id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16477 Crash on Mac waking from sleep yaohe@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-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 0x00000003100bf000 (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 0x000000030f0b3000 (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 0x000000030e0a7000 (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 0x000000030d09b000 (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 0x000000030c08f000 (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 0x000000030b083000 (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 0x000000030a077000 (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 0x000000030906b000 (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 0x000000030805f000 (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 0x0000000307053000 (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 0x0000000306047000 (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 0x000000030503b000 (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 0x000000030402f000 (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 0x00000001f838f840 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD- > coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb"" Chain information for raiA_OD- coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb #1 --- Chain | Description A | No description available > set bgColor white > lighting soft > graphics silhouettes true > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"" Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256, pixel 0.856, shown at level 0.0213, step 1, values float32 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc"" Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32 > ui mousemode right zoom > hide #!2 models > show atoms > style stick Changed 6580 atom styles > nucleotides atoms > style nucleic stick Changed 6575 atom styles > select H 2195 atoms, 204 residues, 1 model selected > delete sel > select clear > show #!2 models > volume #2 level 0.06175 > view > select clear > show #!3 models > hide #!2 models > hide #1 models > volume #3 level 0.1598 > volume #3 level 0.2398 > show #1 models > hide #!3 models > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear Drag select of 3161 atoms, 204 residues, 3480 bonds > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > select #1 4385 atoms, 4907 bonds, 209 residues, 1 model selected > select #1/1-14 Nothing selected > select #1/A:1-14 298 atoms, 332 bonds, 14 residues, 1 model selected > select #1/A:1-14,191-204 593 atoms, 661 bonds, 28 residues, 1 model selected > color sel orange red > select clear > color #1/A:1-14,191-204 orange red > select /A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:23 22 atoms, 24 bonds, 1 residue, 1 model selected > color #1/A:15-23,183-190 purple > select clear > select add /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select add /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:184 44 atoms, 48 bonds, 2 residues, 1 model selected > color sel gray > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:15-23,185-190 purple > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:186 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:15-23,186-190 purple > color sel light gray > select clear > select /A:24 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:25 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:26 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:27 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:50 106 atoms, 113 bonds, 5 residues, 1 model selected > select add /A:49 128 atoms, 137 bonds, 6 residues, 1 model selected > select add /A:48 151 atoms, 162 bonds, 7 residues, 1 model selected > select add /A:47 171 atoms, 183 bonds, 8 residues, 1 model selected > select add /A:46 193 atoms, 207 bonds, 9 residues, 1 model selected > select add /A:45 215 atoms, 231 bonds, 10 residues, 1 model selected > color #1/A:24-27,45-50 royal blue > color sel cornflower blue > select clear > color #1/A:24-27,45-50 cornflower blue > select /A:28 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:29 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /A:30 65 atoms, 70 bonds, 3 residues, 1 model selected > select add /A:31 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:32 105 atoms, 112 bonds, 5 residues, 1 model selected > color #1/A:28-32,40-44 yellow > select clear > color #1/A:33-39 green > select /A:90 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:33-39,85-90 green > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select /A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel gray > select clear > select /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:35 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:35 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:36 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:37 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:38 106 atoms, 113 bonds, 5 residues, 1 model selected > select add /A:39 128 atoms, 137 bonds, 6 residues, 1 model selected > select /A:85 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:34 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select /A:85 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:90 40 atoms, 42 bonds, 2 residues, 1 model selected > color #1/A:34-39,85-90 green > select clear > select /A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:52 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:53 62 atoms, 66 bonds, 3 residues, 1 model selected > select add /A:54 82 atoms, 87 bonds, 4 residues, 1 model selected > color sel cyan > select clear > select add /A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:52 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:53 62 atoms, 66 bonds, 3 residues, 1 model selected > select add /A:54 82 atoms, 87 bonds, 4 residues, 1 model selected > select /A:177 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:176 46 atoms, 50 bonds, 2 residues, 1 model selected > select add /A:175 66 atoms, 71 bonds, 3 residues, 1 model selected > select add /A:174 89 atoms, 96 bonds, 4 residues, 1 model selected > select /A:174 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:51-54, 174-177 cyan > select clear > select /A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:79 46 atoms, 50 bonds, 2 residues, 1 model selected > color #1/A:55-79 orange > select clear > view > color #1/A:55-79 goldenrod rod Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/A:55-79 goldenrod > select /A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:81 42 atoms, 45 bonds, 2 residues, 1 model selected > select clear > select /A:82 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:83 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:84 66 atoms, 71 bonds, 3 residues, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > select /A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:83 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:82 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:181 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:182 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:170 108 atoms, 116 bonds, 5 residues, 1 model selected > select add /A:121 130 atoms, 140 bonds, 6 residues, 1 model selected > select subtract /A:170 107 atoms, 115 bonds, 5 residues, 1 model selected > select subtract /A:121 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:81 107 atoms, 115 bonds, 5 residues, 1 model selected > select add /A:180 127 atoms, 136 bonds, 6 residues, 1 model selected > select add /A:179 150 atoms, 161 bonds, 7 residues, 1 model selected > select add /A:178 173 atoms, 186 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > color sel dark salmon > color sel salmon > color sel light salmon > select clear > select add /A:178 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:179 46 atoms, 50 bonds, 2 residues, 1 model selected > select add /A:180 66 atoms, 71 bonds, 3 residues, 1 model selected > select add /A:181 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:182 108 atoms, 116 bonds, 5 residues, 1 model selected > select clear > select /A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:82 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /A:83 65 atoms, 70 bonds, 3 residues, 1 model selected > select clear > select add /A:178 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:179 46 atoms, 50 bonds, 2 residues, 1 model selected > select /A:180 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:181 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:182 62 atoms, 66 bonds, 3 residues, 1 model selected > color #1/A:81-83, 178-182 salmon > select clear > select add /A:184 22 atoms, 24 bonds, 1 residue, 1 model selected > color #1/A:81-83, 178-184 salmon > select clear > select add /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:183@C3' 1 atom, 1 residue, 1 model selected > select clear > select /A:173 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:172 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select /A:91 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:99 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:100 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:100 45 atoms, 49 bonds, 2 residues, 1 model selected > select add /A:99 67 atoms, 73 bonds, 3 residues, 1 model selected > select subtract /A:99 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:103 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:168 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > color #1/A:119-163 hotpink > select clear > select /A:163 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:118 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:106 46 atoms, 50 bonds, 2 residues, 1 model selected > select /A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:118 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:108 43 atoms, 46 bonds, 2 residues, 1 model selected > color #1/A:108-118 blue > color #1/A:108-118 royalblue > color #1/A:108-118 