id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15859 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001fad44f40 (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, 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chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, 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, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, 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cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yufy/Downloads/eLORE_AF-O64782-F1-model_v2.pdb eLORE_AF-O64782-F1-model_v2.pdb title: AF-O64782-F1-model_v2_cut [more info...] Chain information for eLORE_AF-O64782-F1-model_v2.pdb #1 --- Chain | Description A | No description available > set bgColor white > open /Users/yufy/Downloads/eLORE_SD1-29_Model_1_SRK8.pdb eLORE_SD1-29_Model_1_SRK8.pdb title: At1g61380_SD1-29.B99990001_SRK8 [more info...] Chain information for eLORE_SD1-29_Model_1_SRK8.pdb #2 --- Chain | Description A | No description available > open /Users/yufy/Downloads/eLORE_SD1-29_Model_SRK9.pdb eLORE_SD1-29_Model_SRK9.pdb title: At1g61380_SD1-29.B99990001_SRK9 [more info...] Chain information for eLORE_SD1-29_Model_SRK9.pdb #3 --- Chain | Description A | No description available > hide #2 models > hide #3 models > mlp #1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #1/A #2/A #3/A Alignment identifier is 1 > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 1 [ID: 1] region 3 chains [116-259] RMSD: 2.808 > show #2 models > hide #!1 models > mlp sel & #2 Map values for surface ""eLORE_SD1-29_Model_1_SRK8.pdb_A SES surface"": minimum -27.19, mean -4.328, maximum 24.21 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 models > show #3 models > mlp sel & #3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.34, mean -4.476, maximum 26.37 To also show corresponding color key, enter the above mlp command and add key true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!3 models > show #!1 models > mlp sel & #!1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > select add #1 5347 atoms, 5497 bonds, 684 residues, 6 models selected > select add #2 7283 atoms, 7484 bonds, 936 residues, 6 models selected > select subtract #1 4210 atoms, 4331 bonds, 540 residues, 5 models selected > select subtract #2 1137 atoms, 1172 bonds, 144 residues, 3 models selected > select add #3 3073 atoms, 3159 bonds, 396 residues, 2 models selected > select subtract #3 1 model selected > mlp #!1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > mlp #!1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > mlp #!1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > hide #!1 surfaces > show #!1 surfaces > color #!1 bychain > mlp #!1 Map values for surface ""eLORE_AF-O64782-F1-model_v2.pdb_A SES surface"": minimum -27.94, mean -5.194, maximum 25.3 To also show corresponding color key, enter the above mlp command and add key true > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-282 #2/A:137-282 #3/A:137-282 3453 atoms, 3558 bonds, 438 residues, 3 models selected 1 [ID: 1] region 3 chains [116-261] RMSD: 2.791 > hide #!1 models > show #!3 models > show #!1 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!1 models > show #!1 models > show #!2 models > show #!3 models > hide sel surfaces > select add #1 5375 atoms, 5525 bonds, 688 residues, 6 models selected > select add #2 7297 atoms, 7498 bonds, 938 residues, 6 models selected > select add #3 9219 atoms, 9471 bonds, 1188 residues, 6 models selected > select subtract #3 6146 atoms, 6312 bonds, 792 residues, 5 models selected > select subtract #2 3073 atoms, 3153 bonds, 396 residues, 3 models selected > select subtract #1 1 model selected > hide surfaces > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #!2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with eLORE_SD1-29_Model_1_SRK8.pdb, chain A (#2), sequence alignment score = 1889 RMSD between 203 pruned atom pairs is 1.228 angstroms; (across all 396 pairs: 3.289) Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with eLORE_SD1-29_Model_SRK9.pdb, chain A (#3), sequence alignment score = 1911.5 RMSD between 225 pruned atom pairs is 1.176 angstroms; (across all 396 pairs: 3.154) > matchmaker #!2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with eLORE_SD1-29_Model_1_SRK8.pdb, chain A (#2), sequence alignment score = 1889 RMSD between 203 pruned atom pairs is 1.228 angstroms; (across all 396 pairs: 3.289) Matchmaker eLORE_AF-O64782-F1-model_v2.pdb, chain A (#1) with eLORE_SD1-29_Model_SRK9.pdb, chain A (#3), sequence alignment score = 1911.5 RMSD between 225 pruned atom pairs is 1.176 angstroms; (across all 396 pairs: 3.154) > hide #!1 models > hide #!2 models > show #!3 surfaces > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 1 [ID: 1] region 3 chains [116-259] RMSD: 2.813 > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:212-213 #2/A:212-213 #3/A:212-213 51 atoms, 51 bonds, 6 residues, 3 models selected 1 [ID: 1] region 3 chains [191-192] RMSD: 3.033 > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected 1 [ID: 1] region 3 chains [191] RMSD: 1.970 > select #1/A:226 #2/A:226 #3/A:226 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:226 #2/A:226 #3/A:226 33 atoms, 33 bonds, 3 residues, 3 models selected 1 [ID: 1] region 3 chains [205] RMSD: 1.419 > select #1/A:212-213 #2/A:212-213 #3/A:212-213 51 atoms, 51 bonds, 6 residues, 3 models selected > select #1/A:212-213 #2/A:212-213 #3/A:212-213 51 atoms, 51 bonds, 6 residues, 3 models selected 1 [ID: 1] region 3 chains [191-192] RMSD: 3.033 > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected 1 [ID: 1] region 3 chains [191] RMSD: 1.970 > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:212-213 #2/A:212-213 #3/A:212-213 51 atoms, 51 bonds, 6 residues, 3 models selected 1 [ID: 1] region 3 chains [191-192] RMSD: 3.033 > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:202 #2/A:202 #3/A:202 42 atoms, 45 bonds, 3 residues, 3 models selected > select #1/A:202-295 #2/A:202-295 #3/A:202-295 2208 atoms, 2279 bonds, 282 residues, 3 models selected 1 [ID: 1] region 3 chains [181-274] RMSD: 3.123 > ui mousemode right select > select clear > select #1/A:202-295 #2/A:202-295 #3/A:202-295 2208 atoms, 2279 bonds, 282 residues, 3 models selected > select #1/A:296 #2/A:296 #3/A:296 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:295-296 #2/A:295-296 #3/A:295-296 51 atoms, 48 bonds, 6 residues, 3 models selected 1 [ID: 1] region 3 chains [274-275] RMSD: 1.852 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > select #1/A:296 #2/A:296 #3/A:296 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:295-296 #2/A:295-296 #3/A:295-296 51 atoms, 48 bonds, 6 residues, 3 models selected 1 [ID: 1] region 3 chains [274-275] RMSD: 1.852 > select clear > select #1/A:295-296 #2/A:295-296 #3/A:295-296 51 atoms, 48 bonds, 6 residues, 3 models selected > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected 1 [ID: 1] region 3 chains [274] RMSD: 2.169 > show sel & #!3 atoms > hide sel & #!3 surfaces > show sel & #!3 surfaces > select clear > hide #!3 surfaces > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #1/A #2/A #3/A Alignment identifier is 2 > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:273 #2/A:273 #3/A:273 30 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:273 #2/A:273 #3/A:273 30 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:273 #2/A:273 #3/A:273 30 atoms, 30 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [252] RMSD: 2.171 > show sel & #!3 atoms > select clear > show #!3 surfaces > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [274] RMSD: 2.169 > hide sel & #!3 surfaces > select clear > hide #!3 surfaces > show #!2 models > show #!1 models > show surfaces > hide surfaces > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > select clear > ui mousemode right translate > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!1 surfaces > show #!3 models > hide #!1 models > show #!3 surfaces > hide #!3 surfaces The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #!3 surfaces > coulombic #!3 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > mlp #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > select add #3 3073 atoms, 3159 bonds, 396 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > show sel surfaces > hide sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > show sel surfaces > hide #!3 models > show #!3 models > color sel bychain > color sel bypolymer > rainbow sel > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > ~hbonds > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > select #1/A:87 #2/A:87 #3/A:87 21 atoms, 18 bonds, 3 residues, 3 models selected > select #1/A:87-388 #2/A:87-388 #3/A:87-388 7032 atoms, 7222 bonds, 906 residues, 3 models selected 2 [ID: 2] region 3 chains [66-367] RMSD: 3.044 > coulombic sel & #!3 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > hide sel & #!3 surfaces > show sel & #!3 surfaces > color sel & #!3 bychain > coulombic sel & #!3 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > select #1/A:417 #2/A:417 #3/A:417 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:417 #2/A:417 #3/A:417 18 atoms, 15 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [396] RMSD: 1.307 > color sel & #!3 byhetero > ui mousemode right select > select clear > mlp #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 17874 of 367328 triangles, 6 atoms, 29 residues, 7 bonds Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 4132 of 367328 triangles, 19 residues Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 40125 of 367328 triangles, 7 atoms, 63 residues, 7 bonds Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3810 of 367328 triangles, 13 residues Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 75448 of 367328 triangles, 7 atoms, 128 residues, 7 bonds > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > select clear > select #3/A:266@CA 1 atom, 1 residue, 1 model selected Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 64837 of 367328 triangles, 7 atoms, 88 residues, 7 bonds > show sel atoms > hide sel surfaces > select clear > hide #!3 atoms > show #!3 surfaces > ui mousemode right translate The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:212 #2/A:212 #3/A:212 33 atoms, 33 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [191] RMSD: 1.970 > hide sel & #!3 surfaces > show sel & #!3 atoms > select #1/A:226 #2/A:226 #3/A:226 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:226 #2/A:226 #3/A:226 33 atoms, 33 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [205] RMSD: 1.419 > show sel & #!3 atoms > hide sel & #!3 surfaces > select #1/A:241 #2/A:241 #3/A:241 36 atoms, 36 bonds, 3 residues, 3 models selected > select #1/A:241 #2/A:241 #3/A:241 36 atoms, 36 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [220] RMSD: 0.403 > hide sel & #!3 surfaces > show sel & #!3 atoms The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A #2/A #3/A 9219 atoms, 9471 bonds, 1188 residues, 3 models selected 2 [ID: 2] region 3 chains [1-396] RMSD: 2.850 > hide sel & #!3 surfaces > show sel & #!3 surfaces > hide sel & #!3 surfaces > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:239 #2/A:239 #3/A:239 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:239 #2/A:239 #3/A:239 33 atoms, 33 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [218] RMSD: 1.304 > select #1/A:273 #2/A:273 #3/A:273 30 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:273 #2/A:273 #3/A:273 30 atoms, 30 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [252] RMSD: 2.171 > show sel & #!3 atoms > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [274] RMSD: 2.169 > show sel & #!3 atoms > select #1/A:216 #2/A:216 #3/A:216 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:216 #2/A:216 #3/A:216 18 atoms, 15 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [195] RMSD: 4.411 > show sel & #!3 atoms > select #1/A:221 #2/A:221 #3/A:221 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:221 #2/A:221 #3/A:221 18 atoms, 15 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [200] RMSD: 8.119 > select #1/A:224 #2/A:224 #3/A:224 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:224 #2/A:224 #3/A:224 18 atoms, 15 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [203] RMSD: 6.161 > show sel & #!3 atoms > select #1/A:202 #2/A:202 #3/A:202 42 atoms, 45 bonds, 3 residues, 3 models selected > select #1/A:202 #2/A:202 #3/A:202 42 atoms, 45 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [181] RMSD: 1.864 > show sel & #!3 atoms > select #1/A:270 #2/A:270 #3/A:270 42 atoms, 45 bonds, 3 residues, 3 models selected > select #1/A:270 #2/A:270 #3/A:270 42 atoms, 45 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [249] RMSD: 2.665 > select #1/A:264 #2/A:264 #3/A:264 42 atoms, 45 bonds, 3 residues, 3 models selected > select #1/A:264 #2/A:264 #3/A:264 42 atoms, 45 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [243] RMSD: 1.921 > show sel & #!3 atoms > select #1/A:222 #2/A:222 #3/A:222 36 atoms, 36 bonds, 3 residues, 3 models selected > select #1/A:222 #2/A:222 #3/A:222 36 atoms, 36 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [201] RMSD: 7.915 > show sel & #!3 atoms > mlp sel & #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > mlp sel & #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > hide sel & #!3 surfaces > ui mousemode right select > select #3/A:222@CB 1 atom, 1 residue, 1 model selected > select #3/A:222 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/A:273@CA 1 atom, 1 residue, 1 model selected > select #3/A:273@CA 1 atom, 1 residue, 1 model selected > select #3/A:273 10 atoms, 10 bonds, 1 residue, 1 model selected > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > select #3/A:222 12 atoms, 12 bonds, 1 residue, 1 model selected > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > select #3/A:222@CD1 1 atom, 1 residue, 1 model selected Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 1162 of 367328 triangles, 18 atoms, 19 residues, 20 bonds > hide sel surfaces > select clear Drag select of 1 residues > select clear > open /Users/yufy/switchdrive/Fan- > Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json Failed opening file /Users/yufy/switchdrive/Fan- Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/yufy/switchdrive/Fan- Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_full_data_0.json format pae structure #1 > open /Users/yufy/switchdrive/Fan- > Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lomi_dimer/fold_2024_08_23_lomi_dimer_model_0.cif Chain information for fold_2024_08_23_lomi_dimer_model_0.cif #4 --- Chain | Description A | . B | . > hide #!3 models Drag select of 108 residues Drag select of 57 residues > ui mousemode right translate > ui mousemode right select > select clear > hide #4 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/yufy/switchdrive/Fan- > Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/lore_dimer/fold_2024_08_25_lore_dimer_model_0.cif Chain information for fold_2024_08_25_lore_dimer_model_0.cif #5 --- Chain | Description A B | . Drag select of 37 residues > ui mousemode right translate > ui mousemode right select > select clear > ui mousemode right translate > hide #5 models > show #5 models > open /Users/yufy/switchdrive/Fan- > Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/AthLOREdimer_67ef4/AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #6 --- Chain | Description A B | No description available > hide #5 models > set bgColor black > set bgColor transparent > mlp #6 Map values for surface ""AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A SES surface"": minimum -28.76, mean -4.06, maximum 25.4 Map values for surface ""AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface"": minimum -30.26, mean -4.011, maximum 26.74 To also show corresponding color key, enter the above mlp command and add key true > hide #!6 surfaces > hide #!6 models > show #!3 models > coulombic #!3 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > coulombic #!3 reassignCharges true Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > ui mousemode right select > select clear Drag select of 68 atoms, 136 residues, 68 bonds > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:359 #2/A:359 #3/A:359 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:359-360 #2/A:359-360 #3/A:359-360 54 atoms, 54 bonds, 6 residues, 3 models selected 2 [ID: 2] region 3 chains [338-339] RMSD: 3.580 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > select #3/A:244@CD1 1 atom, 1 residue, 1 model selected Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 120408 of 367328 triangles, 69 atoms, 158 residues, 69 bonds > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select clear > set bgColor white > set bgColor #ffffff00 > color #3 black > color #3 Coral Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #3 coral > select #1/A:224 #2/A:224 #3/A:224 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:224 #2/A:224 #3/A:224 18 atoms, 15 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [203] RMSD: 6.161 > color #3:222 red > color #3:222 blue > color #3:224 blue > color #3:216 blue > select clear > color #3:212 blue > color #3:241 hot pink > color #3:239 hot pink > select #1/A:239 #2/A:239 #3/A:239 33 atoms, 33 bonds, 3 residues, 3 models selected > select #1/A:239 #2/A:239 #3/A:239 33 atoms, 33 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [218] RMSD: 1.304 > show sel & #!3 atoms > color #3:226 hot pink > show sel & #!3 atoms > select clear > color #3:184 turquoise > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [163] RMSD: 2.154 > show sel & #!3 atoms > color #3:237 turquoise > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [216] RMSD: 1.000 > show sel & #!3 atoms > select #1/A:241 #2/A:241 #3/A:241 36 atoms, 36 bonds, 3 residues, 3 models selected > select #1/A:241 #2/A:241 #3/A:241 36 atoms, 36 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [220] RMSD: 0.403 > save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/AthLORE- > BindingPocket.cxs > select clear > select #3/A:273 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:202@CA 1 atom, 1 residue, 1 model selected > select clear > open /Users/yufy/switchdrive/Fan- > Yu_PhD_project/Assay_ProteinWork/protein_prediction_images/AthLOREdimer_67ef4/AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for AthLOREdimer_67ef4_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #7 --- Chain | Description A B | No description available > hide #!3 models > hide #7 models > show #7 models Drag select of 56 residues Drag select of 103 residues > ui mousemode right translate > ui mousemode right select > select clear Drag select of 39 residues > select clear > ui mousemode right translate > hide #7 models > show #!3 models > hide #!3 models > show #7 models > hide #7 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #6.1 models > show #6.1 models > hide #6.1 models > show #6.1 models > hide #6.2 models > show #6.2 models Cell requested for row 6 is out of bounds for table with 9 rows! Resizing table model. > hide #!6 models > show #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #3.1 models > show #3.1 models > hide #!3 models > show #!3 models > hide #3.1 models > show #3.1 models > coulombic #!3 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_SD1-29_Model_SRK9.pdb #/A ALA 417 C) > hide #!3 models > hide #3.1 models > show #!1 models > coulombic #!1 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of eLORE_AF-O64782-F1-model_v2.pdb #/A ALA 417 HXT bonded to atom that should not have hydrogens (copy of eLORE_AF-O64782-F1-model_v2.pdb #/A ALA 417 C) > hide #!1 models > show #!3 models > color #3:239 coral > color #3:226 coral > color #3:241 #8B008B > color #3:241 #FF00FF > save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/AthLORE- > BindingPocket.cxs > save /Users/yufy/Desktop/image1.png supersample 3 > save /Users/yufy/switchdrive/Fan-Yu/LORE_binding_pocket_modeling/LORE- > BindingPocket.ppm width 1257 height 850 supersample 3 > lighting simple > lighting soft > lighting full > lighting simple > lighting full > lighting simple > lighting full > lighting simple > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #1/A #2/A #3/A Alignment identifier is 2 > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:203 #2/A:203 #3/A:203 33 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:203-204 #2/A:203-204 #3/A:203-204 51 atoms, 48 bonds, 6 residues, 3 models selected 2 [ID: 2] region 3 chains [182-183] RMSD: 2.237 > select #1/A:225 #2/A:225 #3/A:225 21 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:203-225 #2/A:203-225 #3/A:203-225 516 atoms, 531 bonds, 69 residues, 3 models selected 2 [ID: 2] region 3 chains [182-204] RMSD: 4.786 > save /Users/yufy/Desktop/image2.png supersample 3 > color (#!3 & sel) cornflower blue > undo > ui mousemode right select > select clear > mlp #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > hide #!3 surfaces > ui mousemode right select Drag select of 80 atoms, 133 residues, 79 bonds > select #3/A:247 12 atoms, 12 bonds, 1 residue, 1 model selected Drag select of 81 atoms, 141 residues, 81 bonds > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-276 #2/A:137-276 #3/A:137-276 3318 atoms, 3417 bonds, 420 residues, 3 models selected 2 [ID: 2] region 3 chains [116-255] RMSD: 2.846 > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 Drag select of 2 residues > select #1/A:137-138 #2/A:137-138 #3/A:137-138 66 atoms, 69 bonds, 6 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 > mlp sel & #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.58, mean -4.477, maximum 26.66 To also show corresponding color key, enter the above mlp command and add key true > surface style #3 solid > surface style #3 mesh > surface style #3 dot > surface style #3 solid > transparency (#!3 & sel) 50 > select clear > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 > open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.asnt Unrecognized file suffix '.asnt' > open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.json Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.json format pae structure #1 > open /Users/yufy/Downloads/Conformer3D_COMPOUND_CID_26612.sdf PubChem entry 26612 > hide #!3 models Drag select of 9 atoms, 7 bonds Drag select of 8 atoms, 9 bonds > ui mousemode right translate > ui mousemode right select > select clear > show #!3 models Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 4502 of 367328 triangles, 9 atoms, 28 residues, 6 bonds > select clear > select #1/A:137 #2/A:137 #3/A:137 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 > color (#!3 & sel) light gray > undo > color (#!3 & sel) light gray > select clear Drag select of 28 atoms, 29 bonds > select clear Drag select of 33 atoms, 32 bonds > ui mousemode right translate > ui mousemode right ""translate selected atoms"" > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,24.008,0,1,0,-5.6817,0,0,1,25.149 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.68499,-0.57923,0.44192,24.18,0.58568,0.79856,0.13885,-6.1185,-0.43332,0.16372,0.88625,25.474 > view matrix models > #8,0.83894,-0.32902,0.4335,24.088,0.29244,0.94432,0.15079,-5.8988,-0.45897,0.00026563,0.88845,25.48 > view matrix models > #8,0.87287,-0.19526,0.44718,24.073,-0.078378,0.84844,0.52345,-5.6507,-0.48162,-0.49196,0.72528,25.466 > ui mousemode right select Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328 triangles, 103 atoms, 396 residues, 100 bonds > select clear > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A #2/A #3/A 9219 atoms, 9471 bonds, 1188 residues, 3 models selected 2 [ID: 2] region 3 chains [1-396] RMSD: 2.850 Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 12 of 367328 triangles > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A #2/A #3/A 9219 atoms, 9471 bonds, 1188 residues, 3 models selected 2 [ID: 2] region 3 chains [1-396] RMSD: 2.850 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98822,0.14155,-0.058171,-0.91946,-0.14052,0.98984,0.021525,4.5149,0.060628,-0.013097,0.99807,-1.8909,#2,0.99173,0.11249,-0.061722,-0.60774,-0.11208,0.99365,0.010095,3.9696,0.062465,-0.0030941,0.99804,-2.1042,#3,0.99047,0.12806,-0.050768,-0.99518,-0.12764,0.99175,0.011501,4.4523,0.051822,-0.0049116,0.99864,-1.962 > view matrix models > #1,0.99126,0.066335,-0.11403,2.0168,-0.075762,0.99388,-0.080417,4.9314,0.108,0.088354,0.99022,-5.3208,#2,0.99249,0.03656,-0.11669,2.3803,-0.047457,0.99463,-0.092011,4.4329,0.1127,0.096858,0.9889,-5.5645,#3,0.993,0.052312,-0.10593,1.95,-0.061956,0.99402,-0.089901,4.8709,0.10059,0.095835,0.9903,-5.4019 > color (#!3 & sel) gray > view matrix models > #1,0.99272,0.034361,-0.11547,2.6336,-0.049897,0.98966,-0.13448,5.5742,0.10965,0.13926,0.98417,-6.2651,#2,0.99303,0.0045432,-0.11775,3.0138,-0.021846,0.98903,-0.14607,5.1005,0.1158,0.14762,0.98224,-6.5319,#3,0.99404,0.02031,-0.10707,2.5692,-0.035684,0.98898,-0.14369,5.5158,0.10297,0.14666,0.98381,-6.3496 > transparency (#!3 & sel) 40 > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 239 of 367328 triangles, 33 atoms, 32 bonds > ui mousemode right ""translate selected models"" > view matrix models > #3.1,1,8.5001e-17,2.3592e-16,-6.62,-1.3357e-16,1,-3.3307e-16,4.2002,-6.9389e-17,-1.6852e-34,1,-2.2772,#8,0.87287,-0.19526,0.44718,17.821,-0.078378,0.84844,0.52345,-0.9334,-0.48162,-0.49196,0.72528,23.16 > view matrix models > #3.1,1,8.5001e-17,2.3592e-16,0.055566,-1.3357e-16,1,-3.3307e-16,-3.4356,-6.9389e-17,-1.6852e-34,1,-2.5932,#8,0.87287,-0.19526,0.44718,24.336,-0.078378,0.84844,0.52345,-8.6778,-0.48162,-0.49196,0.72528,22.417 > undo > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear Drag select of 33 atoms, 32 bonds > ui mousemode right ""translate selected models"" > view matrix models > #8,0.87287,-0.19526,0.44718,17.873,-0.078378,0.84844,0.52345,12.976,-0.48162,-0.49196,0.72528,38.696 > ui mousemode right select > select clear > undo > select #1/A:154 #2/A:154 #3/A:154 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:154-280 #2/A:154-280 #3/A:154-280 2997 atoms, 3087 bonds, 381 residues, 3 models selected 2 [ID: 2] region 3 chains [133-259] RMSD: 2.972 > select #1/A:149-150 #2/A:149-150 #3/A:149-150 45 atoms, 45 bonds, 6 residues, 3 models selected > select #1/A:149-280 #2/A:149-280 #3/A:149-280 3105 atoms, 3198 bonds, 396 residues, 3 models selected 2 [ID: 2] region 3 chains [128-259] RMSD: 2.920 Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 629 of 367328 triangles, 5 residues Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 130056 of 367328 triangles, 85 atoms, 166 residues, 83 bonds > select #1/A:149 #2/A:149 #3/A:149 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:149-280 #2/A:149-280 #3/A:149-280 3105 atoms, 3198 bonds, 396 residues, 3 models selected 2 [ID: 2] region 3 chains [128-259] RMSD: 2.920 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #8 target m > show #8 models > select clear Drag select of 33 atoms, 32 bonds > ui mousemode right ""translate selected models"" > view matrix models > #8,0.87287,-0.19526,0.44718,13.507,-0.078378,0.84844,0.52345,-18.133,-0.48162,-0.49196,0.72528,-6.9555 > hide #8 models > select subtract #8 Nothing selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right select Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328 triangles, 90 atoms, 394 residues, 88 bonds Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 132573 of 367328 triangles, 90 atoms, 396 residues, 88 bonds > color #3 coral > select #1/A:137-138 #2/A:137-138 #3/A:137-138 66 atoms, 69 bonds, 6 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 > mlp sel & #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.83, mean -4.481, maximum 26.5 To also show corresponding color key, enter the above mlp command and add key true > color (#!3 & sel) light sea green > color (#!3 & sel) orange > color (#!3 & sel) dark gray > color (#!3 & sel) dim gray > transparency (#!3 & sel) 50 > hide sel & #!3 cartoons > hide sel & #!3 atoms > hide sel & #!3 cartoons > show sel & #!3 cartoons > cartoon style (#!3 & sel) modeHelix tube sides 20 > undo > show sel & #!3 atoms > hide sel & #!3 atoms > hide sel & #!3 cartoons The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > style sel & #!3 ball Changed 1137 atom styles > style sel & #!3 stick Changed 1137 atom styles > color (#!3 & sel) light gray > color (#!3 & sel) gray > ui tool show ""Side View"" > lighting simple > lighting full > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting full > undo > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting simple > set bgColor gray > set bgColor #80808000 > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > cofr sel > ui tool show ""Selection Inspector"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Render/Select by Attribute"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > transparency (#!3 & sel) 50 > transparency (#!3 & sel) 80 > select #3/A:222@CE1 1 atom, 1 residue, 1 model selected > select #3/A:222@N 1 atom, 1 residue, 1 model selected Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 14426 of 367328 triangles > select #3/A:222@CE1 1 atom, 1 residue, 1 model selected > select #3/A:221@CB 1 atom, 1 residue, 1 model selected > show sel cartoons > select #3/A:222@CB 1 atom, 1 residue, 1 model selected > show sel cartoons > select #3/A:222@CD2 1 atom, 1 residue, 1 model selected > select #3/A:220@O 1 atom, 1 residue, 1 model selected > show sel cartoons > select #1/A:241 #2/A:241 #3/A:241 36 atoms, 36 bonds, 3 residues, 3 models selected > select #1/A:187-241 #2/A:187-241 #3/A:187-241 1257 atoms, 1296 bonds, 165 residues, 3 models selected 2 [ID: 2] region 3 chains [166-220] RMSD: 3.646 > show sel & #!3 cartoons > select clear > select #1/A:242 #2/A:242 #3/A:242 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:242-280 #2/A:242-280 #3/A:242-280 963 atoms, 990 bonds, 117 residues, 3 models selected 2 [ID: 2] region 3 chains [221-259] RMSD: 2.524 > show sel & #!3 cartoons > select clear > transparency #3 60 > graphics silhouettes false > graphics silhouettes true > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:184-185 #2/A:184-185 #3/A:184-185 45 atoms, 42 bonds, 6 residues, 3 models selected > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [163] RMSD: 2.154 > show sel & #!3 cartoons > show sel & #!3 atoms > hide sel & #!3 atoms > select clear > select #1/A:137-138 #2/A:137-138 #3/A:137-138 66 atoms, 69 bonds, 6 residues, 3 models selected > select #1/A:137-280 #2/A:137-280 #3/A:137-280 3411 atoms, 3516 bonds, 432 residues, 3 models selected 2 [ID: 2] region 3 chains [116-259] RMSD: 2.813 > show sel & #!3 cartoons > select clear > mlp #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.83, mean -4.481, maximum 26.5 To also show corresponding color key, enter the above mlp command and add key true > undo > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A:22-135 #2/A:22-135 #3/A:22-135 2607 atoms, 2664 bonds, 342 residues, 3 models selected 2 [ID: 2] region 3 chains [1-114] RMSD: 2.913 > hide #8 target m > hide sel & #!3 atoms > hide sel & #!3 cartoons > hide sel & #!3 surfaces > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:136 #2/A:136 #3/A:136 27 atoms, 24 bonds, 3 residues, 3 models selected > select #1/A:136-137 #2/A:136-137 #3/A:136-137 51 atoms, 48 bonds, 6 residues, 3 models selected 2 [ID: 2] region 3 chains [115-116] RMSD: 2.468 > select #1/A:136 #2/A:136 #3/A:136 27 atoms, 24 bonds, 3 residues, 3 models selected > select #1/A:136 #2/A:136 #3/A:136 27 atoms, 24 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [115] RMSD: 2.625 > hide sel & #!3 cartoons > hide sel & #!3 surfaces > select #3/A:138@CH2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select clear > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A:22-138 #2/A:22-138 #3/A:22-138 2700 atoms, 2763 bonds, 351 residues, 3 models selected 2 [ID: 2] region 3 chains [1-117] RMSD: 2.897 > select #3/A:257@OE1 1 atom, 1 residue, 1 model selected > select clear > select #1/A:281 #2/A:281 #3/A:281 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:281-417 #2/A:281-417 #3/A:281-417 3174 atoms, 3258 bonds, 411 residues, 3 models selected 2 [ID: 2] region 3 chains [260-396] RMSD: 2.835 > hide sel & #!3 cartoons > hide sel & #!3 surfaces > hide sel & #!3 atoms Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 1109 of 367328 triangles, 3 residues > select clear > select #3/A:266@OD2 1 atom, 1 residue, 1 model selected > select clear > ui mousemode right zoom > ui mousemode right translate > ui mousemode right select Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 105 of 367328 triangles > ui mousemode right translate > ui mousemode right select > select #3/A:262@CD1 1 atom, 1 residue, 1 model selected > hide sel atoms > show sel atoms > show sel cartoons > show sel atoms > hide sel surfaces > show sel surfaces > select clear > hide #!3 atoms > select clear > ui mousemode right translate > ui mousemode right clip > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [216] RMSD: 1.000 > ui mousemode right ""move planes"" > ui mousemode right select > select clear > ui mousemode right ""contour level"" > ui mousemode right ""rotate slab"" > ui mousemode right ""crop volume"" > ui mousemode right translate > mlp #!3 Map values for surface ""eLORE_SD1-29_Model_SRK9.pdb_A SES surface"": minimum -27.83, mean -4.481, maximum 26.5 To also show corresponding color key, enter the above mlp command and add key true > transparency #3 60 > select #1/A:22-23 #2/A:22-23 #3/A:22-23 39 atoms, 36 bonds, 6 residues, 3 models selected > select #1/A:22-136 #2/A:22-136 #3/A:22-136 2634 atoms, 2691 bonds, 345 residues, 3 models selected 2 [ID: 2] region 3 chains [1-115] RMSD: 2.911 > hide sel & #!3 surfaces > ui mousemode right select > select #3/A:138@CH2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #3/A:137@CD2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #1/A:281 #2/A:281 #3/A:281 18 atoms, 15 bonds, 3 residues, 3 models selected > select #1/A:281-417 #2/A:281-417 #3/A:281-417 3174 atoms, 3258 bonds, 411 residues, 3 models selected 2 [ID: 2] region 3 chains [260-396] RMSD: 2.835 > hide sel & #!3 surfaces > select #1/A:295 #2/A:295 #3/A:295 33 atoms, 30 bonds, 3 residues, 3 models selected > select #1/A:280-295 #2/A:280-295 #3/A:280-295 363 atoms, 374 bonds, 48 residues, 3 models selected 2 [ID: 2] region 3 chains [259-274] RMSD: 1.281 > show sel & #!3 surfaces Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2032 of 367328 triangles Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3847 of 367328 triangles > select #3/A:290@OH 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #3/A:290@CE2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #3/A:290@CZ 1 atom, 1 residue, 1 model selected Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 3301 of 367328 triangles Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2354 of 367328 triangles Drag select of eLORE_SD1-29_Model_SRK9.pdb_A SES surface, 2265 of 367328 triangles > select #3/A:290@CA 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #1/A:292 #2/A:292 #3/A:292 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:292-296 #2/A:292-296 #3/A:292-296 114 atoms, 111 bonds, 15 residues, 3 models selected 2 [ID: 2] region 3 chains [271-275] RMSD: 1.279 > hide sel & #!3 surfaces > select clear > select #3/A:290@CE1 1 atom, 1 residue, 1 model selected > select clear > select #3/A:290@CD2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #3/A:290@CE1 1 atom, 1 residue, 1 model selected > hide sel surfaces > select #3/A:290@CZ 1 atom, 1 residue, 1 model selected > hide sel surfaces > select clear > hide #!3 surfaces > show #!3 surfaces > select #1/A:23 #2/A:23 #3/A:23 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:23-136 #2/A:23-136 #3/A:23-136 2619 atoms, 2676 bonds, 342 residues, 3 models selected 2 [ID: 2] region 3 chains [2-115] RMSD: 2.882 > hide sel & #!3 surfaces > select #1/A:22 #2/A:22 #3/A:22 15 atoms, 12 bonds, 3 residues, 3 models selected > select #1/A:22-136 #2/A:22-136 #3/A:22-136 2634 atoms, 2691 bonds, 345 residues, 3 models selected 2 [ID: 2] region 3 chains [1-115] RMSD: 2.911 > hide sel & #!3 surfaces > select #1/A:281-282 #2/A:281-282 #3/A:281-282 42 atoms, 39 bonds, 6 residues, 3 models selected > select #1/A:281-417 #2/A:281-417 #3/A:281-417 3174 atoms, 3258 bonds, 411 residues, 3 models selected 2 [ID: 2] region 3 chains [260-396] RMSD: 2.835 > hide sel & #!3 surfaces > select #3/A:138@CH2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select clear > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:180-184 #2/A:180-184 #3/A:180-184 126 atoms, 126 bonds, 15 residues, 3 models selected 2 [ID: 2] region 3 chains [159-163] RMSD: 1.720 > hide sel & #!3 cartoons > show sel & #!3 cartoons > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1/A:184-185 #2/A:184-185 #3/A:184-185 45 atoms, 42 bonds, 6 residues, 3 models selected > select #1/A:184-185 #2/A:184-185 #3/A:184-185 45 atoms, 42 bonds, 6 residues, 3 models selected 2 [ID: 2] region 3 chains [163-164] RMSD: 2.295 > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [163] RMSD: 2.154 > show sel & #!3 atoms > select > #1/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #2/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 > #3/A:26-28,34-36,42-47,56-61,69-72,85-89,92-97,103-106,116-120,126-130,136-139,154-157,162-164,180-185,191-196,199-205,226-231,236-241,249-254,260-265,270-276,291-294,300-303,307-309,324-326,347-351,361-363,381-387,391-396,402-404,412-416 3762 atoms, 3794 bonds, 453 residues, 3 models selected > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected > select #1/A:237 #2/A:237 #3/A:237 12 atoms, 9 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [216] RMSD: 1.000 > show sel & #!3 atoms > select clear > transparency #3 30 > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected > select #1/A:184 #2/A:184 #3/A:184 24 atoms, 21 bonds, 3 residues, 3 models selected 2 [ID: 2] region 3 chains [163] RMSD: 2.154 > hide sel & #!3 atoms > select clear > transparency #3 20 > transparency #3 10 > transparency #3 20 > save /Users/yufy/Desktop/image3.png supersample 3 > show #8 models > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of 33 atoms, 32 bonds > ui mousemode right ""translate selected models"" > view matrix models > #8,0.87287,-0.19526,0.44718,13.046,-0.078378,0.84844,0.52345,9.5173,-0.48162,-0.49196,0.72528,40.263 > view matrix models > #8,0.87287,-0.19526,0.44718,11.832,-0.078378,0.84844,0.52345,11.633,-0.48162,-0.49196,0.72528,41.559 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.8058,-0.52171,0.2802,11.862,0.33667,0.79283,0.50801,11.333,-0.48718,-0.31502,0.81451,41.573 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.8058,-0.52171,0.2802,11.767,0.33667,0.79283,0.50801,11.307,-0.48718,-0.31502,0.81451,41.341 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.75896,-0.62551,0.18087,11.796,0.49983,0.7377,0.45383,11.188,-0.4173,-0.25404,0.87254,41.294 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.75896,-0.62551,0.18087,12.424,0.49983,0.7377,0.45383,9.7686,-0.4173,-0.25404,0.87254,40.057 > view matrix models > #8,0.75896,-0.62551,0.18087,12.25,0.49983,0.7377,0.45383,10.076,-0.4173,-0.25404,0.87254,40.251 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.58296,-0.79671,-0.15941,12.373,0.80507,0.53991,0.24569,9.8491,-0.10968,-0.27156,0.95615,40.028 > view matrix models > #8,0.74877,-0.43468,0.50039,12.262,0.46519,0.8824,0.07044,10.121,-0.47217,0.18003,0.86293,40.321 > hide #8 models > select subtract #8 Nothing selected > ui mousemode right translate > save /Users/yufy/Desktop/image4.png supersample 3 > volume planes z style image imageMode ""full region"" No volumes specified ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 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: MacBookPro17,1 Model Number: Z11C0002BSM/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 13 days, 6 hours, 6 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2422HE: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 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-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX