > select add #8 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected > select add #9 10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 6 models selected > select add #10 12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 9 models selected > select add #11 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected > show sel & #!8 surfaces > hide sel & #!8 surfaces > select subtract #9 18235 atoms, 16623 bonds, 149 pseudobonds, 4053 residues, 17 models selected > select subtract #10 16063 atoms, 14743 bonds, 144 pseudobonds, 3491 residues, 14 models selected > select subtract #11 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 11 models selected > select subtract #8.10 7845 atoms, 7085 bonds, 47 pseudobonds, 1801 residues, 11 models selected > select subtract #8.9 7602 atoms, 6813 bonds, 47 pseudobonds, 1789 residues, 10 models selected > select subtract #8.6 6083 atoms, 5260 bonds, 43 pseudobonds, 1593 residues, 9 models selected > select subtract #8.5 4569 atoms, 3711 bonds, 39 pseudobonds, 1398 residues, 8 models selected > select subtract #8.4 3028 atoms, 2135 bonds, 35 pseudobonds, 1200 residues, 7 models selected > hide sel atoms > select subtract #8.3 1483 atoms, 555 bonds, 31 pseudobonds, 1003 residues, 5 models selected > select add #8.4 3024 atoms, 555 bonds, 31 pseudobonds, 1201 residues, 4 models selected > select add #8.5 4538 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 5 models selected > select add #8.6 6057 atoms, 555 bonds, 31 pseudobonds, 1592 residues, 6 models selected > hide sel atoms > select add #8.3 7602 atoms, 555 bonds, 31 pseudobonds, 1789 residues, 7 models selected > select subtract #8.4 6061 atoms, 555 bonds, 31 pseudobonds, 1591 residues, 8 models selected > select subtract #8.5 4547 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 7 models selected > select subtract #8.6 3028 atoms, 555 bonds, 31 pseudobonds, 1200 residues, 6 models selected > select subtract #8.7 2807 atoms, 308 bonds, 1189 residues, 4 models selected > select subtract #8.8 2580 atoms, 54 bonds, 1178 residues, 3 models selected > show sel atoms > show #!7 models > hide #!7 models > select add #8.10 2823 atoms, 54 bonds, 1190 residues, 2 models selected > select add #8.9 3066 atoms, 54 bonds, 1202 residues, 3 models selected > select subtract #8.3 1521 atoms, 54 bonds, 1005 residues, 4 models selected > hide sel atoms > select add #8.8 1748 atoms, 54 bonds, 1016 residues, 3 models selected > select add #8.7 1969 atoms, 54 bonds, 1027 residues, 4 models selected > select subtract #8.9 1726 atoms, 54 bonds, 1015 residues, 5 models selected > select subtract #8.10 1483 atoms, 54 bonds, 1003 residues, 4 models selected > show sel atoms > select clear > hide #!8 models > show #!10 models > show #!9 models > show #!8 models > hide #!8 models > hide #!9 models > hide #!10 models > show #!11 models > select add #11 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > select subtract #11.8 7548 atoms, 6909 bonds, 16 pseudobonds, 1657 residues, 8 models selected > select add #11.8 7975 atoms, 6909 bonds, 16 pseudobonds, 1678 residues, 7 models selected > select subtract #11.3 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected > select add #11.3 7975 atoms, 5302 bonds, 12 pseudobonds, 1678 residues, 7 models selected > select subtract #11.3 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected > select subtract #11.8 5977 atoms, 5302 bonds, 12 pseudobonds, 1457 residues, 7 models selected > select subtract #11.7 5549 atoms, 4821 bonds, 12 pseudobonds, 1436 residues, 6 models selected > hide sel atoms > show #!10 models > hide #!10 models > select add #11 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 6 models selected > select subtract #11 6 models selected > show #!12 models > hide #!11 models > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #12.3 6758 atoms, 6897 bonds, 67 pseudobonds, 863 residues, 9 models selected > select subtract #12.8 6232 atoms, 6310 bonds, 12 pseudobonds, 837 residues, 7 models selected > select subtract #12.7 5698 atoms, 5709 bonds, 12 pseudobonds, 811 residues, 6 models selected > hide sel atoms > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!12 models > show #!13 models > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected > select subtract #12 6 models selected > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected > select subtract #13.3 6016 atoms, 5691 bonds, 60 pseudobonds, 1165 residues, 9 models selected > select subtract #13.8 5628 atoms, 5256 bonds, 12 pseudobonds, 1146 residues, 7 models selected > select subtract #13.7 5240 atoms, 4821 bonds, 12 pseudobonds, 1127 residues, 6 models selected > hide sel atoms > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected > select subtract #13 6 models selected > show #!14 models > hide #!13 models > show #!15 models > hide #!14 models > show #!16 models > hide #!15 models > select add #16 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected > select subtract #16.3 2211 atoms, 1979 bonds, 5 pseudobonds, 530 residues, 6 models selected > select subtract #16.5 1801 atoms, 1520 bonds, 5 pseudobonds, 510 residues, 5 models selected > hide sel atoms > select add #16 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected > select subtract #16 3 models selected > show #!17 models > hide #!16 models > select add #17 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #17.3 6814 atoms, 6897 bonds, 73 pseudobonds, 919 residues, 9 models selected > select subtract #17.8 6281 atoms, 6299 bonds, 12 pseudobonds, 893 residues, 7 models selected > select subtract #17.7 5754 atoms, 5709 bonds, 12 pseudobonds, 867 residues, 6 models selected > hide sel atoms > select add #17 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected > select subtract #17 6 models selected Cell requested for row 17 is out of bounds for table with 27 rows! Resizing table model. > show #!18 models > hide #!17 models > select add #18 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected > select subtract #18.3 6608 atoms, 6852 bonds, 55 pseudobonds, 749 residues, 9 models selected > select subtract #18.8 6075 atoms, 6254 bonds, 12 pseudobonds, 723 residues, 7 models selected > select subtract #18.7 5548 atoms, 5664 bonds, 12 pseudobonds, 697 residues, 6 models selected > hide sel atoms > hide #!18 models > select add #18 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected > select subtract #18 6 models selected > show #!19 models > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected > select subtract #19.11 7406 atoms, 6860 bonds, 46 pseudobonds, 1566 residues, 12 models selected > select subtract #19.10 7163 atoms, 6588 bonds, 46 pseudobonds, 1554 residues, 11 models selected > select subtract #19.4 5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 10 models selected > select add #19.10 5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected > select add #19.11 6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected > select subtract #19.9 5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected > select subtract #19.8 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected > hide sel atoms > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected > select subtract #19 8 models selected > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!8 models > show #!7 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > show #!15 models > show #!16 models > show #!17 models > show #!18 models > select > #!1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274 530 atoms, 532 bonds, 64 residues, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select O 30159 atoms, 21045 residues, 127 models selected > hide sel atoms > show sel atoms [Repeated 1 time(s)] > select add #1 35149 atoms, 6306 bonds, 55 pseudobonds, 21051 residues, 230 models selected > select add #2 40862 atoms, 13714 bonds, 133 pseudobonds, 21058 residues, 232 models selected > select add #3 46517 atoms, 21027 bonds, 190 pseudobonds, 21062 residues, 234 models selected > select add #4 52139 atoms, 28308 bonds, 264 pseudobonds, 21070 residues, 236 models selected > select add #5 57787 atoms, 35615 bonds, 334 pseudobonds, 21078 residues, 238 models selected > select add #6 59208 atoms, 37450 bonds, 338 pseudobonds, 21079 residues, 239 models selected > select add #7 66012 atoms, 46262 bonds, 411 pseudobonds, 21083 residues, 241 models selected > select add #8 71687 atoms, 53619 bonds, 492 pseudobonds, 21087 residues, 243 models selected > select add #9 73111 atoms, 55456 bonds, 497 pseudobonds, 21088 residues, 245 models selected > select add #10 74561 atoms, 57336 bonds, 502 pseudobonds, 21089 residues, 247 models selected > select add #11 80272 atoms, 64722 bonds, 565 pseudobonds, 21093 residues, 249 models selected > select add #12 87064 atoms, 73522 bonds, 636 pseudobonds, 21097 residues, 251 models selected > select add #13 92720 atoms, 80820 bonds, 700 pseudobonds, 21101 residues, 253 models selected > select add #14 94122 atoms, 82634 bonds, 705 pseudobonds, 21102 residues, 255 models selected > select add #15 95535 atoms, 84461 bonds, 710 pseudobonds, 21104 residues, 257 models selected > select add #16 98255 atoms, 87960 bonds, 720 pseudobonds, 21108 residues, 259 models selected > select add #17 105047 atoms, 96760 bonds, 797 pseudobonds, 21112 residues, 261 models selected > select add #18 111803 atoms, 105500 bonds, 856 pseudobonds, 21116 residues, 263 models selected > select add #19 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 266 models selected > show sel atoms > select subtract #1 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models selected > select subtract #2 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models selected > select subtract #3 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected > select subtract #4 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected > select subtract #5 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected > select subtract #6 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected > select subtract #7 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected > select subtract #8 60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected > select subtract #9 59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected > select subtract #10 56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected > select subtract #11 48873 atoms, 47890 bonds, 372 pseudobonds, 7996 residues, 70 models selected > select subtract #12 40252 atoms, 39090 bonds, 301 pseudobonds, 6899 residues, 61 models selected > select subtract #13 32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected > select subtract #14 30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected > select subtract #15 28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected > select subtract #16 24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected > select subtract #17 16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected > select subtract #18 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected > select subtract #19 8 models selected > select add #1.2 12 pseudobonds, 1 model selected > select subtract #1.2 Nothing selected > select add #1.1 43 pseudobonds, 1 model selected > select add #2.3 1552 atoms, 43 pseudobonds, 199 residues, 2 models selected > select subtract #2.3 43 pseudobonds, 2 models selected > hide #!1 models > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected > select subtract #1 5 models selected > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!14 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > select add #1.2 12 pseudobonds, 1 model selected > select subtract #1.2 Nothing selected > select add #1.1 43 pseudobonds, 1 model selected > select subtract #1.1 Nothing selected > select add #1.3 1535 atoms, 196 residues, 1 model selected > select add #1.5 3064 atoms, 391 residues, 2 models selected > select add #1.6 3484 atoms, 412 residues, 3 models selected > select add #1.7 3919 atoms, 433 residues, 4 models selected > select subtract #1.7 3484 atoms, 412 residues, 5 models selected > select subtract #1.6 3064 atoms, 391 residues, 4 models selected > hide sel atoms Drag select of 46 atoms Drag select of 72 atoms > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 81 atoms > hide sel atoms Drag select of 35 atoms > hide sel atoms Drag select of 1 atoms > hide sel atoms > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected > select subtract #1 5 models selected Cell requested for row 0 is out of bounds for table with 28 rows! Resizing table model. > show #!2 models > hide #!1 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > select subtract #2.10 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected > select add #2.10 8210 atoms, 7136 bonds, 44 pseudobonds, 1896 residues, 10 models selected > select subtract #2.8 7967 atoms, 6864 bonds, 16 pseudobonds, 1884 residues, 10 models selected > select subtract #2.7 7724 atoms, 6592 bonds, 16 pseudobonds, 1872 residues, 9 models selected > select subtract #2.6 6170 atoms, 5003 bonds, 12 pseudobonds, 1674 residues, 8 models selected > select subtract #2.5 4641 atoms, 3439 bonds, 8 pseudobonds, 1479 residues, 7 models selected > select subtract #2.4 3096 atoms, 1859 bonds, 4 pseudobonds, 1281 residues, 6 models selected > hide sel atoms > select add #2.8 3339 atoms, 1859 bonds, 4 pseudobonds, 1293 residues, 5 models selected > select add #2.7 3582 atoms, 1859 bonds, 4 pseudobonds, 1305 residues, 6 models selected > select add #2.6 5136 atoms, 1859 bonds, 4 pseudobonds, 1503 residues, 7 models selected > select add #2.5 6665 atoms, 1859 bonds, 4 pseudobonds, 1698 residues, 8 models selected > select add #2.4 8210 atoms, 1859 bonds, 4 pseudobonds, 1896 residues, 9 models selected > show #!1 models > select subtract #2.3 6658 atoms, 272 bonds, 1697 residues, 9 models selected > select add #2.3 8210 atoms, 272 bonds, 1896 residues, 8 models selected > select subtract #2.4 6665 atoms, 272 bonds, 1698 residues, 9 models selected > select add #2.4 8210 atoms, 272 bonds, 1896 residues, 8 models selected > select subtract #2.3 6658 atoms, 272 bonds, 1697 residues, 9 models selected > select subtract #2.8 6415 atoms, 272 bonds, 1685 residues, 8 models selected > select add #2.8 6658 atoms, 272 bonds, 1697 residues, 7 models selected > hide sel atoms > select add #2.3 8210 atoms, 272 bonds, 1896 residues, 8 models selected > select subtract #2.4 6665 atoms, 272 bonds, 1698 residues, 9 models selected > select subtract #2.5 5136 atoms, 272 bonds, 1503 residues, 8 models selected > select subtract #2.6 3582 atoms, 272 bonds, 1305 residues, 7 models selected > select subtract #2.7 3339 atoms, 272 bonds, 1293 residues, 6 models selected > select subtract #2.8 3096 atoms, 272 bonds, 1281 residues, 5 models selected > select subtract #2.9 2853 atoms, 1269 residues, 4 models selected > select subtract #2.10 2610 atoms, 1257 residues, 3 models selected > show sel atoms > select clear > hide #!1 models > select add #1.8 756 atoms, 648 bonds, 108 residues, 109 models selected > select subtract #1.8 Nothing selected > select add #1.7 435 atoms, 21 residues, 1 model selected > select subtract #1.7 1 model selected > show #!1 models > hide #!1 models > select add #2.9 243 atoms, 12 residues, 1 model selected > select add #2.10 486 atoms, 24 residues, 2 models selected > show sel atoms > hide sel atoms > select add #2.8 729 atoms, 36 residues, 3 models selected > select add #2.7 972 atoms, 48 residues, 4 models selected > select subtract #2.9 729 atoms, 36 residues, 5 models selected > select subtract #2.10 486 atoms, 24 residues, 4 models selected > show sel atoms > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected > select subtract #2 8 models selected > hide #!2 models > hide #!1 models > show #!3 models > select add #3.4 1558 atoms, 198 residues, 1 model selected > select add #3.5 3110 atoms, 395 residues, 2 models selected > select add #3.6 4662 atoms, 592 residues, 3 models selected > select add #3.7 5090 atoms, 613 residues, 4 models selected > select subtract #3.7 4662 atoms, 592 residues, 5 models selected > hide sel atoms > show #!2 models > hide #!2 models > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected > select subtract #3 6 models selected > show #!4 models > hide #!3 models > select add #4.10 243 atoms, 12 residues, 1 model selected > select subtract #4.10 1 model selected > select add #4.10 243 atoms, 12 residues, 1 model selected > select add #4.9 486 atoms, 24 residues, 2 models selected > select add #4.6 2010 atoms, 220 residues, 3 models selected > select add #4.5 3518 atoms, 413 residues, 4 models selected > select add #4.4 5056 atoms, 611 residues, 5 models selected > hide sel atoms > show #!3 models > hide #!3 models > select add #4 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 8 models selected > select subtract #4 8 models selected > show #!19 models > select add #19.11 227 atoms, 12 residues, 1 model selected > select add #19.10 470 atoms, 24 residues, 2 models selected > select add #19.7 1954 atoms, 218 residues, 3 models selected > select add #19.6 3450 atoms, 411 residues, 4 models selected > select add #19.5 4939 atoms, 608 residues, 5 models selected > hide sel atoms > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected > select subtract #19 8 models selected Cell requested for row 17 is out of bounds for table with 30 rows! Resizing table model. > show #!18 models > hide #!19 models > select add #18.6 1848 atoms, 231 residues, 1 model selected > select add #18.5 3696 atoms, 462 residues, 2 models selected > select add #18.4 5544 atoms, 693 residues, 3 models selected > hide sel atoms > select add #18.7 6071 atoms, 719 residues, 4 models selected > select subtract #18.7 5544 atoms, 693 residues, 5 models selected > hide #!18 models > show #!17 models > select add #18 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected > select subtract #18 6 models selected > select add #17.6 1863 atoms, 234 residues, 1 model selected > select add #17.5 3726 atoms, 468 residues, 2 models selected > select add #17.4 5589 atoms, 702 residues, 3 models selected > hide sel atoms > select add #17 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected > select subtract #17 6 models selected Cell requested for row 15 is out of bounds for table with 27 rows! Resizing table model. > show #!16 models > hide #!17 models > select add #16.5 410 atoms, 20 residues, 1 model selected > select subtract #16.5 1 model selected > select add #16.4 1486 atoms, 195 residues, 1 model selected > hide sel atoms > select add #16.1 1486 atoms, 8 pseudobonds, 195 residues, 3 models selected > select subtract #16.1 1486 atoms, 195 residues, 2 models selected > select add #16.2 1486 atoms, 2 pseudobonds, 195 residues, 3 models selected > select subtract #16.2 1486 atoms, 195 residues, 2 models selected > select add #16.3 2972 atoms, 390 residues, 2 models selected > select subtract #16.3 1486 atoms, 195 residues, 3 models selected > select add #16 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected > select subtract #16 3 models selected > hide #!16 models > show #!16 models > show #!15 models > hide #!16 models > show #!14 models > show #!13 models > hide #!14 models > hide #!15 models > hide #15.1 models > show #15.1 models > hide #!15 models > select add #13.8 388 atoms, 19 residues, 1 model selected > select subtract #13.8 1 model selected > select add #13.6 1571 atoms, 200 residues, 1 model selected > select add #13.5 3142 atoms, 400 residues, 2 models selected > select add #13.4 4713 atoms, 600 residues, 3 models selected > hide sel atoms > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected > select subtract #13 6 models selected > show #!12 models > hide #!13 models > select add #12.8 526 atoms, 26 residues, 1 model selected > select subtract #12.8 1 model selected > select add #12.6 1863 atoms, 234 residues, 1 model selected > select add #12.5 3726 atoms, 468 residues, 2 models selected > select add #12.4 5589 atoms, 702 residues, 3 models selected > hide sel atoms > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected > select subtract #12 6 models selected > show #!11 models > hide #!12 models > select add #11.6 1571 atoms, 200 residues, 1 model selected > select add #11.5 3142 atoms, 400 residues, 2 models selected > select add #11.4 4713 atoms, 600 residues, 3 models selected > hide sel atoms > select add #11.7 5141 atoms, 621 residues, 4 models selected > select subtract #11.7 4713 atoms, 600 residues, 5 models selected > select subtract #11.6 3142 atoms, 400 residues, 4 models selected > select subtract #11.5 1571 atoms, 200 residues, 3 models selected > select subtract #11.4 1 model selected > show #!10 models > hide #!11 models > hide #!10 models > show #!10 models > hide #!4 models > show #!9 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!9 models > select add #8.10 243 atoms, 12 residues, 1 model selected > select add #8.9 486 atoms, 24 residues, 2 models selected > select add #8.6 2005 atoms, 220 residues, 3 models selected > select add #8.5 3519 atoms, 415 residues, 4 models selected > select add #8.4 5060 atoms, 613 residues, 5 models selected > hide sel atoms > select add #8 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 8 models selected > select subtract #8 8 models selected > hide #!8 models > show #!8 models > hide #!8 models > show #!7 models > select add #7.6 1865 atoms, 234 residues, 1 model selected > select add #7.5 3730 atoms, 468 residues, 2 models selected > select add #7.4 5595 atoms, 702 residues, 3 models selected > hide sel atoms > select add #7 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected > select subtract #7 6 models selected > show #!6 models > hide #!7 models > hide #!6 models > show #!6 models > show #!5 models > hide #!6 models > select add #5.9 243 atoms, 12 residues, 1 model selected > select add #5.10 466 atoms, 23 residues, 2 models selected > select add #5.6 2002 atoms, 221 residues, 3 models selected > select add #5.5 3537 atoms, 417 residues, 4 models selected > select add #5.4 5089 atoms, 616 residues, 5 models selected > hide sel atoms > select add #5 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected > select subtract #5 8 models selected > show #!4 models > hide #!5 models > show #!3 models > hide #!4 models > show #!1 models > show #!2 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > show #!15 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models Drag select of 883 atoms, 15 bonds > hide sel atoms Drag select of 560 atoms, 6 bonds > hide sel atoms Drag select of 49 atoms > hide sel atoms Drag select of 358 atoms, 3 bonds > hide sel atoms Drag select of 604 atoms > hide sel atoms Drag select of 106 atoms > hide sel atoms Drag select of 22 atoms > hide sel atoms Drag select of 610 atoms, 3 bonds > hide sel atoms Drag select of 112 atoms > hide sel atoms Drag select of 252 atoms, 1 bonds > hide sel atoms Drag select of 4 atoms > hide sel atoms Drag select of 3 atoms > hide sel atoms Drag select of 47 atoms, 8 bonds > hide sel atoms Drag select of 77 atoms > hide sel atoms Drag select of 15 atoms > hide sel atoms > select ions 61 atoms, 61 residues, 19 models selected > select solvent 8211 atoms, 8211 residues, 18 models selected > hide sel atoms > save ""/Users/kompa012/Desktop/P53/Before mutation 1.cxs"" > hide #!2 models > show #!2 models > hide #!2 models > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > style sel sphere Changed 12 atom styles > style sel stick Changed 12 atom styles > show #!2 models > select Y220 Expected an objects specifier or a keyword > select #1 Y220 Expected a keyword > select #1, Y220 Expected an objects specifier or a keyword > select #1 :Y220 Nothing selected > select #1-19 :Y220 Nothing selected > select #1-19 :220 698 atoms, 696 bonds, 60 residues, 19 models selected > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > style sel sphere Changed 228 atom styles > style sel stick Changed 228 atom styles > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!10 models > show #!9 models > show #!10 models > select add #9.2 228 atoms, 228 bonds, 1 pseudobond, 19 residues, 37 models selected > select subtract #9.2 228 atoms, 228 bonds, 19 residues, 36 models selected > select add #9.1 228 atoms, 228 bonds, 4 pseudobonds, 19 residues, 37 models selected > select subtract #9.1 228 atoms, 228 bonds, 19 residues, 36 models selected > select clear > select ligand 172 atoms, 129 bonds, 43 residues, 4 models selected > hide sel atoms > select add #8 8188 atoms, 7432 bonds, 81 pseudobonds, 1838 residues, 6 models selected > select subtract #8 100 atoms, 75 bonds, 25 residues, 11 models selected > select add #9 2021 atoms, 1891 bonds, 5 pseudobonds, 398 residues, 5 models selected > select subtract #9 72 atoms, 54 bonds, 18 residues, 2 models selected > select add #10 2176 atoms, 1883 bonds, 5 pseudobonds, 563 residues, 4 models selected > select subtract #10 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > select subtract #1.3 216 atoms, 216 bonds, 18 residues, 35 models selected > lighting full > lighting simple > lighting soft Cell requested for row 8 is out of bounds for table with 28 rows! Resizing table model. > select add #1.9 228 atoms, 225 bonds, 21 residues, 38 models selected > select add #1.8 984 atoms, 873 bonds, 129 residues, 147 models selected > select clear > select add #1.8 756 atoms, 648 bonds, 108 residues, 109 models selected > select add #1.9 768 atoms, 657 bonds, 111 residues, 113 models selected > hide sel atoms > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected > select subtract #1 5 models selected > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > style sel sphere Changed 228 atom styles > select #1-19 /A :248 207 atoms, 188 bonds, 19 residues, 19 models selected > select add #1 6792 atoms, 6484 bonds, 55 pseudobonds, 1143 residues, 151 models selected > select subtract #1 196 atoms, 178 bonds, 18 residues, 39 models selected > color (#!2-19 & sel) black > style sel sphere Changed 196 atom styles > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > style sel sphere Changed 209 atom styles > ui tool show ""Color Actions"" > select clear > set bgColor white > set bgColor #ffffff00 > lighting flat > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > lighting full > graphics silhouettes false > lighting flat > graphics silhouettes false > graphics silhouettes true > select clear > color #1 #0009d1ff > color #1 #0017d1ff > color #1 #00d1c3ff > color #1 #00d1b9ff > color #1 #74d100ff > color #1 #70d100ff > color #1 #5bd100ff > color #1 #60d100ff > color #2 #85d406ff > color #2 #87d401ff > color #3 #b1dc05ff > color #4 #d0d405ff > color #5 #d4ba04ff > color #6 #db9704ff > color #7 #d16404ff > color #8 #f4520cff > color #9 #ff2f10ff > color #10 #940907ff > color #9 #ff1f1aff > color #10 #a71728ff > color #11 #fc1a3dff > color #10 #ff3b4cff > color #10 #ff1ed9ff > color #10 #ff08ceff > color #10 #ff00efff > color #9 #ff00adff > color #11 #e406ffff > color #12 #ce02fcff > color #13 #b700fcff > color #14 #826cffff > color #14 #b000ffff > color #14 #ad00ffff > color #15 #ff7c70ff > color #15 #8308ffff > color #16 #edff78ff > color #16 #3907ffff > color #16 #4a11ffff > color #17 #0d00fcff > color #18 #0040e1ff > color #19 #008afaff > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select #1-19 /A :248 207 atoms, 188 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select clear > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > style sel sphere Changed 12 atom styles > color (#!1 & sel) black > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel sphere Changed 11 atom styles > color (#!1 & sel) black > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel sphere Changed 11 atom styles > color (#!1 & sel) black > select clear [Repeated 1 time(s)] > lighting flat > lighting simple > lighting shadows true > lighting shadows false > ui tool show ""Side View"" > select add #8 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected > select add #9 10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 14 models selected > select add #10 12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 17 models selected > select add #11 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 20 models selected > select add #12 28805 atoms, 27260 bonds, 225 pseudobonds, 5530 residues, 29 models selected > select add #13 36392 atoms, 34558 bonds, 289 pseudobonds, 6895 residues, 38 models selected > select add #14 38485 atoms, 36372 bonds, 294 pseudobonds, 7442 residues, 47 models selected > select add #15 40594 atoms, 38199 bonds, 299 pseudobonds, 7993 residues, 52 models selected > select add #16 44291 atoms, 41698 bonds, 309 pseudobonds, 8718 residues, 57 models selected > select add #17 52968 atoms, 50498 bonds, 386 pseudobonds, 9871 residues, 63 models selected > select add #18 61424 atoms, 59238 bonds, 445 pseudobonds, 10851 residues, 72 models selected > select add #19 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 82 models selected > select add #7 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 93 models selected > select add #6 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 101 models selected > select add #5 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 106 models selected > select add #4 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 117 models selected > select add #3 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 128 models selected > select add #2 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 137 models selected > select add #1 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 261 models selected > color (#1.8.1-108#1.9.1-3#!1-19 & sel) dark gray > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select #1-19 /A :248 207 atoms, 188 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > color (#!1-19 & sel) black > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) black > select #!1/B:167-170,177-181,278-287 167 atoms, 169 bonds, 19 residues, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) black > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!1 & sel) black > select clear Cell requested for row 15 is out of bounds for table with 28 rows! Resizing table model. > select #1-19 :AP, TP, GP, CP Nothing selected > select #1-19 :AP Nothing selected > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected > select add #4 15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 12 models selected > select add #5 22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 23 models selected > select add #6 24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 33 models selected > select add #7 33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 38 models selected > select add #8 41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 47 models selected > select add #9 43471 atoms, 41742 bonds, 364 pseudobonds, 7863 residues, 58 models selected > select add #10 45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 61 models selected > select add #11 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 64 models selected > select add #12 62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 73 models selected > select add #13 69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 82 models selected > select add #14 71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 91 models selected > select add #15 74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 96 models selected > select add #16 77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 