lblue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A:108-118 blue > select clear > color #1/A:108-118 darkblue > select /A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:101-107,164-170 limegreen > select clear > color #1/A:101-107,164-170 lime > select clear > select add /A:171 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:172 45 atoms, 49 bonds, 2 residues, 1 model selected > select add /A:173 65 atoms, 70 bonds, 3 residues, 1 model selected > select add /A:100 87 atoms, 94 bonds, 4 residues, 1 model selected > select add /A:91 107 atoms, 115 bonds, 5 residues, 1 model selected > color #1/A:91-100, 171-173 lightgray > color #1/A:91-100, 171-173 gray > color #1/A:91-100, 171-173 darkgray > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:183 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:165 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:33 45 atoms, 49 bonds, 2 residues, 1 model selected > color #1/A:33, 84, 91-100, 171-173 darkgray > select clear > select add /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select add /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:183 45 atoms, 49 bonds, 2 residues, 1 model selected > color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray > select clear > color byhetero > select clear > undo > select clear > view > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > volume #2 level 0.06614 > hide #!2 models > view > show #!2 models > volume #2 level 0.07928 > volume #2 color #b2b2b283 > view > show #!3 models > hide #!3 models > hide #!2 models > save ""/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs"" > show #!2 models > hide #!2 models > select Mg 5 atoms, 5 residues, 1 model selected > hide sel target a > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near #1 distance 5.14 > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select clear > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"" Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256, pixel 0.856, shown at level 0.0213, step 1, values float32 > volume #4 level 0.04781 > volume #4 color #b2b2b27a > select clear > view > hide #!2 models > show #!2 models > hide #1 models > hide #!4 models > volume #2 level 0.06335 > select clear > view > view name p1 > ui tool show ""Side View"" > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > surface dust size 3 Missing or invalid ""surfaces"" argument: invalid surfaces specifier > surface dust Missing or invalid ""surfaces"" argument: empty atom specifier > surface dust #2 size 3 > select clear > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > color single #2 > show #1 models > hide #!2 models > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #2 near sel distance 5.14 > select clear > hide #1 models > select clear > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > turn y 90 > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3 > transparentBackground true > view name p2 > view p1 > turn y 90 > turn y 190 > view p1 > view > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc"" Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256, pixel 0.856, shown at level 0.0194, step 1, values float32 > volume #5 color #b2b2b2 > volume #5 level 0.04769 > ui mousemode right ""rotate selected models"" > select add #5 2 models selected > view matrix models > #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003 > fitmap #5 inMap #2 Fit map cryosparc_P44_J208_006_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 57510 points correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5 steps = 160, shift = 7.08, angle = 13.6 degrees Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99520792 0.09266609 -0.03121206 -1.90478254 -0.08638041 0.68359534 -0.72473156 121.64881794 -0.04582162 0.72395470 0.68832403 -45.65379273 Axis 0.99239916 0.01000804 -0.12265292 Axis point 0.00000000 113.18746461 118.36999355 Rotation angle (degrees) 46.87724941 Shift along axis 4.92673271 > select clear > select add #5 2 models selected > view matrix models > #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296 > view matrix models > #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269 > fitmap #5 inMap #2 Fit map cryosparc_P44_J208_006_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 57510 points correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4 steps = 420, shift = 27.3, angle = 61.9 degrees Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.82309682 0.56737562 0.02442404 134.59045503 -0.45808180 -0.63789380 -0.61907396 298.40293952 -0.33566753 -0.52074601 0.78495280 110.25649577 Axis 0.09010312 0.32997103 -0.93968109 Axis point 119.35289183 147.39940598 0.00000000 Rotation angle (degrees) 146.93150884 Shift along axis 6.98539970 > select clear > view p1 > select clear > hide #!2 models > open ""/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN- > coot-13_isolde_real_space_refined_065_isolde.pdb"" Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6 --- Chain | Description A | No description available > select add #6 5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected > view matrix models > #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11 > view matrix models > #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21 > fitmap #6 inMap #5 Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms average map value = 0.01605, steps = 132 shifted from previous position = 4.23 rotated from previous position = 9.84 degrees atoms outside contour = 4651, contour level = 0.047687 Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.86772792 -0.39727738 0.29869543 2.06277270 0.42913695 0.90201861 -0.04694588 -47.94991180 -0.25077830 0.16891749 0.95319313 19.39883446 Axis 0.21254395 0.54102425 0.81370623 Axis point 94.65981773 -21.12486692 0.00000000 Rotation angle (degrees) 30.51798290 Shift along axis -9.71868299 > view matrix models > #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027 > view matrix models > #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164 > fitmap #6 inMap #5 Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms average map value = 0.07683, steps = 172 shifted from previous position = 10.1 rotated from previous position = 25.4 degrees atoms outside contour = 1263, contour level = 0.047687 Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999995 0.00001997 0.00032109 -0.03981368 -0.00001996 1.00000000 -0.00003851 0.01104931 -0.00032109 0.00003851 0.99999995 0.04171659 Axis 0.11885500 0.99099744 -0.06162443 Axis point 130.60221565 0.00000000 125.36760562 Rotation angle (degrees) 0.01856408 Shift along axis 0.00364702 > ui mousemode right zoom > select clear > view p1 > select clear > view p1 > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > hide #!6 models > show #!6 models > hide #!5 models > select clear Drag select of 249 residues, 1 pseudobonds, 498 shapes > nucleotides sel atoms > style nucleic & sel stick Changed 5353 atom styles > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > show #1 models > hide #!6 models > show #!6 models > select #6/A:240 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:14 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:240 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:1 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:253 22 atoms, 24 bonds, 1 residue, 1 model selected > P1a and P1b color #6/A:1-14,240-253 orange red Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red > color #6/A:1-14,240-253 orange red > select clear > select #6/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select #6/A:239 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:238 45 atoms, 49 bonds, 2 residues, 1 model selected > select #6/A:235 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:239 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:20 43 atoms, 46 bonds, 2 residues, 1 model selected > select #6/A:19 20 atoms, 21 bonds, 1 residue, 1 model selected > color #6/A:15-19,235-239 purple > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > hide #1 models > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:59 42 atoms, 45 bonds, 2 residues, 1 model selected > select add #6/A:20 65 atoms, 70 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color #6/A:20-60 darkgoldenrod > select clear > view > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > color #6/A:20-60 pylegoldenrod Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #6/A:20-60 palegoldenrod > select clear > view > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > color #6/A:20-60 tan > select clear > show #!2 models > hide #!2 models > show #1 models > hide #!6 models > show #!6 models > select #1/A:23 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel purple > select clear > select #6/A:20 23 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select clear > hide #1 models > select #6/A:20 23 atoms, 25 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!6 models > show #!6 models > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:59 20 atoms, 21 bonds, 1 residue, 1 model selected > color #6/A:15-20,60,235-239 purple > select clear > hide #1 models > show #!2 models > show #1 models > hide #!2 models > color #6/A:21-59 tan > hide #1 models > show #1 models > select #6/A:61 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:64 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #1/A:50 66 atoms, 71 bonds, 3 residues, 2 models selected > select subtract #1/A:50 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #6/A:87 66 atoms, 71 bonds, 3 residues, 1 model selected > select add #6/A:82 88 atoms, 95 bonds, 4 residues, 1 model selected > color #6/A:61-64,82-87 cornflower blue > select #6/A:65 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:65 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:69 42 atoms, 45 bonds, 2 residues, 1 model selected > select #6/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:65-69,77-81 yellow > select clear > select #6/A:70 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:71 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:76 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:71 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:76 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:123 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:118 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:71-76,118-123 green > undo > color #6/A:71-76,118-123 green > select clear > hide #1 models > show #1 models > select #6/A:88 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:91 40 atoms, 42 bonds, 2 residues, 1 model selected > select add #6/A:92 63 atoms, 67 bonds, 3 residues, 1 model selected > select subtract #6/A:92 40 atoms, 42 bonds, 2 residues, 1 model selected > select #6/A:226 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:223 46 atoms, 50 bonds, 2 residues, 1 model selected > select subtract #6/A:223 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:223 46 atoms, 50 bonds, 2 residues, 1 model selected > color #6/A:88-91,223-226 cyan > select clear > select #1/A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:112 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > hide #1 models > show #1 models > hide #1 models > show #1 models > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:112 20 atoms, 21 bonds, 1 residue, 1 model selected > hide #1 models > show #1 models > hide #!6 models > select #1/A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:33,80,84,91-100,171-173,183,185 darkgray > select clear > show #!2 models > hide #1 models > show #1 models > hide #!2 models > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > color #2 near 1 distance 5 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > colorzone #2 near 1 distance 5 Unknown command: colorzone #2 near 1 distance 5 > color zone #2 near 1 distance 5 Invalid ""near"" argument: invalid atoms specifier > color zone #2 near #1 distance 5 > select clear > hide #!2 models > hide #1 models > view p1 > show #1 models > show #!2 models > hide #1 models > show #!6 models > hide #!2 models > color #6/A:92-112 goldenrod > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #1 models > show #!2 models > hide #!2 models > show #1 models > hide #1 models > select #6/A:70 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #1 models > select #1/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:114 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:115 42 atoms, 45 bonds, 2 residues, 1 model selected > select add #6/A:116 65 atoms, 70 bonds, 3 residues, 1 model selected > select #6/A:227 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:233 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:114-116,227-233 salmon > hide #1 models > show #1 models > hide #!6 models > show #!6 models > select #1/A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:232 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #1 models > show #1 models > hide #1 models > select #6/A:234 23 atoms, 25 bonds, 1 residue, 1 model selected > color #6/A:70,232,234 darkgray > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select #6/A:219 23 atoms, 25 bonds, 1 residue, 1 model selected > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:219 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:213 46 atoms, 50 bonds, 2 residues, 1 model selected > select #6/A:140 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:134 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > color #6/A:134-140,213-219 lime > select #6/A:141 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:174 23 atoms, 25 bonds, 1 residue, 1 model selected > color #6/A:141-174 darkblue > select clear > select #6/A:212 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:175 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:175-212 hotpink > hide #1 models > view p1 > select clear > show #1 models > hide #1 models > select #6/A:124 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:133 42 atoms, 45 bonds, 2 residues, 1 model selected > select #6/A:222 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:220 42 atoms, 45 bonds, 2 residues, 1 model selected > color #6/A:70,113,117,124-133,220-222,232,234 darkgray > select clear > view p1 > show #!5 models > volume #5 level 0.05695 > ui tool show ""Color Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #5 near #6 distance 5.14 > color zone #5 near #6 distance 5.1 > color zone #5 near #6 distance 5 > hide #!5 models > show #!5 models > hide #!6 models > volume #5 level 0.05886 > volume #5 level 0.05504 > show #!2 models > hide #!2 models > show #1 models > show #!6 models > hide #!6 models > hide #!5 models > show #!2 models > hide #1 models > save /Users/heyao/Desktop/fig1.cxs > show #!6 models > hide #!2 models > show #!2 models > hide #!6 models > show #1 models > hide #!2 models > show #!2 models > hide #1 models > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > turn x 180 > turn z 180 > save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3 > transparentBackground true > show #1 models > hide #1 models > hide #!2 models > show #!6 models > hide #!6 models > show #!5 models > ui tool show ""Hide Dust"" > surface dust #5 size 5.14 > surface dust #5 size 4.94 > surface dust #5 size 1.19 > surface dust #5 size 1.74 > surface dust #5 size 1 > surface dust #5 size 3 > save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3 > transparentBackground true > turn z 180 > save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3 > transparentBackground true > view p1 > save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3 > transparentBackground true > view > select clear > volume #5 level 0.07883 > view p1 > volume #5 level 0.04591 > view p1 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc"" Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32 > volume #7 level 0.09953 > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617 > fitmap #7 inMap #5 Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map cryosparc_P44_J208_006_volume_map.mrc using 33096 points correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7 steps = 164, shift = 18.4, angle = 13.5 degrees Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999995 -0.00009731 0.00030468 -0.02233620 0.00009737 0.99999998 -0.00018529 0.01126621 -0.00030466 0.00018532 0.99999994 0.01925316 Axis 0.50131231 0.82422219 0.26333202 Axis point 60.44868633 0.00000000 78.51712028 Rotation angle (degrees) 0.02117924 Shift along axis 0.00315842 > select clear > hide #!5 models > volume #7 level 0.1479 > volume #7 level 0.1142 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface dust #7 size 5.14 > color zone #7 near #6 distance 5.14 > select clear > volume #7 level 0.09513 > surface dust #7 size 5.17 > surface dust #7 size 2.59 > hide #!7 models > show #1 models > hide #1 models > show #!2 models > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc"" Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256, pixel 0.856, shown at level 0.0109, step 1, values float32 > volume #8 level 0.05676 > select add #8 2 models selected > view matrix models > #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51 > view matrix models > #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04 > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected Must specify one map, got 0 > fitmap #8 inMap #2 Fit map cryosparc_P44_J119_007_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 32003 points correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41 steps = 120, shift = 7.63, angle = 7.11 degrees Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.67932839 -0.70734554 0.19538482 233.17463966 -0.32924966 0.53174106 0.78028592 -1.20521285 -0.65582589 0.46573999 -0.59412007 187.73366128 Axis -0.31995815 0.86585704 0.38460157 Axis point 145.04886475 0.00000000 58.92440994 Rotation angle (degrees) 150.55799757 Shift along axis -3.44700659 > select clear > select add #8 2 models selected > view matrix models > #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71 > fitmap #8 inMap #2 Fit map cryosparc_P44_J119_007_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 32003 points correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2 steps = 132, shift = 2.14, angle = 21.9 degrees Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.98172391 0.09005861 0.16765326 -29.84294848 -0.01268335 -0.84802486 0.52980466 149.11768328 0.18988760 -0.52224830 -0.83138403 232.76992784 Axis -0.99504515 -0.02102952 -0.09717466 Axis point 0.00000000 108.37326391 96.40524730 Rotation angle (degrees) 148.08599472 Shift along axis 3.93986945 > select clear > hide #!8 models > show #!8 models > hide #!2 models > show #!2 models > select clear > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN- > coot-11_isolde.pdb"" Chain information for initial_model_AN-coot-11_isolde.pdb #9 --- Chain | Description A | No description available > select add #9 3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected > hide #!2 models > view matrix models > #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07 > fitmap #9 inMap #8 Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms average map value = 0.06906, steps = 132 shifted from previous position = 6.96 rotated from previous position = 16.8 degrees atoms outside contour = 1046, contour level = 0.056762 Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.99999922 0.00120715 0.00033324 -0.17137916 -0.00120711 0.99999926 -0.00015796 0.15354463 -0.00033343 0.00015757 0.99999994 0.01154017 Axis 0.12499238 0.26409247 -0.95636399 Axis point 125.34278901 142.88874346 0.00000000 Rotation angle (degrees) 0.07231914 Shift along axis 0.00809228 > select clear > ui mousemode right zoom > view p1 > select clear > hide #!8 models > select clear Drag select of 155 residues, 2 pseudobonds, 310 shapes > nucleotides sel atoms > style nucleic & sel stick Changed 3336 atom styles > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > show #!8 models > hide #!8 models > show #1 models > select clear > select #1/A:191 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:150 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:14 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:150 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:163 23 atoms, 25 bonds, 1 residue, 1 model selected > color #9/A:1-14,150-163 orange red > select clear > select #1/A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select #1/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:23 42 atoms, 45 bonds, 2 residues, 2 models selected > select #1/A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:149 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:145 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:15-23,145-149 purple > undo > hide #1 models > hide #!9 models > show #!5 models > hide #!5 models > show #!6 models > show #!9 models > hide #!6 models > undo No undo action is available > undo No undo action is available > undo No undo action is available > undo No undo action is available > select clear > color #9/A:15-23,145-149 purple > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > select #1/A:24 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #1/A:27 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #1/A:50 66 atoms, 71 bonds, 3 residues, 1 model selected > select add #9/A:45 88 atoms, 95 bonds, 4 residues, 2 models selected > color #9/A:24-27,45-50 cornflower blue > select clear > hide #!9 models > show #!9 models > hide #1 models > show #1 models > select #9/A:28 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:32 42 atoms, 45 bonds, 2 residues, 1 model selected > select #9/A:40 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:44 45 atoms, 49 bonds, 2 residues, 1 model selected > color #9/A:28-32,40-44 yellow > select clear > select #1/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:39 46 atoms, 50 bonds, 2 residues, 1 model selected > select #9/A:92 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:87 20 atoms, 21 bonds, 1 residue, 1 model selected > color #9/A:34-39,87-92 green > select clear > hide #1 models > show #1 models > hide #1 models > select #9/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel darg gray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel darkgray > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!9 models > show #!9 models > select #1/A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:54 40 atoms, 42 bonds, 2 residues, 1 model selected > select clear > select #9/A:136 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:133 46 atoms, 50 bonds, 2 residues, 1 model selected > color #9/A:51-54,133-136 cyan > select clear > hide #1 models > show #1 models > select #9/A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:81 20 atoms, 21 bonds, 1 residue, 1 model selected > hide #1 models > select clear > select #9/A:81 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > color #9/A:55-81 goldenrod > select clear > hide #1 models > show #1 models > select #9/A:83 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:85 45 atoms, 49 bonds, 2 residues, 1 model selected > select #1/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:83 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:85 45 atoms, 49 bonds, 2 residues, 1 model selected > select #1/A:184 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:143 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:143 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:137 23 atoms, 25 bonds, 1 residue, 1 model selected > color #9/A:83-85,137-143 salmon > select clear > select #1/A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #1/A:185 45 atoms, 49 bonds, 2 residues, 1 model selected > hide #1 models > show #1 models > hide #1 models > select add #9/A:142 67 atoms, 73 bonds, 3 residues, 2 models selected > select add #9/A:144 89 atoms, 97 bonds, 4 residues, 2 models selected > color #9/A:33, 82, 86, 142,144 darkgray > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > select #9/A:93 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > select #9/A:121 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #1 models > select add #9/A:108 43 atoms, 46 bonds, 2 residues, 1 model selected > show #1 models > hide #1 models > color #9/A:108-121 darkblue > select clear > select add #9/A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > select add #1/A:101 43 atoms, 46 bonds, 2 residues, 2 models selected > select add #9/A:102 65 atoms, 70 bonds, 3 residues, 2 models selected > select #1/A:102 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #!9 models > show #!9 models > hide #1 models > select #9/A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:128 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:127 43 atoms, 46 bonds, 2 residues, 1 model selected > select add #9/A:126 66 atoms, 71 bonds, 3 residues, 1 model selected > show #1 models > select add #9/A:129 88 atoms, 95 bonds, 4 residues, 1 model selected > select #9/A:103 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:107 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > color #9/A:103-107,126-129 lime > select clear > hide #1 models > select #9/A:102 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:130 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:132 42 atoms, 45 bonds, 2 residues, 1 model selected > select #9/A:93 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:102 42 atoms, 45 bonds, 2 residues, 1 model selected > color #9/A:33,82,86,93-102,130-132,142,144 darkgray > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > save /Users/heyao/Desktop/fig1.cxs > show #!8 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #8 near #9 distance 5.14 > color zone #8 near #9 distance 4.96 > color zone #8 near #9 distance 3.98 > surface dust #8 size 5.14 > volume #8 level 0.06701 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc"" Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32 > volume #10 level 0.1802 > select add #10 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13 > volume #10 level 0.08858 > view matrix models > #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58 Must specify one map, got 0 > fitmap #10 inMap #8 Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map cryosparc_P44_J119_007_volume_map.mrc using 27855 points correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1 steps = 120, shift = 6.72, angle = 13 degrees Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.99999985 0.00045450 0.00030702 -0.07641814 -0.00045451 0.99999989 0.00002918 0.05384633 -0.00030700 -0.00002931 0.99999995 0.03236712 Axis -0.05324606 0.55895242 -0.82748840 Axis point 109.35316698 167.30731259 0.00000000 Rotation angle (degrees) 0.03147028 Shift along axis 0.00738308 > select clear > save /Users/heyao/Desktop/fig1.cxs > surface dust #10 size 5.14 > color zone #10 near #9 distance 5.14 > hide #!8 models > hide #!9 models > volume #10 level 0.08349 > view p1 > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!10 models > show #!8 models > hide #!10 models > show #!10 models > hide #!8 models > volume #10 level 0.08172 > volume #10 level 0.07116 > show #!8 models > volume #8 level 0.05258 > volume #8 level 0.04487 > select #8 2 models selected > show #!9 models > hide #!8 models > select clear > show #!8 models > color #8 #d6d6d6ff models > color #8 silver models > color zone #10 near #9 distance 5.14 > color zone #8 near #9 distance 5.14 > select clear > hide #!8 models > hide #!9 models > show #1 models > hide #1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > color #3 #b2b2b2ff models > color zone #3 near #1 distance 5.14 > view > view p1 > volume #3 level 0.1706 > volume #3 level 0.19 > volume #3 level 0.2 > volume #3 level 0.1481 > view > view p1 > show #1 models > hide #!2 models Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near sel distance 5 > hide #!2 models > show #!2 models > hide #1 models > view p1 > volume #2 level 0.07 > volume #2 level 0.05 > volume #2 level 0.06 > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view p1 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!5 models > volume #5 level 0.05207 > view p1 > save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!5 models > show #!10 models > show #!8 models > hide #!10 models > view p1 > volume #8 level 0.05187 > volume #8 level 0.04053 > view p1 > view > view p1 > save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3 > transparentBackground true > show #!2 models > hide #!2 models > show #!2 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > show #!8 models > view p1 > hide #!8 models > show #!8 models > hide #!2 models > volume #8 level 0.05 > view p1 > save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3 > transparentBackground true > save /Users/heyao/Desktop/fig1.cxs > show #!2 models > hide #!8 models > view p2 > turn y 180 > save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!2 models > show #!2 models > hide #!2 models > show #!5 models > save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3 > transparentBackground true > volume #5 level 0.04797 > save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!5 models > show #!10 models > hide #!10 models > show #!8 models > view p1 > show #!3 models > hide #!3 models > show #!2 models > hide #!8 models > view p1 > turn y 90 > turn x 90 > hide #!2 models > show #1 models > select clear > view p1 > save /Users/heyao/Desktop/31.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/32.png width 2000 height 2000 supersample 3 > transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/heyao/Desktop/fig1.cxs Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256, pixel 0.856, shown at level 0.06, step 1, values float32 Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.856, shown at level 0.148, step 1, values float32 Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256, pixel 0.856, shown at level 0.0478, step 1, values float32 Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256, pixel 0.856, shown at level 0.0521, step 1, values float32 Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 0.856, shown at level 0.0951, step 1, values float32 Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256, pixel 0.856, shown at level 0.05, step 1, values float32 Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 0.856, shown at level 0.0712, step 1, values float32 Log from Sat Dec 14 18:45:20 2024You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD- > coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb"" Chain information for raiA_OD- coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb #1 --- Chain | Description A | No description available > set bgColor white > lighting soft > graphics silhouettes true > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"" Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256, pixel 0.856, shown at level 0.0213, step 1, values float32 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc"" Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32 > ui mousemode right zoom > hide #!2 models > show atoms > style stick Changed 6580 atom styles > nucleotides atoms > style nucleic stick Changed 6575 atom styles > select H 2195 atoms, 204 residues, 1 model selected > delete sel > select clear > show #!2 models > volume #2 level 0.06175 > view > select clear > show #!3 models > hide #!2 models > hide #1 models > volume #3 level 0.1598 > volume #3 level 0.2398 > show #1 models > hide #!3 models > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear Drag select of 3161 atoms, 204 residues, 3480 bonds > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > select #1 4385 atoms, 4907 bonds, 209 residues, 1 model selected > select #1/1-14 Nothing selected > select #1/A:1-14 298 atoms, 332 bonds, 14 residues, 1 model selected > select #1/A:1-14,191-204 593 atoms, 661 bonds, 28 residues, 1 model selected > color sel orange red > select clear > color #1/A:1-14,191-204 orange red > select /A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:23 22 atoms, 24 bonds, 1 residue, 1 model selected > color #1/A:15-23,183-190 purple > select clear > select add /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select add /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:184 44 atoms, 48 bonds, 2 residues, 1 model selected > color sel gray > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:15-23,185-190 purple > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:186 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:15-23,186-190 purple > color sel light gray > select clear [Repeated 2 time(s)] > select /A:24 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:25 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:26 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:27 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:50 106 atoms, 113 bonds, 5 residues, 1 model selected > select add /A:49 128 atoms, 137 bonds, 6 residues, 1 model selected > select add /A:48 151 atoms, 162 bonds, 7 residues, 1 model selected > select add /A:47 171 atoms, 183 bonds, 8 residues, 1 model selected > select add /A:46 193 atoms, 207 bonds, 9 residues, 1 model selected > select add /A:45 215 atoms, 231 bonds, 10 residues, 1 model selected > color #1/A:24-27,45-50 royal blue > color sel cornflower blue > select clear > color #1/A:24-27,45-50 cornflower blue > select /A:28 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:29 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /A:30 65 atoms, 70 bonds, 3 residues, 1 model selected > select add /A:31 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:32 105 atoms, 112 bonds, 5 residues, 1 model selected > color #1/A:28-32,40-44 yellow > select clear > color #1/A:33-39 green > select /A:90 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:33-39,85-90 green > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select /A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel gray > select clear > select /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:35 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:35 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:36 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:37 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:38 106 atoms, 113 bonds, 5 residues, 1 model selected > select add /A:39 128 atoms, 137 bonds, 6 residues, 1 model selected > select /A:85 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:34 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select /A:85 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:90 40 atoms, 42 bonds, 2 residues, 1 model selected > color #1/A:34-39,85-90 green > select clear > select /A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:52 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:53 62 atoms, 66 bonds, 3 residues, 1 model selected > select add /A:54 82 atoms, 87 bonds, 4 residues, 1 model selected > color sel cyan > select clear > select add /A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:52 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:53 62 atoms, 66 bonds, 3 residues, 1 model selected > select add /A:54 82 atoms, 87 bonds, 4 residues, 1 model selected > select /A:177 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:176 46 atoms, 50 bonds, 2 residues, 1 model selected > select add /A:175 66 atoms, 71 bonds, 3 residues, 1 model selected > select add /A:174 89 atoms, 96 bonds, 4 residues, 1 model selected > select /A:174 23 atoms, 25 bonds, 1 residue, 1 model selected > color #1/A:51-54, 174-177 cyan > select clear > select /A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:79 46 atoms, 50 bonds, 2 residues, 1 model selected > color #1/A:55-79 orange > select clear > view [Repeated 1 time(s)] > color #1/A:55-79 goldenrod rod Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/A:55-79 goldenrod > select /A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:81 42 atoms, 45 bonds, 2 residues, 1 model selected > select clear > select /A:82 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:83 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:84 66 atoms, 71 bonds, 3 residues, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > select /A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:83 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:82 43 atoms, 46 bonds, 2 residues, 1 model selected > select add /A:181 63 atoms, 67 bonds, 3 residues, 1 model selected > select add /A:182 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:170 108 atoms, 116 bonds, 5 residues, 1 model selected > select add /A:121 130 atoms, 140 bonds, 6 residues, 1 model selected > select subtract /A:170 107 atoms, 115 bonds, 5 residues, 1 model selected > select subtract /A:121 85 atoms, 91 bonds, 4 residues, 1 model selected > select add /A:81 107 atoms, 115 bonds, 5 residues, 1 model selected > select add /A:180 127 atoms, 136 bonds, 6 residues, 1 model selected > select add /A:179 150 atoms, 161 bonds, 7 residues, 1 model selected > select add /A:178 173 atoms, 186 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > color sel dark salmon > color sel salmon > color sel light salmon > select clear > select add /A:178 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:179 46 atoms, 50 bonds, 2 residues, 1 model selected > select add /A:180 66 atoms, 71 bonds, 3 residues, 1 model selected > select add /A:181 86 atoms, 92 bonds, 4 residues, 1 model selected > select add /A:182 108 atoms, 116 bonds, 5 residues, 1 model selected > select clear > select /A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:82 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /A:83 65 atoms, 70 bonds, 3 residues, 1 model selected > select clear > select add /A:178 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:179 46 atoms, 50 bonds, 2 residues, 1 model selected > select /A:180 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:181 40 atoms, 42 bonds, 2 residues, 1 model selected > select add /A:182 62 atoms, 66 bonds, 3 residues, 1 model selected > color #1/A:81-83, 178-182 salmon > select clear > select add /A:184 22 atoms, 24 bonds, 1 residue, 1 model selected > color #1/A:81-83, 178-184 salmon > select clear > select add /A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:183@C3' 1 atom, 1 residue, 1 model selected > select clear > select /A:173 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:172 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select /A:91 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:99 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:100 22 atoms, 24 bonds, 1 residue, 1 model selected > select /A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:100 45 atoms, 49 bonds, 2 residues, 1 model selected > select add /A:99 67 atoms, 73 bonds, 3 residues, 1 model selected > select subtract /A:99 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:103 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /A:168 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > color #1/A:119-163 hotpink > select clear > select /A:163 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select /A:118 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:106 46 atoms, 50 bonds, 2 residues, 1 model selected > select /A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:118 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:108 43 atoms, 46 bonds, 2 residues, 1 model selected > color #1/A:108-118 blue > color #1/A:108-118 royalblue > color #1/A:108-118 lblue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A:108-118 blue > select clear > color #1/A:108-118 darkblue > select /A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:101-107,164-170 limegreen > select clear > color #1/A:101-107,164-170 lime > select clear > select add /A:171 22 atoms, 24 bonds, 1 residue, 1 model selected > select add /A:172 45 atoms, 49 bonds, 2 residues, 1 model selected > select add /A:173 65 atoms, 70 bonds, 3 residues, 1 model selected > select add /A:100 87 atoms, 94 bonds, 4 residues, 1 model selected > select add /A:91 107 atoms, 115 bonds, 5 residues, 1 model selected > color #1/A:91-100, 171-173 lightgray > color #1/A:91-100, 171-173 gray > color #1/A:91-100, 171-173 darkgray > select clear > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:183 45 atoms, 49 bonds, 2 residues, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select /A:165 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /A:84 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:33 45 atoms, 49 bonds, 2 residues, 1 model selected > color #1/A:33, 84, 91-100, 171-173 darkgray > select clear > select add /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select add /A:29 20 atoms, 21 bonds, 1 residue, 1 model selected > select /A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > select add /A:183 45 atoms, 49 bonds, 2 residues, 1 model selected > color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray > select clear > color byhetero > select clear [Repeated 1 time(s)] > undo [Repeated 4 time(s)] > select clear > view > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > volume #2 level 0.06614 > hide #!2 models > view [Repeated 1 time(s)] > show #!2 models > volume #2 level 0.07928 > volume #2 color #b2b2b283 > view [Repeated 1 time(s)] > show #!3 models > hide #!3 models > hide #!2 models > save ""/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs"" > show #!2 models > hide #!2 models > select Mg 5 atoms, 5 residues, 1 model selected > hide sel target a > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near #1 distance 5.14 > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select clear > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"" Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256, pixel 0.856, shown at level 0.0213, step 1, values float32 > volume #4 level 0.04781 > volume #4 color #b2b2b27a > select clear > view > hide #!2 models > show #!2 models > hide #1 models > hide #!4 models > volume #2 level 0.06335 > select clear > view > view name p1 > ui tool show ""Side View"" > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > surface dust size 3 Missing or invalid ""surfaces"" argument: invalid surfaces specifier > surface dust Missing or invalid ""surfaces"" argument: empty atom specifier > surface dust #2 size 3 > select clear > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 [Repeated 2 time(s)] > color single #2 > show #1 models > hide #!2 models > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #2 near sel distance 5.14 > select clear > hide #1 models > select clear > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 [Repeated 2 time(s)] > turn y 90 [Repeated 1 time(s)] > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > turn x 90 > save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3 > transparentBackground true > view name p2 > view p1 > turn y 90 [Repeated 1 time(s)] > turn y 190 [Repeated 1 time(s)] > view p1 > view > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc"" Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256, pixel 0.856, shown at level 0.0194, step 1, values float32 > volume #5 color #b2b2b2 > volume #5 level 0.04769 > ui mousemode right ""rotate selected models"" > select add #5 2 models selected > view matrix models > #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003 > fitmap #5 inMap #2 Fit map cryosparc_P44_J208_006_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 57510 points correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5 steps = 160, shift = 7.08, angle = 13.6 degrees Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99520792 0.09266609 -0.03121206 -1.90478254 -0.08638041 0.68359534 -0.72473156 121.64881794 -0.04582162 0.72395470 0.68832403 -45.65379273 Axis 0.99239916 0.01000804 -0.12265292 Axis point 0.00000000 113.18746461 118.36999355 Rotation angle (degrees) 46.87724941 Shift along axis 4.92673271 > select clear > select add #5 2 models selected > view matrix models > #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296 > view matrix models > #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269 > fitmap #5 inMap #2 Fit map cryosparc_P44_J208_006_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 57510 points correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4 steps = 420, shift = 27.3, angle = 61.9 degrees Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.82309682 0.56737562 0.02442404 134.59045503 -0.45808180 -0.63789380 -0.61907396 298.40293952 -0.33566753 -0.52074601 0.78495280 110.25649577 Axis 0.09010312 0.32997103 -0.93968109 Axis point 119.35289183 147.39940598 0.00000000 Rotation angle (degrees) 146.93150884 Shift along axis 6.98539970 > select clear > view p1 > select clear > hide #!2 models > open ""/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN- > coot-13_isolde_real_space_refined_065_isolde.pdb"" Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6 --- Chain | Description A | No description available > select add #6 5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected > view matrix models > #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11 > view matrix models > #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21 > fitmap #6 inMap #5 Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms average map value = 0.01605, steps = 132 shifted from previous position = 4.23 rotated from previous position = 9.84 degrees atoms outside contour = 4651, contour level = 0.047687 Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.86772792 -0.39727738 0.29869543 2.06277270 0.42913695 0.90201861 -0.04694588 -47.94991180 -0.25077830 0.16891749 0.95319313 19.39883446 Axis 0.21254395 0.54102425 0.81370623 Axis point 94.65981773 -21.12486692 0.00000000 Rotation angle (degrees) 30.51798290 Shift along axis -9.71868299 > view matrix models > #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027 > view matrix models > #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164 > fitmap #6 inMap #5 Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms average map value = 0.07683, steps = 172 shifted from previous position = 10.1 rotated from previous position = 25.4 degrees atoms outside contour = 1263, contour level = 0.047687 Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999995 0.00001997 0.00032109 -0.03981368 -0.00001996 1.00000000 -0.00003851 0.01104931 -0.00032109 0.00003851 0.99999995 0.04171659 Axis 0.11885500 0.99099744 -0.06162443 Axis point 130.60221565 0.00000000 125.36760562 Rotation angle (degrees) 0.01856408 Shift along axis 0.00364702 > ui mousemode right zoom > select clear > view p1 > select clear > view p1 > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > hide #!6 models > show #!6 models > hide #!5 models > select clear Drag select of 249 residues, 1 pseudobonds, 498 shapes > nucleotides sel atoms > style nucleic & sel stick Changed 5353 atom styles > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > show #1 models > hide #!6 models > show #!6 models > select #6/A:240 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:14 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:240 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:1 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:253 22 atoms, 24 bonds, 1 residue, 1 model selected > P1a and P1b color #6/A:1-14,240-253 orange red Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red > color #6/A:1-14,240-253 orange red > select clear [Repeated 1 time(s)] > select #6/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select #6/A:239 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:238 45 atoms, 49 bonds, 2 residues, 1 model selected > select #6/A:235 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:239 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:20 43 atoms, 46 bonds, 2 residues, 1 model selected > select #6/A:19 20 atoms, 21 bonds, 1 residue, 1 model selected > color #6/A:15-19,235-239 purple > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > hide #1 models > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:59 42 atoms, 45 bonds, 2 residues, 1 model selected > select add #6/A:20 65 atoms, 70 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color #6/A:20-60 darkgoldenrod > select clear > view > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > color #6/A:20-60 pylegoldenrod Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #6/A:20-60 palegoldenrod > select clear > view > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > color #6/A:20-60 tan > select clear [Repeated 1 time(s)] > show #!2 models > hide #!2 models > show #1 models > hide #!6 models > show #!6 models > select #1/A:23 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel purple > select clear > select #6/A:20 23 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select clear [Repeated 1 time(s)] > hide #1 models > select #6/A:20 23 atoms, 25 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!6 models > show #!6 models > select #6/A:60 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:59 20 atoms, 21 bonds, 1 residue, 1 model selected > color #6/A:15-20,60,235-239 purple > select clear > hide #1 models > show #!2 models > show #1 models > hide #!2 models > color #6/A:21-59 tan > hide #1 models > show #1 models > select #6/A:61 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:64 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #1/A:50 66 atoms, 71 bonds, 3 residues, 2 models selected > select subtract #1/A:50 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #6/A:87 66 atoms, 71 bonds, 3 residues, 1 model selected > select add #6/A:82 88 atoms, 95 bonds, 4 residues, 1 model selected > color #6/A:61-64,82-87 cornflower blue > select #6/A:65 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:65 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:69 42 atoms, 45 bonds, 2 residues, 1 model selected > select #6/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:65-69,77-81 yellow > select clear [Repeated 1 time(s)] > select #6/A:70 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #6/A:71 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:76 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:71 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:76 45 atoms, 49 bonds, 2 residues, 1 model selected > select clear > select #6/A:123 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:118 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:71-76,118-123 green > undo > color #6/A:71-76,118-123 green > select clear > hide #1 models > show #1 models > select #6/A:88 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:91 40 atoms, 42 bonds, 2 residues, 1 model selected > select add #6/A:92 63 atoms, 67 bonds, 3 residues, 1 model selected > select subtract #6/A:92 40 atoms, 42 bonds, 2 residues, 1 model selected > select #6/A:226 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:223 46 atoms, 50 bonds, 2 residues, 1 model selected > select subtract #6/A:223 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:223 46 atoms, 50 bonds, 2 residues, 1 model selected > color #6/A:88-91,223-226 cyan > select clear > select #1/A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:112 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > hide #1 models > show #1 models > hide #1 models > show #1 models > select #6/A:92 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:112 20 atoms, 21 bonds, 1 residue, 1 model selected > hide #1 models > show #1 models > hide #!6 models > select #1/A:80 20 atoms, 21 bonds, 1 residue, 1 model selected > color #1/A:33,80,84,91-100,171-173,183,185 darkgray > select clear > show #!2 models > hide #1 models > show #1 models > hide #!2 models > select clear Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > color #2 near 1 distance 5 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > colorzone #2 near 1 distance 5 Unknown command: colorzone #2 near 1 distance 5 > color zone #2 near 1 distance 5 Invalid ""near"" argument: invalid atoms specifier > color zone #2 near #1 distance 5 > select clear > hide #!2 models > hide #1 models > view p1 > show #1 models > show #!2 models > hide #1 models > show #!6 models > hide #!2 models > color #6/A:92-112 goldenrod > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #1 models > show #!2 models > hide #!2 models > show #1 models > hide #1 models > select #6/A:70 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #1 models > select #1/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:114 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/A:115 42 atoms, 45 bonds, 2 residues, 1 model selected > select add #6/A:116 65 atoms, 70 bonds, 3 residues, 1 model selected > select #6/A:227 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:233 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:114-116,227-233 salmon > hide #1 models > show #1 models > hide #!6 models > show #!6 models > select #1/A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:232 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:185 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #1 models > show #1 models > hide #1 models > select #6/A:234 23 atoms, 25 bonds, 1 residue, 1 model selected > color #6/A:70,232,234 darkgray > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > select #6/A:219 23 atoms, 25 bonds, 1 residue, 1 model selected > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #1/A:170 23 atoms, 25 bonds, 1 residue, 1 model selected > select #6/A:219 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #6/A:213 46 atoms, 50 bonds, 2 residues, 1 model selected > select #6/A:140 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:134 23 atoms, 25 bonds, 1 residue, 1 model selected > select clear > color #6/A:134-140,213-219 lime > select #6/A:141 20 atoms, 21 bonds, 1 residue, 1 model selected > select #6/A:174 23 atoms, 25 bonds, 1 residue, 1 model selected > color #6/A:141-174 darkblue > select clear > select #6/A:212 22 atoms, 24 bonds, 1 residue, 1 model selected > select #6/A:175 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:175-212 hotpink > hide #1 models > view p1 > select clear > show #1 models > hide #1 models > select #6/A:124 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:133 42 atoms, 45 bonds, 2 residues, 1 model selected > select #6/A:222 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/A:220 42 atoms, 45 bonds, 2 residues, 1 model selected > color #6/A:70,113,117,124-133,220-222,232,234 darkgray > select clear > view p1 > show #!5 models > volume #5 level 0.05695 > ui tool show ""Color Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #5 near #6 distance 5.14 > color zone #5 near #6 distance 5.1 > color zone #5 near #6 distance 5 [Repeated 2 time(s)] > hide #!5 models > show #!5 models > hide #!6 models > volume #5 level 0.05886 > volume #5 level 0.05504 > show #!2 models > hide #!2 models > show #1 models > show #!6 models > hide #!6 models > hide #!5 models > show #!2 models > hide #1 models > save /Users/heyao/Desktop/fig1.cxs > show #!6 models > hide #!2 models > show #!2 models > hide #!6 models > show #1 models > hide #!2 models > show #!2 models > hide #1 models > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 [Repeated 1 time(s)] > turn x 180 [Repeated 1 time(s)] > turn z 180 > save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3 > transparentBackground true > show #1 models > hide #1 models > hide #!2 models > show #!6 models > hide #!6 models > show #!5 models > ui tool show ""Hide Dust"" > surface dust #5 size 5.14 > surface dust #5 size 4.94 > surface dust #5 size 1.19 > surface dust #5 size 1.74 > surface dust #5 size 1 > surface dust #5 size 3 [Repeated 1 time(s)] > save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3 > transparentBackground true > turn z 180 > save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3 > transparentBackground true > view p1 > save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3 > transparentBackground true > view [Repeated 3 time(s)] > select clear > volume #5 level 0.07883 > view p1 > volume #5 level 0.04591 > view p1 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc"" Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32 > volume #7 level 0.09953 > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617 > fitmap #7 inMap #5 Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map cryosparc_P44_J208_006_volume_map.mrc using 33096 points correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7 steps = 164, shift = 18.4, angle = 13.5 degrees Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999995 -0.00009731 0.00030468 -0.02233620 0.00009737 0.99999998 -0.00018529 0.01126621 -0.00030466 0.00018532 0.99999994 0.01925316 Axis 0.50131231 0.82422219 0.26333202 Axis point 60.44868633 0.00000000 78.51712028 Rotation angle (degrees) 0.02117924 Shift along axis 0.00315842 > select clear > hide #!5 models > volume #7 level 0.1479 > volume #7 level 0.1142 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface dust #7 size 5.14 > color zone #7 near #6 distance 5.14 > select clear > volume #7 level 0.09513 > surface dust #7 size 5.17 > surface dust #7 size 2.59 > hide #!7 models > show #1 models > hide #1 models > show #!2 models > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc"" Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256, pixel 0.856, shown at level 0.0109, step 1, values float32 > volume #8 level 0.05676 > select add #8 2 models selected > view matrix models > #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51 > view matrix models > #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04 > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected Must specify one map, got 0 > fitmap #8 inMap #2 Fit map cryosparc_P44_J119_007_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 32003 points correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41 steps = 120, shift = 7.63, angle = 7.11 degrees Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.67932839 -0.70734554 0.19538482 233.17463966 -0.32924966 0.53174106 0.78028592 -1.20521285 -0.65582589 0.46573999 -0.59412007 187.73366128 Axis -0.31995815 0.86585704 0.38460157 Axis point 145.04886475 0.00000000 58.92440994 Rotation angle (degrees) 150.55799757 Shift along axis -3.44700659 > select clear > select add #8 2 models selected > view matrix models > #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71 > fitmap #8 inMap #2 Fit map cryosparc_P44_J119_007_volume_map.mrc in map cryosparc_P44_J306_007_volume_map.mrc using 32003 points correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2 steps = 132, shift = 2.14, angle = 21.9 degrees Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.98172391 0.09005861 0.16765326 -29.84294848 -0.01268335 -0.84802486 0.52980466 149.11768328 0.18988760 -0.52224830 -0.83138403 232.76992784 Axis -0.99504515 -0.02102952 -0.09717466 Axis point 0.00000000 108.37326391 96.40524730 Rotation angle (degrees) 148.08599472 Shift along axis 3.93986945 > select clear > hide #!8 models > show #!8 models > hide #!2 models > show #!2 models > select clear > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN- > coot-11_isolde.pdb"" Chain information for initial_model_AN-coot-11_isolde.pdb #9 --- Chain | Description A | No description available > select add #9 3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected > hide #!2 models > view matrix models > #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07 > fitmap #9 inMap #8 Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms average map value = 0.06906, steps = 132 shifted from previous position = 6.96 rotated from previous position = 16.8 degrees atoms outside contour = 1046, contour level = 0.056762 Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.99999922 0.00120715 0.00033324 -0.17137916 -0.00120711 0.99999926 -0.00015796 0.15354463 -0.00033343 0.00015757 0.99999994 0.01154017 Axis 0.12499238 0.26409247 -0.95636399 Axis point 125.34278901 142.88874346 0.00000000 Rotation angle (degrees) 0.07231914 Shift along axis 0.00809228 > select clear > ui mousemode right zoom > view p1 > select clear > hide #!8 models > select clear Drag select of 155 residues, 2 pseudobonds, 310 shapes > nucleotides sel atoms > style nucleic & sel stick Changed 3336 atom styles > cartoon style sel xsection oval width 1.6 thickness 1.6 > select clear > show #!8 models > hide #!8 models > show #1 models > select clear > select #1/A:191 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:150 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:14 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:150 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:163 23 atoms, 25 bonds, 1 residue, 1 model selected > color #9/A:1-14,150-163 orange red > select clear > select #1/A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select #1/A:15 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:23 42 atoms, 45 bonds, 2 residues, 2 models selected > select #1/A:190 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:149 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:145 22 atoms, 24 bonds, 1 residue, 1 model selected > color #6/A:15-23,145-149 purple [Repeated 1 time(s)] > undo [Repeated 2 time(s)] > hide #1 models > hide #!9 models > show #!5 models > hide #!5 models > show #!6 models > show #!9 models > hide #!6 models > undo [Repeated 10 time(s)]No undo action is available > undo No undo action is available > undo No undo action is available > undo No undo action is available > select clear [Repeated 1 time(s)] > color #9/A:15-23,145-149 purple > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > select #1/A:24 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #1/A:27 46 atoms, 50 bonds, 2 residues, 1 model selected > select add #1/A:50 66 atoms, 71 bonds, 3 residues, 1 model selected > select add #9/A:45 88 atoms, 95 bonds, 4 residues, 2 models selected > color #9/A:24-27,45-50 cornflower blue > select clear > hide #!9 models > show #!9 models > hide #1 models > show #1 models > select #9/A:28 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:32 42 atoms, 45 bonds, 2 residues, 1 model selected > select #9/A:40 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:44 45 atoms, 49 bonds, 2 residues, 1 model selected > color #9/A:28-32,40-44 yellow > select clear > select #1/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > select #1/A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:34 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:39 46 atoms, 50 bonds, 2 residues, 1 model selected > select #9/A:92 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:87 20 atoms, 21 bonds, 1 residue, 1 model selected > color #9/A:34-39,87-92 green > select clear > hide #1 models > show #1 models > hide #1 models > select #9/A:33 22 atoms, 24 bonds, 1 residue, 1 model selected > color sel darg gray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel darkgray > select clear > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!9 models > show #!9 models > select #1/A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:51 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:54 40 atoms, 42 bonds, 2 residues, 1 model selected > select clear > select #9/A:136 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:133 46 atoms, 50 bonds, 2 residues, 1 model selected > color #9/A:51-54,133-136 cyan > select clear > hide #1 models > show #1 models > select #9/A:55 23 atoms, 25 bonds, 1 residue, 1 model selected > select #9/A:81 20 atoms, 21 bonds, 1 residue, 1 model selected > hide #1 models > select clear > select #9/A:81 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > color #9/A:55-81 goldenrod > select clear > hide #1 models > show #1 models > select #9/A:83 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:85 45 atoms, 49 bonds, 2 residues, 1 model selected > select #1/A:81 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:83 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:85 45 atoms, 49 bonds, 2 residues, 1 model selected > select #1/A:184 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:143 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:143 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:137 23 atoms, 25 bonds, 1 residue, 1 model selected > color #9/A:83-85,137-143 salmon > select clear > select #1/A:183 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #1/A:185 45 atoms, 49 bonds, 2 residues, 1 model selected > hide #1 models > show #1 models > hide #1 models > select add #9/A:142 67 atoms, 73 bonds, 3 residues, 2 models selected > select add #9/A:144 89 atoms, 97 bonds, 4 residues, 2 models selected > color #9/A:33, 82, 86, 142,144 darkgray > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > select #9/A:93 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > select #9/A:121 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #1 models > select add #9/A:108 43 atoms, 46 bonds, 2 residues, 1 model selected > show #1 models > hide #1 models > color #9/A:108-121 darkblue > select clear > select add #9/A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > show #1 models > select add #1/A:101 43 atoms, 46 bonds, 2 residues, 2 models selected > select add #9/A:102 65 atoms, 70 bonds, 3 residues, 2 models selected > select #1/A:102 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:101 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #!9 models > show #!9 models > hide #1 models > select #9/A:107 20 atoms, 21 bonds, 1 residue, 1 model selected > select #9/A:128 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:127 43 atoms, 46 bonds, 2 residues, 1 model selected > select add #9/A:126 66 atoms, 71 bonds, 3 residues, 1 model selected > show #1 models > select add #9/A:129 88 atoms, 95 bonds, 4 residues, 1 model selected > select #9/A:103 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #9/A:107 43 atoms, 46 bonds, 2 residues, 1 model selected > select clear > color #9/A:103-107,126-129 lime > select clear > hide #1 models > select #9/A:102 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/A:130 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #9/A:132 42 atoms, 45 bonds, 2 residues, 1 model selected > select #9/A:93 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #9/A:102 42 atoms, 45 bonds, 2 residues, 1 model selected > color #9/A:33,82,86,93-102,130-132,142,144 darkgray > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > save /Users/heyao/Desktop/fig1.cxs > show #!8 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #8 near #9 distance 5.14 > color zone #8 near #9 distance 4.96 > color zone #8 near #9 distance 3.98 > surface dust #8 size 5.14 > volume #8 level 0.06701 > open ""/Users/heyao/My > Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc"" Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32 > volume #10 level 0.1802 > select add #10 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13 > volume #10 level 0.08858 > view matrix models > #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58 Must specify one map, got 0 > fitmap #10 inMap #8 Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map cryosparc_P44_J119_007_volume_map.mrc using 27855 points correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1 steps = 120, shift = 6.72, angle = 13 degrees Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.99999985 0.00045450 0.00030702 -0.07641814 -0.00045451 0.99999989 0.00002918 0.05384633 -0.00030700 -0.00002931 0.99999995 0.03236712 Axis -0.05324606 0.55895242 -0.82748840 Axis point 109.35316698 167.30731259 0.00000000 Rotation angle (degrees) 0.03147028 Shift along axis 0.00738308 > select clear > save /Users/heyao/Desktop/fig1.cxs > surface dust #10 size 5.14 > color zone #10 near #9 distance 5.14 > hide #!8 models > hide #!9 models > volume #10 level 0.08349 > view p1 > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!10 models > show #!8 models > hide #!10 models > show #!10 models > hide #!8 models > volume #10 level 0.08172 > volume #10 level 0.07116 > show #!8 models > volume #8 level 0.05258 > volume #8 level 0.04487 > select #8 2 models selected > show #!9 models > hide #!8 models > select clear > show #!8 models > color #8 #d6d6d6ff models > color #8 silver models > color zone #10 near #9 distance 5.14 [Repeated 1 time(s)] > color zone #8 near #9 distance 5.14 > select clear > hide #!8 models > hide #!9 models > show #1 models > hide #1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > color #3 #b2b2b2ff models > color zone #3 near #1 distance 5.14 > view > view p1 > volume #3 level 0.1706 > volume #3 level 0.19 > volume #3 level 0.2 > volume #3 level 0.1481 > view > view p1 > show #1 models > hide #!2 models Drag select of 3156 atoms, 204 residues, 3480 bonds > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near sel distance 5 > hide #!2 models > show #!2 models > hide #1 models > view p1 > volume #2 level 0.07 > volume #2 level 0.05 > volume #2 level 0.06 > view p1 > save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view p1 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!5 models > volume #5 level 0.05207 > view p1 > save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3 > transparentBackground true > hide #!5 models > show #!10 models > show #!8 models > hide #!10 models > view p1 > volume #8 level 0.05187 > volume #8 level 0.04053 > view p1 > view > view p1 > save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 > turn z 180 > save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3 > transparentBackground true > show #!2 models > hide #!2 models > show #!2 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > show #!8 models > view p1 > hide #!8 models > show #!8 models > hide #!2 models > volume #8 level 0.05 > view p1 > save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3 > transparentBackground true > turn y 180 > save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3 > transparentBackground true > view p2 [Repeated 1 time(s)] > turn z 180 > save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3 > transparentBackground true > save /Users/heyao/Desktop/fig1.cxs ——— End of log from Sat Dec 14 18:45:20 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 3 days, 25 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ROG PG278QR: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 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-ISOLDE: 1.8 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-PICKLUSTER: 0.5 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 assigned normal Window Toolkit all ChimeraX