id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17082 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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 Thread 0x00000003c5f53000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321c3b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000315437000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031442b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031341f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000312413000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311407000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003103fb000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f3ef000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030e3e3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030d3d7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030c3cb000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, 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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 [deleted to fit within ticket limits] > 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 > 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 > 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 > 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"" > open ""/Users/kompa012/Desktop/P53/Before mutation.cxs"" opened ChimeraX session > show #!11 models > hide #!8 models > save /Users/kompa012/Desktop/P53/4hje.png width 3000 height 2520 supersample > 3 transparentBackground true > open ""/Users/kompa012/Desktop/P53/Y220C mutation.cxs"" 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"" > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 3d0a #19/F DG 4 O4'; 2ac0 #2/A LYS 292 N; 2ata #5/C LYS 291 N; 2ahi #4/A GLY 293 N; 2ata #5/B LYS 292 N; 2ata #5/D LYS 291 N; 3d0a #19/B PRO 153 N; 3d0a #19/D ARG 110 NE; 3d0a #19/D ARG 283 NE 1055 hydrogen bonds found > show #!26 models > show #!24 models > show #!23 models > show #!19 models > hide #!19 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 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, 10 hours, 51 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 closed normal Window Toolkit duplicate all ChimeraX