101 models selected > select add #17 86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 107 models selected > select add #18 94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 116 models selected > select add #19 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 126 models selected > show sel cartoons > select add #1 109087 atoms, 105204 bonds, 859 pseudobonds, 19224 residues, 250 models selected > select add #2 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models selected > select subtract #19.4 115783 atoms, 111064 bonds, 933 pseudobonds, 20924 residues, 266 models selected > select subtract #19.11 115556 atoms, 110812 bonds, 898 pseudobonds, 20912 residues, 265 models selected > select subtract #19.10 115313 atoms, 110540 bonds, 898 pseudobonds, 20900 residues, 264 models selected > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > select subtract #1 108717 atoms, 104234 bonds, 843 pseudobonds, 19775 residues, 147 models selected > select subtract #2 100507 atoms, 96826 bonds, 765 pseudobonds, 17879 residues, 139 models selected > select subtract #3 93414 atoms, 89513 bonds, 708 pseudobonds, 17024 residues, 128 models selected > select subtract #4 85379 atoms, 82232 bonds, 634 pseudobonds, 15191 residues, 119 models selected > select subtract #5 77598 atoms, 74925 bonds, 564 pseudobonds, 13636 residues, 108 models selected > select subtract #6 75666 atoms, 73090 bonds, 560 pseudobonds, 13270 residues, 98 models selected > select subtract #7 67073 atoms, 64278 bonds, 487 pseudobonds, 12209 residues, 93 models selected > select subtract #9 65124 atoms, 62441 bonds, 482 pseudobonds, 11829 residues, 84 models selected > select subtract #8 57036 atoms, 55084 bonds, 401 pseudobonds, 10016 residues, 81 models selected > select subtract #10 54864 atoms, 53204 bonds, 396 pseudobonds, 9454 residues, 70 models selected > select subtract #11 46889 atoms, 45818 bonds, 333 pseudobonds, 7776 residues, 67 models selected > select subtract #12 38268 atoms, 37018 bonds, 262 pseudobonds, 6679 residues, 58 models selected > select subtract #13 30681 atoms, 29720 bonds, 198 pseudobonds, 5314 residues, 49 models selected > select subtract #14 28588 atoms, 27906 bonds, 193 pseudobonds, 4767 residues, 40 models selected > select subtract #15 26479 atoms, 26079 bonds, 188 pseudobonds, 4216 residues, 35 models selected > select subtract #16 22782 atoms, 22580 bonds, 178 pseudobonds, 3491 residues, 30 models selected > select subtract #17 14105 atoms, 13780 bonds, 101 pseudobonds, 2338 residues, 24 models selected > select subtract #18 5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 15 models selected > select add #19.10 5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected > select add #19.11 6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected > select subtract #19.9 5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected > select subtract #19.8 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected > hide sel atoms > hide sel cartoons > select add #8 13778 atoms, 11923 bonds, 93 pseudobonds, 3172 residues, 10 models selected > select subtract #8 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 15 models selected > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected > select subtract #19 8 models selected > hide #!19 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > show #!12 models > show #!11 models > show #!10 models > show #!9 models > show #!8 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > select add #1 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected > select add #2 14806 atoms, 13714 bonds, 133 pseudobonds, 3021 residues, 124 models selected > select add #3 21899 atoms, 21027 bonds, 190 pseudobonds, 3876 residues, 135 models selected > select add #4 29934 atoms, 28308 bonds, 264 pseudobonds, 5709 residues, 144 models selected > select add #5 37715 atoms, 35615 bonds, 334 pseudobonds, 7264 residues, 155 models selected > select add #6 39647 atoms, 37450 bonds, 338 pseudobonds, 7630 residues, 165 models selected > select add #7 48240 atoms, 46262 bonds, 411 pseudobonds, 8691 residues, 170 models selected > select add #9 50189 atoms, 48099 bonds, 416 pseudobonds, 9071 residues, 179 models selected > select add #8 58277 atoms, 55456 bonds, 497 pseudobonds, 10884 residues, 182 models selected > select add #10 60449 atoms, 57336 bonds, 502 pseudobonds, 11446 residues, 193 models selected > select add #11 68424 atoms, 64722 bonds, 565 pseudobonds, 13124 residues, 196 models selected > select add #12 77045 atoms, 73522 bonds, 636 pseudobonds, 14221 residues, 205 models selected > select add #13 84632 atoms, 80820 bonds, 700 pseudobonds, 15586 residues, 214 models selected > select add #14 86725 atoms, 82634 bonds, 705 pseudobonds, 16133 residues, 223 models selected > select add #15 88834 atoms, 84461 bonds, 710 pseudobonds, 16684 residues, 228 models selected > select add #16 92531 atoms, 87960 bonds, 720 pseudobonds, 17409 residues, 233 models selected > select add #17 101208 atoms, 96760 bonds, 797 pseudobonds, 18562 residues, 239 models selected > select add #18 109664 atoms, 105500 bonds, 856 pseudobonds, 19542 residues, 248 models selected > select add #19 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models selected > hide sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 13700 atom styles > nucleotides sel tube/slab shape box > select subtract #1 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models selected > select add #1.7 111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models selected > select subtract #1.7 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 146 models selected > select add #1.7 111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models selected > select add #1.6 111556 atoms, 106306 bonds, 882 pseudobonds, 20037 residues, 147 models selected > select add #1 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 263 models selected > select subtract #1 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models selected > select subtract #2 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models selected > select subtract #3 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected > select subtract #4 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected > select subtract #5 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected > select subtract #6 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected > select subtract #7 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected > select subtract #8 60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected > select subtract #9 59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected > select subtract #10 56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected > select subtract #12 48227 atoms, 46476 bonds, 364 pseudobonds, 8577 residues, 70 models selected > select subtract #13 40640 atoms, 39178 bonds, 300 pseudobonds, 7212 residues, 61 models selected > select subtract #11 32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected > select subtract #14 30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected > select subtract #15 28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected > select subtract #16 24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected > select subtract #17 16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected > select subtract #18 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected > select subtract #19 8 models selected > select add #1.7 435 atoms, 21 residues, 1 model selected > select add #1.6 855 atoms, 42 residues, 2 models selected > show sel cartoons > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > show #!11 models > hide #!10 models > hide #!11 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > color (#!1 & sel) blue > select subtract #1.6 435 atoms, 21 residues, 3 models selected > select subtract #1.7 1 model selected > select add #1.4 1522 atoms, 194 residues, 1 model selected > show sel cartoons > hide sel atoms > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > show sel & #!1 atoms > select subtract #1.3 198 atoms, 180 bonds, 18 residues, 35 models selected > select add #1.3 1733 atoms, 180 bonds, 214 residues, 35 models selected > hide sel & #!1 atoms > select clear > show #!2 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected > hide sel atoms > select subtract #2 8 models selected > select add #2.10 243 atoms, 12 residues, 1 model selected > select subtract #2.10 1 model selected > select add #2.10 243 atoms, 12 residues, 1 model selected > select add #2.9 486 atoms, 24 residues, 2 models selected > select subtract #2.10 243 atoms, 12 residues, 3 models selected > select subtract #2.9 1 model selected > select add #2.8 243 atoms, 12 residues, 1 model selected > select add #2.7 486 atoms, 24 residues, 2 models selected > show sel cartoons > select subtract #2.7 243 atoms, 12 residues, 3 models selected > select subtract #2.8 1 model selected > select add #2.3 1552 atoms, 199 residues, 1 model selected > show sel cartoons > select add #2.8 1795 atoms, 211 residues, 2 models selected > select add #2.7 2038 atoms, 223 residues, 3 models selected > select subtract #2.3 486 atoms, 24 residues, 4 models selected > color (#!2 & sel) blue > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected > select subtract #2 8 models selected > show #!3 models > select add #3.8 427 atoms, 21 residues, 1 model selected > select add #3.7 855 atoms, 42 residues, 2 models selected > show sel cartoons > color (#!3 & sel) blue > select subtract #3.7 427 atoms, 21 residues, 3 models selected > select subtract #3.8 1 model selected > select add #3.3 1552 atoms, 197 residues, 1 model selected > show sel cartoons > hide sel atoms Cell requested for row 8 is out of bounds for table with 27 rows! Resizing table model. > select add #3 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 4 models selected > select subtract #3 6 models selected > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > show #!4 models > select add #4.10 243 atoms, 12 residues, 1 model selected > select subtract #4.10 1 model selected > select add #4.8 224 atoms, 11 residues, 1 model selected > select add #4.7 426 atoms, 21 residues, 2 models selected > select add #4.3 1977 atoms, 220 residues, 3 models selected > show sel cartoons > hide sel atoms > show sel atoms > select subtract #4.7 1775 atoms, 210 residues, 4 models selected > select subtract #4.8 1551 atoms, 199 residues, 3 models selected > hide sel atoms > select subtract #4.3 1 model selected > select add #4.8 224 atoms, 11 residues, 1 model selected > select add #4.7 426 atoms, 21 residues, 2 models selected > color (#!4 & sel) blue > show #!5 models > select add #4 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected > select subtract #4 8 models selected > select add #5.8 222 atoms, 11 residues, 1 model selected > select add #5.7 425 atoms, 21 residues, 2 models selected > show sel cartoons > color (#!5 & sel) blue > select subtract #5.8 203 atoms, 10 residues, 3 models selected > select subtract #5.7 1 model selected > select add #5.3 1546 atoms, 197 residues, 1 model selected > show sel cartoons > hide sel atoms > select add #5 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected > select subtract #5 8 models selected > show #!6 models > select add #6 1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 2 models selected > select subtract #6 2 models selected > select add #6.3 205 atoms, 10 residues, 1 model selected > show sel cartoons > color (#!6 & sel) blue > select subtract #6.3 1 model selected > select add #6.2 1571 atoms, 200 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #6 1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 3 models selected > select subtract #6 2 models selected > hide #!6 models > select add #5 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 3 models selected > select subtract #5 8 models selected > select add #5.3 1546 atoms, 197 residues, 1 model selected > show sel cartoons > select add #5 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected > select subtract #5 8 models selected > show #!6 models > show #!7 models > select add #7.8 535 atoms, 26 residues, 1 model selected > select add #7.7 1060 atoms, 52 residues, 2 models selected > show sel cartoons > color (#!7 & sel) blue > select subtract #7.7 535 atoms, 26 residues, 3 models selected > select subtract #7.8 1 model selected > select add #7.3 1865 atoms, 234 residues, 1 model selected > hide sel atoms > show sel cartoons > select subtract #7.3 1 model selected > show #!8 models > select add #8.8 227 atoms, 11 residues, 1 model selected > select add #8.7 448 atoms, 22 residues, 2 models selected > show sel cartoons > color (#!8 & sel) blue > select subtract #8.7 227 atoms, 11 residues, 3 models selected > select subtract #8.8 1 model selected > select add #8.3 1545 atoms, 197 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > show sel cartoons > select subtract #8.3 1 model selected > show #!9 models > select add #9.2 1 pseudobond, 1 model selected > select subtract #9.2 Nothing selected > select add #9 1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #9 2 models selected > select add #9.4 221 atoms, 11 residues, 1 model selected > nucleotides sel tube/slab shape box > show sel cartoons > color (#!9 & sel) blue > select subtract #9.4 1 model selected > select add #9.3 1535 atoms, 197 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #9 1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 4 models selected > select subtract #9 2 models selected > show #!10 models > select add #10 2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #10.4 1947 atoms, 1629 bonds, 5 pseudobonds, 550 residues, 5 models selected > select subtract #10.3 404 atoms, 51 bonds, 353 residues, 2 models selected > select add #10.3 1947 atoms, 51 bonds, 550 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #10.4 2172 atoms, 51 bonds, 562 residues, 2 models selected > select subtract #10.3 629 atoms, 51 bonds, 365 residues, 3 models selected > show sel cartoons > color (#!10 & sel) blue > select add #10 2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 4 models selected > select subtract #10 2 models selected > show #!11 models > hide #!10 models > hide #!11 models > show #!10 models > show #!11 models > select add #11.3 1571 atoms, 200 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #11.7 1999 atoms, 221 residues, 2 models selected > select add #11.8 2426 atoms, 242 residues, 3 models selected > select subtract #11.3 855 atoms, 42 residues, 4 models selected > show sel cartoons > color (#!11 & sel) blue > select add #11 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 5 models selected > select subtract #11 6 models selected > show #!12 models > select add #12.8 526 atoms, 26 residues, 1 model selected > select add #12.7 1060 atoms, 52 residues, 2 models selected > show sel cartoons > color (#!12 & sel) blue > select subtract #12.7 526 atoms, 26 residues, 3 models selected > select subtract #12.8 1 model selected > select add #12.4 1863 atoms, 234 residues, 1 model selected > select subtract #12.4 1 model selected > select add #12.3 1863 atoms, 234 residues, 1 model selected > show sel cartoons > hide sel atoms > show #!13 models > select add #12 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 4 models selected > select subtract #12 6 models selected > select add #13.3 1571 atoms, 200 residues, 1 model selected > show sel cartoons > hide sel atoms > select subtract #13.3 1 model selected > select add #13.8 388 atoms, 19 residues, 1 model selected > select add #13.7 776 atoms, 38 residues, 2 models selected > show sel cartoons > color (#!13 & sel) blue > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 5 models selected > select subtract #13 6 models selected > show #!14 models > select add #14.4 225 atoms, 12 residues, 1 model selected > show sel cartoons > color (#!14 & sel) blue > select add #14.3 1755 atoms, 209 residues, 2 models selected > select subtract #14.4 1530 atoms, 197 residues, 3 models selected > show sel cartoons > hide sel atoms > select add #14 2093 atoms, 1814 bonds, 5 pseudobonds, 547 residues, 4 models selected > select subtract #14 2 models selected > show #!15 models > select add #15.4 225 atoms, 12 residues, 1 model selected > show sel cartoons > color (#!15 & sel) blue > select add #15.3 1764 atoms, 209 residues, 2 models selected > select subtract #15.4 1539 atoms, 197 residues, 3 models selected > hide sel atoms > show sel cartoons > select add #15 2109 atoms, 1827 bonds, 5 pseudobonds, 551 residues, 4 models selected > select subtract #15 2 models selected > show #!16 models > select add #16.5 410 atoms, 20 residues, 1 model selected > color (#!16 & sel) blue > show sel cartoons > select add #16.4 1896 atoms, 215 residues, 2 models selected > select subtract #16.5 1486 atoms, 195 residues, 3 models selected > select add #16.5 1896 atoms, 215 residues, 2 models selected > select subtract #16.5 1486 atoms, 195 residues, 3 models selected > select add #16.3 2972 atoms, 390 residues, 2 models selected > select subtract #16.4 1486 atoms, 195 residues, 3 models selected > show sel cartoons > hide sel atoms > select add #16.4 2972 atoms, 390 residues, 2 models selected > select subtract #16.4 1486 atoms, 195 residues, 3 models selected > select subtract #16.3 1 model selected > show #!17 models > select add #17.8 533 atoms, 26 residues, 1 model selected > select add #17.7 1060 atoms, 52 residues, 2 models selected > show sel cartoons > color (#!17 & sel) blue > select subtract #17.7 533 atoms, 26 residues, 3 models selected > select subtract #17.8 1 model selected > select add #17.3 1863 atoms, 234 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #17 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 4 models selected > select subtract #17 6 models selected > show #!18 models > select add #18.8 533 atoms, 26 residues, 1 model selected > select add #18.7 1060 atoms, 52 residues, 2 models selected > color (#!18 & sel) blue > show sel cartoons > select subtract #18.7 533 atoms, 26 residues, 3 models selected > select subtract #18.8 1 model selected > select add #18.3 1848 atoms, 231 residues, 1 model selected > show sel cartoons > hide sel atoms > select add #18 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 4 models selected > select subtract #18 6 models selected > show #!19 models > select add #19.11 227 atoms, 12 residues, 1 model selected > select subtract #19.11 1 model selected > select add #19.9 216 atoms, 11 residues, 1 model selected > select add #19.8 429 atoms, 23 residues, 2 models selected > show sel cartoons > color (#!19 & sel) blue > select subtract #19.8 216 atoms, 11 residues, 3 models selected > select subtract #19.9 1 model selected > select add #19.4 1514 atoms, 196 residues, 1 model selected > show sel cartoons > hide sel atoms > select add #19 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 5 models selected > select subtract #19 8 models selected > select #1-19 /A :282 209 atoms, 190 bonds, 19 residues, 19 models selected > show sel atoms > select #1-19 /A :248 207 atoms, 188 bonds, 19 residues, 19 models selected > show sel atoms > select #1-19 /A :220 228 atoms, 228 bonds, 19 residues, 19 models selected > show sel atoms Drag select of 23 atoms > hide sel atoms Drag select of 11 atoms, 10 bonds > hide sel atoms > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #!1/B:220 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:248 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > select #!1/B:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear Drag select of 123 residues, 341 shapes, 1 atoms > hide sel cartoons > hide sel atoms > select clear > save ""/Users/kompa012/Desktop/P53/Superposition of P53.png"" width 3000 > height 2520 supersample 3 transparentBackground true > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > save /Users/kompa012/Desktop/P53/1tup.png width 3000 height 2520 supersample > 3 transparentBackground true > show #!2 models > hide #!1 models > select add #2.8 243 atoms, 12 residues, 1 model selected > select add #2.7 486 atoms, 24 residues, 2 models selected > show sel atoms > select subtract #2.7 243 atoms, 12 residues, 3 models selected > select subtract #2.8 1 model selected Drag select of 7 residues, 7 shapes > select subtract #2.8 81 atoms, 6 residues, 4 models selected > select subtract #2.7 21 atoms, 3 residues, 3 models selected > select add #2.9 264 atoms, 15 residues, 2 models selected > select add #2.10 507 atoms, 27 residues, 3 models selected > show sel cartoons > hide sel cartoons > save /Users/kompa012/Desktop/P53/2ac0.png width 3000 height 2520 supersample > 3 transparentBackground true Cell requested for row 11 is out of bounds for table with 29 rows! Resizing table model. > show #!4 models > hide #!2 models > show #!2 models > show #!5 models > hide #!4 models > hide #!5 models > show #!4 models > show #!5 models > select add #2 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 6 models selected > select subtract #2 8 models selected > hide #!4 models > hide #!5 models > show #!5 models > show #!4 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > show #!2 models > hide #!4 models > hide #!5 models > show #!4 models > hide #!2 models > save /Users/kompa012/Desktop/P53/2ahi.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!4 models > show #!4 models > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!6 models > show #!18 models > hide #!18 models > show #!17 models > hide #!17 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > hide #!14 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!16 models > show #!15 models > show #!14 models > hide #!15 models > hide #!16 models > show #!19 models > hide #!14 models > save /Users/kompa012/Desktop/P53/3d0a.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!19 models > show #!18 models > show #!17 models > hide #!17 models > hide #!18 models > show #!18 models > show #!17 models > hide #!17 models > show #!17 models > hide #!18 models > show #!18 models > hide #!17 models > show #!17 models > hide #!18 models > show #!18 models > hide #!17 models > show #!17 models > hide #!18 models > show #!18 models > hide #!17 models > show #!17 models > hide #!18 models > hide #!17 models > show #!17 models > show #!18 models > hide #!17 models > save /Users/kompa012/Desktop/P53/3q06.png width 3000 height 2520 supersample > 3 transparentBackground true > show #!17 models > hide #!18 models > save /Users/kompa012/Desktop/P53/3q05.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!17 models > show #!16 models > select add #16.5 410 atoms, 20 residues, 1 model selected > select subtract #16.5 1 model selected > select add #16.4 1486 atoms, 195 residues, 1 model selected > select subtract #16.4 1 model selected > select add #16.3 1486 atoms, 195 residues, 1 model selected > select subtract #16.3 1 model selected > show #!15 models > hide #!15 models > show #!19 models > hide #!19 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > open /Users/kompa012/Desktop/P53/3kz8.pdb1 3kz8.pdb1 title: Diversity In DNA recognition by P53 revealed by crystal structures with hoogsteen base pairs (P53-DNA complex 3) [more info...] 87 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 3kz8.pdb1 --- Chain | Description 20.1/A 20.1/B | No description available 20.2/A 20.2/B | No description available 20.1/C | No description available 20.2/C | No description available 87 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker [Repeated 1 time(s)] > matchmaker #20.1/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 3kz8.pdb1, chain A (#20.1), sequence alignment score = 948.3 RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs: 2.497) > matchmaker #20.2/A to #12/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain A (#20.2), sequence alignment score = 882.9 RMSD between 180 pruned atom pairs is 0.876 angstroms; (across all 195 pairs: 1.248) > matchmaker #20.2/B to #12/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain B (#20.2), sequence alignment score = 891.9 RMSD between 180 pruned atom pairs is 0.881 angstroms; (across all 195 pairs: 1.263) > show #!12 models > matchmaker #20.1/C to #12/K pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8 #12/K Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.1), sequence alignment score = 33.8 RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs: 1.781) > matchmaker #20.2/C to #12/K pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.2/C to 3ts8 #12/K Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.2), sequence alignment score = 35.9 RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs: 1.781) > matchmaker #20.1/C to #12/L pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8 #12/L Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 3ts8, chain L (#12) with 3kz8.pdb1, chain C (#20.1), sequence alignment score = 38.7 RMSD between 17 pruned atom pairs is 1.147 angstroms; (across all 20 pairs: 1.783) > hide #!12 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!12 models > hide #!16 models > hide #!20.1 models > show #!20.1 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!12 models > ui tool show ""Crystal Contacts"" > show #!16 models > hide #!20 models > crystalcontacts #20.1 distance 8 11 pairs of asymmetric units of 3kz8.pdb1 contact at distance 8.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 961 0 1 0 0 1 0 1 437 0 3 0 0 1 0 1 298 0 3 0 -1 1 0 1 222 0 0 0 0 -1 0 1 172 0 0 0 0 1 0 1 59 0 0 0 1 0 0 1 56 0 0 0 -1 0 0 1 35 0 1 0 0 2 0 1 34 0 1 0 0 0 0 1 9 0 3 0 -1 0 0 1 7 0 3 0 0 0 0 1 > select add #21 40667 atoms, 38489 bonds, 110 pseudobonds, 7975 residues, 34 models selected > show sel atoms > show sel cartoons > show sel surfaces > crystalcontacts #20.1 distance 4 9 pairs of asymmetric units of 3kz8.pdb1 contact at distance 4.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 321 0 1 0 0 1 0 1 67 0 3 0 0 1 0 1 66 0 3 0 -1 1 0 1 43 0 0 0 0 -1 0 1 41 0 0 0 0 1 0 1 18 0 0 0 1 0 0 1 11 0 0 0 -1 0 0 1 3 0 1 0 0 2 0 1 3 0 1 0 0 0 0 1 > select clear > select add #20 7394 atoms, 6998 bonds, 12 pseudobonds, 1450 residues, 6 models selected > show #!20 models > close #20 > select add #21.9 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected > select add #21.8 7394 atoms, 6998 bonds, 20 pseudobonds, 1450 residues, 6 models selected > select add #21.7 11091 atoms, 10497 bonds, 30 pseudobonds, 2175 residues, 9 models selected > select add #21.6 14788 atoms, 13996 bonds, 40 pseudobonds, 2900 residues, 12 models selected > select add #21.5 18485 atoms, 17495 bonds, 50 pseudobonds, 3625 residues, 15 models selected > select add #21.4 22182 atoms, 20994 bonds, 60 pseudobonds, 4350 residues, 18 models selected > select add #21.3 25879 atoms, 24493 bonds, 70 pseudobonds, 5075 residues, 21 models selected > hide sel atoms > hide sel cartoons > select add #21.2 29576 atoms, 27992 bonds, 80 pseudobonds, 5800 residues, 24 models selected > hide sel atoms > hide sel cartoons > select add #21.1 33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 27 models selected > select add #21 33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected > select subtract #21 Nothing selected > select add #21.1 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected > show sel surfaces > hide sel surfaces > select subtract #21.1.5 3287 atoms, 3040 bonds, 10 pseudobonds, 705 residues, 6 models selected > hide sel cartoons > hide sel atoms Drag select of 92 atoms, 101 bonds, 7 residues > hide sel atoms > hide sel cartoons > select subtract #21.1.5 1 model selected > select add #21.1.5 410 atoms, 20 residues, 1 model selected > nucleotides sel tube/slab shape box Drag select of 27 atoms, 221 residues, 1 pseudobonds, 78 shapes > show #!15 models > show #!14 models > show #!2 models > hide #!16 models > hide #!15 models > hide #!14 models > select add #16 3959 atoms, 3499 bonds, 10 pseudobonds, 738 residues, 7 models selected > select subtract #16 262 atoms, 13 residues, 5 models selected > select add #21 33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 29 models selected > select subtract #21 3 models selected > select add #21.1.3 1486 atoms, 195 residues, 1 model selected > select add #21.1.5 1896 atoms, 215 residues, 2 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!16 models > select add #21 33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 30 models selected > show #!15 models > hide #!21 models > hide #!16 models > show #!14 models > hide #!14 models > hide #!15 models > select subtract #21 3 models selected > show #!15 models > show #!14 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!14 models > hide #!15 models > hide #!11 models > show #!11 models > show #!21 models > show #!16 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > select add #21 33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #21,0.98958,0.012409,-0.14344,0.91941,-0.039208,0.98185,-0.18555,1.6593,0.13854,0.18924,0.97211,-2.389 > hide #!11 models > view matrix models > #21,0.98313,0.082637,-0.16316,0.71163,-0.11628,0.97101,-0.20883,2.6873,0.14117,0.22428,0.96425,-2.5673 > view matrix models > #21,0.98538,0.07809,-0.15144,0.64248,-0.10827,0.97326,-0.20261,2.5513,0.13157,0.21604,0.96748,-2.4375 > show #!2 models > hide #!16 models > hide #!21 models > ui mousemode right select > select clear > show #!19 models > hide #!19 models > hide #!2 models > show #!21 models > show #!16 models > show #!15 models > show #!14 models > hide #!21 models > hide #!16 models > ui tool show ""Crystal Contacts"" > crystalcontacts #15 distance 4 10 pairs of asymmetric units of 3igl contact at distance 4.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 201 0 1 0 0 2 0 1 99 0 0 0 0 1 0 1 86 0 0 0 0 -1 0 1 80 0 3 0 0 2 0 1 65 0 3 0 -1 2 0 1 21 0 1 0 0 1 0 1 12 0 0 0 1 0 0 1 9 0 0 0 -1 0 0 1 1 0 3 0 0 1 0 1 1 0 3 0 -1 1 0 1 > crystalcontacts #14 distance 4 10 pairs of asymmetric units of 3igk contact at distance 4.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 174 0 1 0 0 2 0 1 101 0 0 0 0 -1 0 1 86 0 0 0 0 1 0 1 72 0 3 0 -1 2 0 1 64 0 3 0 0 2 0 1 22 0 1 0 0 1 0 1 12 0 0 0 1 0 0 1 9 0 0 0 -1 0 0 1 3 0 3 0 0 1 0 1 1 0 3 0 -1 1 0 1 > hide #!22 models > hide #!20 models > hide #!15 models > show #!15 models > hide #!15 models > show #!15 models > hide #!14 models > show #!14 models > show #!16 models > hide #!16 models > show #!16 models > hide #!15 models > hide #!14 models > show #!13 models > hide #!16 models > show #!7 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > hide #!7 models > show #!10 models > show #!9 models > show #!8 models > hide #!9 models > hide #!10 models > show #!10 models > show #!9 models > hide #!9 models > hide #!10 models > show #!9 models > hide #!8 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!9 models > show #!8 models > show #!11 models > hide #!8 models > show #!8 models > hide #!8 models > show #!6 models > show #!3 models > hide #!11 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > ui tool show Matchmaker > hide #!3 models > show #!2 models > show #!3 models > hide #!2 models > save /Users/kompa012/Desktop/P53/5lgy.png width 3000 height 2520 supersample > 3 transparentBackground true [Repeated 1 time(s)] > show #!18 models > hide #!3 models > show #!17 models > hide #!18 models > show #!18 models > hide #!17 models > show #!17 models > hide #!18 models > hide #!17 models > show #!16 models > show #!21 models > save /Users/kompa012/Desktop/P53/3kz8.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!16 models > hide #!21 models > show #!13 models Drag select of 11 atoms, 11 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms > save /Users/kompa012/Desktop/P53/3kmd.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!13 models > select add #13 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected > select subtract #13 6 models selected > show #!12 models > save /Users/kompa012/Desktop/P53/3ts8.png width 3000 height 2520 supersample > 3 transparentBackground true > show #!7 models > hide #!12 models > save /Users/kompa012/Desktop/P53/4mzr.png width 3000 height 2520 supersample > 3 transparentBackground true > hide #!7 models > show #!8 models > save /Users/kompa012/Desktop/P53/4ibu.png width 3000 height 2520 supersample > 3 transparentBackground true > save ""/Users/kompa012/Desktop/P53/Before mutation.cxs"" > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > show #!13 models > hide #!12 models > hide #!13 models > show #!14 models > show #!13 models > show #!12 models > show #!15 models > show #!16 models > show #!17 models > show #!18 models > show #!19 models > open 6shz fromDatabase pdb format mmcif Summary of feedback from opening 6shz fetched from pdb --- note | Fetching compressed mmCIF 6shz from http://files.rcsb.org/download/6shz.cif 6shz title: p53 cancer mutant Y220C [more info...] Chain information for 6shz #23 --- Chain | Description | UniProt A B | Cellular tumor antigen p53 | P53_HUMAN 94-311 Non-standard residues in 6shz #23 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) ZN — zinc ion 6shz mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 134 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2J1x fromDatabase pdb format mmcif Summary of feedback from opening 2J1x fetched from pdb --- note | Fetching compressed mmCIF 2j1x from http://files.rcsb.org/download/2j1x.cif 2j1x title: Human p53 core domain mutant M133L-V203A-Y220C-N239Y-N268D [more info...] Chain information for 2j1x #24 --- Chain | Description | UniProt A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312 Non-standard residues in 2j1x #24 --- ZN — zinc ion 2j1x mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 35 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 1uol fromDatabase pdb format mmcif Summary of feedback from opening 1uol fetched from pdb --- note | Fetching compressed mmCIF 1uol from http://files.rcsb.org/download/1uol.cif 1uol title: Crystal structure of the human p53 core domain mutant M133L/V203A/N239Y/N268D at 1.9 A resolution. [more info...] Chain information for 1uol #25 --- Chain | Description | UniProt A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312 Non-standard residues in 1uol #25 --- ZN — zinc ion 1uol mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > open 8a32 fromDatabase pdb format mmcif Summary of feedback from opening 8a32 fetched from pdb --- note | Fetching compressed mmCIF 8a32 from http://files.rcsb.org/download/8a32.cif 8a32 title: p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769 [more info...] Chain information for 8a32 #26 --- Chain | Description | UniProt A B | Cellular tumor antigen p53 | P53_HUMAN 94-312 Non-standard residues in 8a32 #26 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) KVA — 4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid ZN — zinc ion 8a32 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 102 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #25/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment score = 927.9 RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs: 2.313) > matchmaker #25/B to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1uol, chain B (#25), sequence alignment score = 927.9 RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 195 pairs: 2.289) > matchmaker #25/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment score = 927.9 RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs: 2.313) > matchmaker #24/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 2j1x, chain A (#24), sequence alignment score = 909.6 RMSD between 187 pruned atom pairs is 0.557 angstroms; (across all 195 pairs: 2.329) > matchmaker #23/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 6shz, chain A (#23), sequence alignment score = 916.9 RMSD between 189 pruned atom pairs is 0.550 angstroms; (across all 197 pairs: 2.279) > matchmaker #26/A to #12/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ts8, chain A (#12) with 8a32, chain A (#26), sequence alignment score = 916.2 RMSD between 189 pruned atom pairs is 0.590 angstroms; (across all 197 pairs: 2.303) > hide #!12 models > matchmaker #25/A to #24/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2j1x, chain A (#24) with 1uol, chain A (#25), sequence alignment score = 1098.9 RMSD between 195 pruned atom pairs is 0.170 angstroms; (across all 195 pairs: 0.170) > hide #!23 models > hide #!26 models > ui tool show ""Show Sequence Viewer"" > sequence chain #24/A Alignment identifier is 24/A > sequence chain #25/A Alignment identifier is 25/A > sequence chain #26/A Alignment identifier is 26/A > sequence chain #23/A Alignment identifier is 23/A > select #25/A:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #25/A:220-221 21 atoms, 21 bonds, 2 residues, 1 model selected > select #25/A:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #25/A:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #25 3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 2 models selected > color (#!25 & sel) dark gray > select subtract #25 Nothing selected > select add #24 3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected > color (#!24 & sel) yellow > select add #26 6990 atoms, 6292 bonds, 16 pseudobonds, 1628 residues, 4 models selected > select subtract #24 3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected > show #!26 models > color (#!26 & sel) orange > color (#!26 & sel) red > select add #23 7103 atoms, 6283 bonds, 16 pseudobonds, 1755 residues, 4 models selected > select subtract #26 3572 atoms, 3124 bonds, 8 pseudobonds, 913 residues, 2 models selected > show #!23 models > color (#!23 & sel) forest green > select add #24 7031 atoms, 6257 bonds, 16 pseudobonds, 1699 residues, 4 models selected > select add #26 10562 atoms, 9416 bonds, 24 pseudobonds, 2541 residues, 6 models selected > select add #25 14027 atoms, 12560 bonds, 32 pseudobonds, 3324 residues, 8 models selected > show sel surfaces > hide sel surfaces > select subtract #23 10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 14 models selected > select add #23.3 11975 atoms, 9436 bonds, 24 pseudobonds, 2609 residues, 13 models selected > hide sel cartoons > select subtract #23.3 10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected > select add #23.2 11978 atoms, 9436 bonds, 24 pseudobonds, 2608 residues, 13 models selected > select subtract #23.2 10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected > select subtract #24.3 8922 atoms, 7868 bonds, 20 pseudobonds, 2216 residues, 12 models selected > select add #24.3 10455 atoms, 7868 bonds, 20 pseudobonds, 2411 residues, 11 models selected > select subtract #24.2 8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 11 models selected > select subtract #24.3 7392 atoms, 6303 bonds, 16 pseudobonds, 2021 residues, 10 models selected > select add #24.3 8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 9 models selected > select subtract #25 5460 atoms, 3159 bonds, 8 pseudobonds, 1433 residues, 8 models selected > select subtract #26 1929 atoms, 591 residues, 4 models selected > select subtract #24.3 396 atoms, 396 residues, 2 models selected > select add #24.3 1929 atoms, 591 residues, 1 model selected > select subtract #24.3 396 atoms, 396 residues, 2 models selected > select add #24.2 1926 atoms, 591 residues, 1 model selected > show sel cartoons > select subtract #24.2 396 atoms, 396 residues, 2 models selected > select add #24.2 1926 atoms, 591 residues, 1 model selected > select subtract #24.2 396 atoms, 396 residues, 2 models selected > select add #24 3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected > select subtract #24 2 models selected > select add #25.2 1536 atoms, 195 residues, 1 model selected > show sel cartoons > select add #25 3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 3 models selected > select subtract #25 2 models selected > select add #26.2 1521 atoms, 197 residues, 1 model selected > show sel cartoons > select add #26 3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected > select subtract #26 2 models selected Drag select of 277 atoms, 16 pseudobonds, 244 bonds > hide sel atoms > select #25/A:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #25/A:220 12 atoms, 12 bonds, 1 residue, 1 model selected > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > show sel atoms > hide #!25 models > hide #!24 models > hide #!23 models > show #!11 models > hide #!26 models > select add #23 3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 9 models selected > select subtract #23 24 atoms, 22 bonds, 3 residues, 8 models selected > select add #23 3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 8 models selected > select subtract #23 24 atoms, 22 bonds, 3 residues, 8 models selected > select add #24 3477 atoms, 3150 bonds, 8 pseudobonds, 788 residues, 7 models selected > select subtract #24 18 atoms, 17 bonds, 2 residues, 6 models selected > select add #25 3471 atoms, 3149 bonds, 8 pseudobonds, 784 residues, 5 models selected > select subtract #25 6 atoms, 5 bonds, 1 residue, 4 models selected > select add #26 3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected > select subtract #26 2 models selected > save ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" ——— End of log from Wed Mar 12 16:42:08 2025 ——— opened ChimeraX session > hide #!11 models > show #!25 models > show #!24 models > show #!26 models > hide #!26 models > show #!23 models > show #!26 models > hide #!25 models > hide #!26 models > show #!25 models > hide #!23 models > show #!26 models > hide #!24 models > hide #!26 models > select #23-26 /A :151 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :153 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > hide sel & #!25 atoms > select #23-26 /A :155 28 atoms, 24 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :222 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :220, 222, 153 86 atoms, 83 bonds, 12 residues, 4 models selected > select #23-26 /A :220, 222, 151 86 atoms, 83 bonds, 12 residues, 4 models selected > color (#!25 & sel) black > select #23-26 /A :223 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > hide sel & #!25 cartoons > show sel & #!25 cartoons > hide sel & #!25 atoms > select #23-26 /A :145 32 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :223 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :147 28 atoms, 24 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > select ~sel & ##selected 13999 atoms, 12536 bonds, 32 pseudobonds, 3320 residues, 8 models selected > select #23-26 /A :151,153,155 84 atoms, 80 bonds, 12 residues, 4 models selected > show sel & #!25 atoms > select #23-26 /A :151,153,155,223,220,147 170 atoms, 159 bonds, 24 residues, 4 models selected > show sel & #!25 cartoons > show sel & #!25 atoms > select #23-26 /A :222 28 atoms, 28 bonds, 4 residues, 4 models selected > hide sel & #!25 atoms > color (#!25 & sel) light gray > color (#!25 & sel) dark gray > select #23-26 /A :151,153,155,223,220,147 170 atoms, 159 bonds, 24 residues, 4 models selected > color (#!25 & sel) black > ui tool show H-Bonds > save ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" ——— End of log from Wed Mar 12 17:13:32 2025 ——— opened ChimeraX session > style sel & #!25 ball Changed 47 atom styles > color (#!25 & sel) byelement > distance #25/A:153@CA #25/A:220@CD2 Distance between 1uol #25/A PRO 153 CA and TYR 220 CD2: 6.945Å > close #27 > hide sel & #!25 cartoons > distance #25/A:223@CD #25/A:220@OH Distance between 1uol #25/A PRO 223 CD and TYR 220 OH: 3.634Å > distance #25/A:147@CG2 #25/A:220@OH Distance between 1uol #25/A VAL 147 CG2 and TYR 220 OH: 3.539Å > distance #25/A:151@CD #25/A:220@OH Distance between 1uol #25/A PRO 151 CD and TYR 220 OH: 4.277Å > distance #25/A:155@O #25/A:220@N Distance between 1uol #25/A THR 155 O and TYR 220 N: 2.885Å > ui mousemode right select > select #25/A:153@CA 1 atom, 1 residue, 1 model selected > select #23-26 /A :153 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 cartoons > hide sel & #!25 atoms > color (#!25 & sel) dark gray > select clear > select #23-26 /A :155 28 atoms, 24 bonds, 4 residues, 4 models selected > select #23-26 /A :222 28 atoms, 28 bonds, 4 residues, 4 models selected > show sel & #!25 atoms > style sel & #!25 ball Changed 7 atom styles > color (#!25 & sel) byelement > hide #27.1 models > show #27.1 models > select #23-26 /A :22 Nothing selected > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style (#!25 & sel) ringFill thick Changed 1 residue ring style > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style (#!25 & sel) ringFill thin Changed 1 residue ring style > select clear > select #23-26 /A :222, 153 56 atoms, 56 bonds, 8 residues, 4 models selected > select #23-26 /A :222, 151 56 atoms, 56 bonds, 8 residues, 4 models selected > style (#!25 & sel) ringFill thin Changed 2 residue ring styles > color (#!25 & sel) black > color (#!25 & sel) byelement > select clear > select #23-26 /A :156-146 Nothing selected > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!25 cartoons > show sel & #!25 atoms > hide (#!25 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!25 & sel-residues) > show (#!25 & sel-residues & backbone) target ab > select #23-26 /A :219-224 179 atoms, 188 bonds, 1 pseudobond, 24 residues, 5 models selected > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!25 cartoons > show sel & #!25 atoms > hide (#!25 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!25 & sel-residues) > show (#!25 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147 142 atoms, 131 bonds, 4 pseudobonds, 20 residues, 5 models selected > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected > show (#!25 & sel-residues & sidechain) target ab > select clear > select #25/A:145 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #25/A:230@C 1 atom, 1 residue, 1 model selected > select #25/A:230@CA 1 atom, 1 residue, 1 model selected > select #25/A:230@CA 1 atom, 1 residue, 1 model selected > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style sel & #!25 sphere Changed 12 atom styles > select clear > select #23-26 /A :220 30 atoms, 27 bonds, 4 residues, 4 models selected > style sel & #!25 ball Changed 12 atom styles > select clear > hide #27.1 models > hide #!27 models > show #!26 models > hide #!25 models > show #!25 models > show #!24 models > hide #!25 models > hide #!26 models > show #!25 models > hide #!25 models > show #!23 models > hide #!23 models > hide #!24 models > show #!24 models > show #!26 models > hide #!26 models > show #!25 models > show #!23 models > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 4 pseudobonds, 24 residues, 5 models selected > style sel & #!23-25 ball Changed 129 atom styles > show sel & #!23-25 atoms > color (#!23-25 & sel) byelement > style (#!23-25 & sel) ringFill thin Changed 18 residue ring styles > hide #!25 models > hide #!24 models > show #!24 models > hide #!23 models > show #!23 models > hide #!24 models > show #!25 models > hide #!23 models > show #!27 models > select clear [Repeated 1 time(s)] > ui tool show ""Side View"" > save ""/Users/kompa012/Desktop/P53/1uol Y220 .png"" width 3000 height 2320 > supersample 3 transparentBackground true > hide #!25 models > show #!24 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > select #23-26 /A :220,155 58 atoms, 51 bonds, 1 pseudobond, 8 residues, 5 models selected > hide sel & #!24 cartoons > ui mousemode right distance > distance #24/A:220@N #24/A:155@O Distance between 2j1x #24/A CYS 220 N and THR 155 O: 2.911Å > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!24 cartoons > hide sel & #!24 atoms > show sel & #!24 atoms > hide sel & #!24 cartoons > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > select up 707 atoms, 732 bonds, 1 pseudobond, 92 residues, 9 models selected > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > hide sel & #!24 cartoons [Repeated 1 time(s)] > show sel & #!24 atoms > hide (#!24 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!24 & sel-residues) > show (#!24 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > show (#!24 & sel-residues & sidechain) target ab > ui mousemode right select > select clear > select #23-26 /A :151,223,222 84 atoms, 88 bonds, 12 residues, 4 models selected > color (#!24 & sel) black > color (#!24 & sel) byelement > select clear > show #!23 models > hide #!24 models > select #23-26 /A :151,223,222 84 atoms, 88 bonds, 12 residues, 4 models selected > color (#!23 & sel) black > color (#!23 & sel) byelement > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!23 cartoons > show sel & #!23 atoms > hide (#!23 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!23 & sel-residues) > show (#!23 & sel-residues & backbone) target ab > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!23 cartoons > show sel & #!23 atoms > hide (#!23 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!23 & sel-residues) > show (#!23 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > show (#!23 & sel-residues & sidechain) target ab > show #!24 models > select clear > save ""/Users/kompa012/Desktop/P53/6shz_2j1x C220.png"" width 3000 height 2320 > supersample 3 transparentBackground true > hide #!24 models > hide #!23 models > show #!26 models > show #!25 models > hide #!25 models > select add #26 3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected > select solvent 19518 atoms, 19518 residues, 51 models selected > hide sel & #!26 atoms > select clear > show #!24 models > hide #!24 models > hide #!26 models > show #!26 models > select #23-26 /A :219-230 331 atoms, 340 bonds, 1 pseudobond, 48 residues, 5 models selected > hide sel & #!26 cartoons > show sel & #!26 cartoons > style sel & #!26 ball Changed 79 atom styles > hide (#!26 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!26 & sel-residues) > show (#!26 & sel-residues & backbone) target ab > select #23-26 /A :146-156 340 atoms, 356 bonds, 44 residues, 4 models selected > hide sel & #!26 cartoons > show sel & #!26 atoms > style sel & #!26 ball Changed 85 atom styles > hide (#!26 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!26 & sel-residues) > show (#!26 & sel-residues & backbone) target ab > select #23-26 /A :151,155,223,220,147,222 170 atoms, 163 bonds, 5 pseudobonds, 24 residues, 5 models selected > color (#!26 & sel) black > style (#!26 & sel) ringFill thin Changed 6 residue ring styles > show (#!26 & sel-residues & sidechain) target ab > color (#!26 & sel) byelement > select add #26.3 1690 atoms, 163 bonds, 5 pseudobonds, 223 residues, 9 models selected > select subtract #26.2 1649 atoms, 124 bonds, 5 pseudobonds, 217 residues, 10 models selected > select add #26.1 1649 atoms, 124 bonds, 13 pseudobonds, 217 residues, 10 models selected > select add #26 3660 atoms, 3283 bonds, 13 pseudobonds, 860 residues, 10 models selected > show sel & #!26 surfaces > hide sel & #!26 surfaces > select ligand 274 atoms, 218 bonds, 60 residues, 16 models selected > style sel & #!26 ball Changed 48 atom styles > color (#!26 & sel) byelement > style sel & #!26 stick Changed 48 atom styles > ui mousemode right distance > distance #26/A:220@N #26/A:155@O Distance between 8a32 #26/A CYS 220 N and THR 155 O: 2.934Å > style (#!26 & sel) ringFill thin Changed 4 residue ring styles > color (#!26 & sel) black > color (#!26 & sel) byelement > distance #26/A:401@O #26/A:151@CD Distance between 8a32 #26/A KVA 401 O and PRO 151 CD: 6.205Å > distance #26/A:401@O1 #26/A:147@CG2 Distance between 8a32 #26/A KVA 401 O1 and VAL 147 CG2: 5.072Å > show #27.1 models > hide #27.1 models > show #27.1 models > hide #27.1 models > distance #26/A:401@O2 #26/A:147@CG2 Distance between 8a32 #26/A KVA 401 O2 and VAL 147 CG2: 3.735Å > show #27.1 models > hide #27.1 models > ui mousemode right select > hide #!26 atoms > undo [Repeated 1 time(s)] > hide #!27 models > show #!27 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > ui mousemode right ""delete markers"" [Repeated 1 time(s)] > ui mousemode right distance > ~distance #26/A:401@O #26/A:151@CD > ~distance #26/A:401@O1 #26/A:147@CG2 > save ""/Users/kompa012/Desktop/P53/8a32 C220 woth cjc769.png"" width 3000 > height 2320 supersample 3 transparentBackground true > save ""/Users/kompa012/Desktop/P53/Y220C mutation details.cxs"" ——— End of log from Thu Mar 13 10:36:24 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S0005DLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 13 days, 23 hours, 45 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 272P7VU: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect new normal Unassigned