id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17696 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001fc52fac0 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, 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824 \n__CTF 824 1 \n__DATA 29.2M 1078 \n__DATA_CONST 53.5M 1083 \n__DATA_DIRTY 2899K 323 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 568.6M 254 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2195K 1 \n__TEXT 1.1G 1102 \ndyld private memory 592K 6 \nmapped file 633.2M 110 \nshared memory 3184K 26 \n=========== ======= ======= \nTOTAL 35.9G 6472 \nTOTAL, minus reserved VM space 35.3G 6472 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""e31c6638a66bae05b4c42da66404da29be6e10bb"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/admin/Desktop/FGH-allS DNA.cxs"" Log from Wed May 14 14:35:55 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/admin/Desktop/FGH-allS DNA.cxs"" Log from Wed May 14 13:57:59 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. [deleted to fit within ticket limits] > hbonds sel showDist true restrict cross select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 2_All-S_DNA_ir-F.pdb 66 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A LYS 428 NZ /D GLU 68 OE2 /A LYS 428 3HZ 3.542 2.919 /D ASN 12 ND2 /K DT 14 OP1 /D ASN 12 2HD2 3.351 2.512 /D LYS 24 NZ /K DC 12 O2 /D LYS 24 1HZ 2.578 1.977 /D LYS 24 NZ /K DC 12 OP2 /D LYS 24 3HZ 2.831 2.079 /D ARG 87 NH2 /B GLU 435 O /D ARG 87 1HH2 3.528 2.879 /D TYR 346 OH /K DG 13 OP1 /D TYR 346 HH 3.427 2.705 /D GLN 373 NE2 /E ASP 823 OD1 /D GLN 373 1HE2 3.310 2.483 /D GLN 373 NE2 /E ASP 823 OD2 /D GLN 373 1HE2 3.125 2.459 /D ARG 420 NE /E ASP 827 OD2 /D ARG 420 HE 3.242 2.483 /E ARG 230 NH1 /D SER 221 OG /E ARG 230 1HH1 3.066 2.357 /J DG 11 N1 /K DC 30 N3 /J DG 11 H1 2.872 2.075 /J DG 11 N2 /K DC 30 N3 /J DG 11 H21 3.565 2.917 /J DG 11 N2 /K DC 30 O2 /J DG 11 H21 2.647 1.840 /J DG 12 N1 /K DC 29 N3 /J DG 12 H1 2.866 2.019 /J DG 12 N2 /K DC 29 N3 /J DG 12 H21 3.618 2.961 /J DG 12 N2 /K DC 29 O2 /J DG 12 H21 2.764 1.927 /J DT 13 N3 /K DA 27 N1 /J DT 13 H3 2.922 2.262 /J DC 15 N4 /K DG 26 O6 /J DC 15 H41 2.871 2.054 /J DT 16 N3 /K DA 25 N1 /J DT 16 H3 2.743 2.012 /J DC 17 N4 /K DG 24 O6 /J DC 17 H41 2.883 2.046 /J DC 18 N4 /K DG 23 O6 /J DC 18 H41 2.912 2.055 /J DC 19 N4 /K DG 22 O6 /J DC 19 H41 2.913 2.068 /J DA 20 N6 /K DT 21 O4 /J DA 20 H61 2.931 2.082 /J DG 21 N1 /K DC 20 N3 /J DG 21 H1 2.900 2.056 /J DG 21 N2 /K DC 20 N3 /J DG 21 H21 3.636 2.980 /J DG 21 N2 /K DC 20 O2 /J DG 21 H21 2.807 1.988 /J DT 22 N3 /K DA 19 N1 /J DT 22 H3 2.802 1.952 /J DC 23 N4 /K DG 18 O6 /J DC 23 H41 2.902 2.043 /J DA 24 N6 /K DT 17 O4 /J DA 24 H61 2.883 2.080 /J DC 25 N4 /K DG 16 O6 /J DC 25 H42 2.906 2.051 /J DG 26 N1 /K DC 15 N3 /J DG 26 H1 2.912 2.079 /J DG 26 N2 /K DC 15 N3 /J DG 26 H21 3.655 3.001 /J DG 26 N2 /K DC 15 O2 /J DG 26 H21 2.829 2.003 /J DA 27 N6 /K DT 14 O4 /J DA 27 H61 3.420 2.797 /J DG 29 N1 /K DG 13 N7 /J DG 29 H1 3.247 2.523 /J DT 30 N3 /K DA 11 N1 /J DT 30 H3 3.126 2.507 /K DC 9 N4 /J DA 34 N6 /K DC 9 H41 3.080 2.473 /K DA 10 N6 /J DT 31 O4 /K DA 10 H62 3.679 3.012 /K DA 11 N6 /J DT 30 O4 /K DA 11 H61 3.027 2.305 /K DC 15 N4 /J DG 26 O6 /K DC 15 H41 2.898 2.040 /K DG 16 N1 /J DC 25 N3 /K DG 16 H1 2.871 2.086 /K DG 16 N2 /J DC 25 N3 /K DG 16 H21 3.611 2.979 /K DG 16 N2 /J DC 25 O2 /K DG 16 H21 2.742 1.921 /K DT 17 N3 /J DA 24 N1 /K DT 17 H3 2.832 2.216 /K DG 18 N1 /J DC 23 N3 /K DG 18 H1 2.860 2.001 /K DG 18 N2 /J DC 23 N3 /K DG 18 H21 3.586 2.925 /K DG 18 N2 /J DC 23 O2 /K DG 18 H21 2.741 1.892 /K DA 19 N6 /J DT 22 O4 /K DA 19 H61 2.923 2.067 /K DC 20 N4 /J DG 21 O6 /K DC 20 H41 2.908 2.051 /K DT 21 N3 /J DA 20 N1 /K DT 21 H3 2.892 2.032 /K DG 22 N1 /J DC 19 N3 /K DG 22 H1 2.892 2.051 /K DG 22 N2 /J DC 19 N3 /K DG 22 H21 3.632 2.981 /K DG 22 N2 /J DC 19 O2 /K DG 22 H21 2.769 1.927 /K DG 23 N1 /J DC 18 N3 /K DG 23 H1 2.876 2.027 /K DG 23 N2 /J DC 18 N3 /K DG 23 H21 3.618 2.963 /K DG 23 N2 /J DC 18 O2 /K DG 23 H21 2.745 1.894 /K DG 24 N1 /J DC 17 N3 /K DG 24 H1 2.884 2.045 /K DG 24 N2 /J DC 17 N3 /K DG 24 H21 3.630 2.981 /K DG 24 N2 /J DC 17 O2 /K DG 24 H21 2.792 1.940 /K DA 25 N6 /J DT 16 O4 /K DA 25 H61 3.017 2.373 /K DG 26 N1 /J DC 15 N3 /K DG 26 H1 2.895 2.273 /K DG 26 N2 /J DC 15 N3 /K DG 26 H21 3.677 3.125 /K DG 26 N2 /J DC 15 O2 /K DG 26 H21 2.815 2.156 /K DA 27 N6 /J DT 13 O4 /K DA 27 H61 2.869 2.246 /K DC 29 N4 /J DG 12 O6 /K DC 29 H41 2.885 2.033 /K DC 30 N4 /J DG 11 O6 /K DC 30 H41 2.992 2.235 66 hydrogen bonds found > select ((/J & ::polymer_type>0 ) & ((/D & ::polymer_type>0 ) :<3.5)) | ((/D & ::polymer_type>0 ) & ((/J & ::polymer_type>0 ) :<3.5)) 344 atoms, 353 bonds, 13 residues, 1 model selected > select ((/J & ::polymer_type>0 ) & ((/D & ::polymer_type>0 ) :<3.5)) | ((/D & ::polymer_type>0 ) & ((/J & ::polymer_type>0 ) :<3.5)) 344 atoms, 353 bonds, 13 residues, 1 model selected > help help:user/selectcontacts.html > contacts sel select true makePseudobonds false 405 contacts > ui tool show Contacts > select clear > hide atoms > ui tool show H-Bonds > size pseudobondRadius +0.5 Changed 66 pseudobond radii > show atoms > size pseudobondRadius -0.5 Changed 66 pseudobond radii > size pseudobondRadius -0.1 Cannot reduce pseudobond radius to <= 0 > size pseudobondRadius -0.1 Cannot reduce pseudobond radius to <= 0 > size pseudobondRadius -0.1 Cannot reduce pseudobond radius to <= 0 > size pseudobondRadius \- 0.1 Invalid ""pseudobondRadius"" argument: Expected a number >= 0 or a +/- delta > size pseudobondRadius /- 0.1 Invalid ""pseudobondRadius"" argument: Expected a number >= 0 or a +/- delta > size pseudobondRadius -0.1 Cannot reduce pseudobond radius to <= 0 > size pseudobondRadius - Invalid ""pseudobondRadius"" argument: Expected a number >= 0 or a +/- delta > size pseudobondRadius -1 Cannot reduce pseudobond radius to <= 0 > size pseudobondRadius \- 0.5 Invalid ""pseudobondRadius"" argument: Expected a number >= 0 or a +/- delta > size pseudobondRadius \- .5 Invalid ""pseudobondRadius"" argument: Expected a number >= 0 or a +/- delta > hide atoms > size pseudobondRadius .5 Changed 66 pseudobond radii > show atoms > size pseudobondRadius .1 Changed 66 pseudobond radii > size pseudobondRadius 0.3 Changed 66 pseudobond radii > size pseudobondRadius 0.2 Changed 66 pseudobond radii > hbonds /J /D saltOnly=false, restrict=cross, select=true, reveal=true, > showDist=true, color=green, radius=0.1, dashes=5, name=j_d_hbonds Expected a keyword > ui tool show Shell > hbonds #J to #D color green distance true radius 0.1 dashes 5 name > j_d_hbonds Expected a keyword > hide atoms > hbonds /j restrict /d 6 hydrogen bonds found > hbonds /j restrict /d reveal true 6 hydrogen bonds found > `open help:user/tutorials/binding-sites.html` Unknown command: `open help:user/tutorials/binding-sites.html` > open help:user/tutorials/binding-sites.html Opened help:user/tutorials/binding-sites.html > label @@display > hbonds /j restrict /e reveal true 0 hydrogen bonds found > hbonds /j restrict /d/e reveal true 6 hydrogen bonds found > hbonds /j/k restrict /d/e reveal true 11 hydrogen bonds found > abel @@display Unknown command: abel @@display > abel @@display Unknown command: abel @@display > label @@display > size pseudobondRadius 0.2 Changed 11 pseudobond radii > hbonds /j/k restrict /d/e reveal true name 1 11 hydrogen bonds found > select 1 Expected an objects specifier or a keyword > label height 1.0 > select add #1 65734 atoms, 66619 bonds, 22 pseudobonds, 4000 residues, 4 models selected > color (#!1 & sel) byhetero > select clear > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" ——— End of log from Wed May 14 10:48:39 2025 ——— opened ChimeraX session > label height 2.0 > color label Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > label color red > label color yellow > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" > select /K:24@O4' 1 atom, 1 residue, 1 model selected > label delete > select /D:344@CZ 1 atom, 1 residue, 1 model selected > select clear > select add /D:360 17 atoms, 17 bonds, 1 residue, 1 model selected > select add /E:302@CZ 18 atoms, 17 bonds, 2 residues, 1 model selected > label sel > label delete > lighting soft > lighting simple > lighting soft > set bgColor white > lighting full > lighting soft > set bgColor black > lighting shadows true intensity 0.5 > graphics silhouettes true > lighting flat > lighting full > lighting soft > label @ca > label delete > select clear > view hbood Expected an objects specifier or a view name or a keyword > view /j/k > lighting full > set bgColor white > lighting full > lighting shadows false > graphics silhouettes false > graphics silhouettes true > select /D:336@CG 1 atom, 1 residue, 1 model selected > select /D:9@CD 1 atom, 1 residue, 1 model selected > select clear > select /E:299 10 atoms, 9 bonds, 1 residue, 1 model selected > select add /D:98 17 atoms, 19 bonds, 1 residue, 1 model selected > select /D:9,12 36 atoms, 34 bonds, 2 residues, 1 model selected > select /D:9,12,264,267,336,344,364 145 atoms, 138 bonds, 7 residues, 1 model selected > select /D:9,12,264,267,336,344,346 142 atoms, 136 bonds, 7 residues, 1 model selected > select /D:9,12,24,267,336,344,346,302 167 atoms, 161 bonds, 8 residues, 1 model selected > select /D:9,12,24,267,336,344,346, /E:302 Expected an objects specifier or a keyword > select /D:9,12,24,267,336,344,346 /E:302 171 atoms, 164 bonds, 8 residues, 1 model selected > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" > abel @@display Unknown command: abel @@display > label @@display > label @display > label delete > label @display [Repeated 1 time(s)] > label sel > label height 1.0 > label color yellow > label height 2.0 > label height 1.5 > label color black > select ~sel & ##selected 65563 atoms, 66455 bonds, 22 pseudobonds, 3992 residues, 3 models selected > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" > select clear > label height 2.0 > label color yellow > select clear > set bgColor black > select /i/h Nothing selected > select /l/m 1051 atoms, 1133 bonds, 33 residues, 1 model selected > hbonds /l/m restrict /c/f reveal true 0 hydrogen bonds found > select ~sel & ##selected 64683 atoms, 65486 bonds, 11 pseudobonds, 3967 residues, 2 models selected > select ~sel & ##selected 1051 atoms, 1133 bonds, 33 residues, 1 model selected > select ~sel & ##selected 64683 atoms, 65486 bonds, 11 pseudobonds, 3967 residues, 2 models selected > select clear > hbonds /l/m restrict /G/f reveal true 4 hydrogen bonds found > select clear > size pseudobondRadius 1.5 Changed 15 pseudobond radii > size pseudobondRadius .5 Changed 15 pseudobond radii > size pseudobondRadius .2 Changed 15 pseudobond radii > select /G:339,12,24 60 atoms, 57 bonds, 3 residues, 1 model selected > label sel > label sel color yellow height 2.0 > label sel color yellow height 1.5 > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" > select clear > view list Named views: 1 > view 1 > view /j/k > view name 1 > view /m/l > view name 2 > view > view name 3 > view list Named views: 1, 2, 3 > view 3 > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" ——— End of log from Wed May 14 13:57:59 2025 ——— opened ChimeraX session > changechains sel Missing or invalid ""fromIds"" argument: Expected a text string > changechains /E Missing or invalid ""fromIds"" argument: Expected a text string > open 6oej 6oej title: Crystal structure of the non-neutralizing and ADCC-potent antibody C11 In complex with hiv-1 clade A/E GP120 [more info...] Chain information for 6oej #2 --- Chain | Description | UniProt A G | clade A/E 93TH057 HIV-1 gp120 core | A0A0M3KKW9_9HIV1 44-492 B H | C11 Fab heavy chain | C L | C11 Fab light chain | Non-standard residues in 6oej #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 6oej mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > changechains glycosylations Chain IDs of 8 residues changed > info 6 models #1, 2_All-S_DNA_ir-F.pdb, shown 65734 atoms, 66619 bonds, 4000 residues, 10 chains (E,A,J,K,B,F,D,G,L,M) 11 1, 4 hydrogen bonds #1.1, hydrogen bonds, shown, 4 pseudobonds #1.2, labels, shown, 22 triangles #1.3, 1, shown, 11 pseudobonds #2, 6oej, shown 12140 atoms, 12455 bonds, 1556 residues, 6 chains (G,H,L,A,B,C) 10 missing structure #2.1, missing structure, shown, 10 pseudobonds > log metadata #2 Metadata for 6oej #2 --- Title | Crystal structure of the non-neutralizing and ADCC-potent antibody C11 In complex with hiv-1 clade A/E GP120 Citation | Tolbert, W.D., Van, V., Sherburn, R., Tuyishime, M., Yan, F., Nguyen, D.N., Stanfield-Oakley, S., Easterhoff, D., Bonsignori, M., Haynes, B.F., Moody, M.A., Ray, K., Ferrari, G., Lewis, G.K., Pazgier, M. (2020). Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial. Mbio, 11. PMID: 32605979. DOI: 10.1128/mBio.00208-20 Non-standard residues | BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Gene sources | Human immunodeficiency virus 1 Homo sapiens Experimental method | X-ray diffraction Resolution | 3.45Å > 6oej title Unknown command: 6oej title > Chain information for 6oej #2 Unknown command: Chain information for 6oej #2 > changechains /G G C Proposed chainID change conflicts with existing residue 6oej #2/C ASN 31 > close #2 > changechains /G G C Chain IDs of 440 residues changed > info 4 models #1, 2_All-S_DNA_ir-F.pdb, shown 65734 atoms, 66619 bonds, 4000 residues, 10 chains (E,A,J,K,B,F,D,C,L,M) 11 1, 4 hydrogen bonds #1.1, hydrogen bonds, shown, 4 pseudobonds #1.2, labels, shown, 22 triangles #1.3, 1, shown, 11 pseudobonds > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" > ui tool show ""Change Chain IDs"" > changechains L H Chain IDs of 16 residues changed > changechains M I Chain IDs of 17 residues changed Must select one or more chain IDs from the list on the left > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" ——— End of log from Wed May 14 14:35:55 2025 ——— opened ChimeraX session > set bgColor white > save ""/Users/admin/Desktop/FGH-2S DNA.cxs"" > select clear > show surfaces > hide #1.1 models > hide #1.2 models > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting flat > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting full > hide #1.10 models > show #1.10 models > hide #1.10 models > show #1.10 models > hide #1.12 models > hide #1.13 models > show atoms > hide cartoons > delete h Missing or invalid ""atoms"" argument: invalid atoms specifier > delete atoms h Expected a keyword > show #1.12 models > show #1.13 models > show cartoons > hide #1.10 models > show #1.10 models > hide #1.12 models > hide #1.13 models > hide atoms > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > show surfaces > hide #1.12 models > hide #1.13 models > color #1.12 #f9697cff > color #1.12 #f97973ff > undo [Repeated 8 time(s)] > color #1.12 lime > save ""/Users/admin/Desktop/FGH all S.tif"" width 1344 height 903 supersample > 3 transparentBackground true > show #1.1 models > hide #1.1 models > show #1.12 models > show #1.13 models > color #1.12 #00ff0078 > color #1.13 #00ff007f > color #1.13 #00ff0080 > color #1.7 #cecaf17c > color #1.7 #cecaf17d > color #1.8 #b2d9f77d > select clear > hide #1.12 models > hide #1.13 models > show #1.12 models > show #1.13 models > hide #1.12 models > hide #1.13 models > show #1.12 models > show #1.13 models > color #1.12 lime > color #1.13 lime > color #1.8 #b2d9f7ff > lighting simple > lighting soft > lighting full > lighting soft > color #1.7 #cecaf1ff > save ""/Users/admin/Desktop/FGH all S.tif"" width 1344 height 903 supersample > 3 transparentBackground true > save ""/Users/admin/Desktop/FGH all S-1.tif"" width 1344 height 903 > supersample 3 transparentBackground true > select /h/i 1051 atoms, 1133 bonds, 33 residues, 1 model selected > view sel > view > view name 4 > save ""/Users/admin/Desktop/FGH all S-2.tif"" width 1344 height 903 > supersample 3 transparentBackground true > view name 4 > select clear > save ""/Users/admin/Desktop/FGH all S-2.tif"" width 1344 height 903 > supersample 3 transparentBackground true > save ""/Users/admin/Desktop/FGH all S-1.tif"" width 1344 height 903 > supersample 3 transparentBackground true > view name 6 > view name 5 > view list Named views: 1, 2, 3, 4, 5, 6 > view 5 > view 6 > save ""/Users/admin/Desktop/FGH all S.tif"" width 1344 height 903 supersample > 3 transparentBackground true > save ""/Users/admin/Desktop/FGH-allS DNA.cxs"" ——— End of log from Thu May 15 17:19:26 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac13,1 Model Number: MJMV3LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 3天23小时25分钟 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Redmi 238 NFS: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Redmi 238 NFS: Resolution: 1080 x 1920 UI Looks like: 1080 x 1920 @ 60.00Hz Mirror: Off Online: Yes Rotation: 90 Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-Clipper: 0.24.0 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX