id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8920 Save X3D: numpy array used as boolean amendezt@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC) Description Trying to save p53 structure in format x3d Log: UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/China_hCoV-19_phylo_20230307.cxs Log from Thu Apr 27 09:24:57 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Wed Apr 26 14:37:38 2023UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/bioinformatica/Downloads/P53_1.pdb Summary of feedback from opening /Users/bioinformatica/Downloads/P53_1.pdb --- warnings | Ignored bad PDB record found on line 10318 END Start residue of secondary structure not found: HELIX 1 1 GLN B 167 THR B 170 1 4 Start residue of secondary structure not found: HELIX 2 2 PRO B 177 ARG B 181 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO B 278 GLU B 287 1 10 Start residue of secondary structure not found: SHEET 1 1 1 ARG B 110 GLY B 112 0 Start residue of secondary structure not found: SHEET 2 2 1 CYS B 124 SER B 127 0 65 messages similar to the above omitted P53_1.pdb title: Tumor suppressor P53 complexed with DNA [more info...] Chain information for P53_1.pdb --- Chain | Description 1.9/A 1.9/B 1.9/C | P53 tumor suppressor 1.1/B | P53 tumor suppressor 1.2/B 1.4/B 1.7/B 1.8/B | P53 tumor suppressor 1.3/B 1.5/B 1.6/B | P53 tumor suppressor 1.9/D | No description available > ui mousemode right select Drag select of 132 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of 17 atoms, 110 residues, 4 pseudobonds, 13 bonds Drag select of 38 residues Drag select of 9 atoms, 139 residues, 1 pseudobonds, 8 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear Drag select of 11 residues Drag select of 8 residues > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select 9564 atoms, 9432 bonds, 16 pseudobonds, 1292 residues, 14 models selected > color sel byhetero > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: P53_1.pdb #1.5/B SER 96 OG, P53_1.pdb #1.5/B LEU 289 OXT, P53_1.pdb #1.6/B SER 96 OG, P53_1.pdb #1.6/B LEU 289 OXT, P53_1.pdb #1.1/B SER 96 OG, and 6 other atoms > color sel bychain > ui mousemode right select > select clear > ui mousemode right select Drag select of P53_1.pdb_A SES surface, 70598 of 88382 triangles, P53_1.pdb_B SES surface, 56419 of 88366 triangles, P53_1.pdb_C SES surface, 68040 of 88170 triangles, P53_1.pdb_D SES surface, 80025 of 88172 triangles, 139 residues > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 15010 of 17442 triangles, 10 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 94275 of 170986 triangles, 148 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 17248 of 17430 triangles, 11 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 139303 of 167568 triangles, 17 atoms, 182 residues, 4 pseudobonds, 13 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 73451 of 169976 triangles, 79 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 11 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 16983 of 17450 triangles, 11 residues > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 158434 of 167568 triangles, 17 atoms, 189 residues, 4 pseudobonds, 13 bonds > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 11 residues > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_A SES surface, P53_1.pdb_B SES surface, P53_1.pdb_C SES surface, P53_1.pdb_D SES surface, 52 atoms, 988 residues, 12 pseudobonds, 39 bonds > show sel cartoons > show sel atoms > show sel cartoons > show sel cartoons > show sel atoms > show sel cartoons > transparency (#!1.1-9 & sel) 90 > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected atoms"" > ui mousemode right translate > set bgColor white > ui mousemode right select > select clear > select 9564 atoms, 9432 bonds, 16 pseudobonds, 1292 residues, 14 models selected > transparency (#!1.1-9 & sel) 90 > transparency (#!1.1-9 & sel) 70 > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 134541 of 169976 triangles, 817 atoms, 182 residues, 4 pseudobonds, 688 bonds > set bgColor gray > set bgColor black > set bgColor white > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 17264 of 17450 triangles, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 166570 of 170986 triangles, 930 atoms, 194 residues, 4 pseudobonds, 788 bonds > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 150274 of 167568 triangles, 900 atoms, 189 residues, 4 pseudobonds, 762 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 5996 of 17430 triangles, 23 atoms, 6 residues, 19 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 134629 of 167568 triangles, 861 atoms, 184 residues, 4 pseudobonds, 729 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 77898 of 169976 triangles, 539 atoms, 120 residues, 2 pseudobonds, 461 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 12537 of 17450 triangles, 51 atoms, 10 residues, 44 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 104554 of 169976 triangles, 717 atoms, 165 residues, 4 pseudobonds, 606 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 14116 of 17450 triangles, 56 atoms, 10 residues, 50 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 16285 of 17442 triangles, 61 atoms, 11 residues, 54 bonds > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 163569 of 170260 triangles, 927 atoms, 193 residues, 4 pseudobonds, 781 bonds > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 129556 of 167568 triangles, P53_1.pdb_B SES surface, 485 of 17430 triangles, 823 atoms, 179 residues, 4 pseudobonds, 694 bonds Drag select of P53_1.pdb_B SES surface, 162685 of 167568 triangles, P53_1.pdb_B SES surface, 990 atoms, 205 residues, 4 pseudobonds, 840 bonds > color (#!1.6,8 & sel) orange > transparency (#!1.6,8 & sel) 80 > ui mousemode right select > select clear > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 123477 of 170260 triangles, 771 atoms, 166 residues, 4 pseudobonds, 654 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 25136 of 169976 triangles, 118 atoms, 41 residues, 1 pseudobonds, 97 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 62181 of 170260 triangles, 399 atoms, 92 residues, 3 pseudobonds, 347 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 159760 of 169976 triangles, 899 atoms, 191 residues, 4 pseudobonds, 761 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 25367 of 167568 triangles, 119 atoms, 35 residues, 103 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 16499 of 17430 triangles, 62 atoms, 11 residues, 56 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 4923 of 17430 triangles, 16 atoms, 5 residues, 12 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 107494 of 167568 triangles, 684 atoms, 146 residues, 4 pseudobonds, 581 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 68886 of 170986 triangles, 497 atoms, 118 residues, 1 pseudobonds, 421 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 7439 of 17442 triangles, 29 atoms, 9 residues, 24 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 15325 of 17430 triangles, 58 atoms, 11 residues, 53 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 87376 of 169976 triangles, 561 atoms, 123 residues, 2 pseudobonds, 477 bonds Drag select of P53_1.pdb_B SES surface, 6756 of 17450 triangles, 24 atoms, 6 residues, 20 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 65654 of 169976 triangles, 351 atoms, 88 residues, 293 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 6992 of 17450 triangles, 25 atoms, 5 residues, 23 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 16949 of 17612 triangles, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear Drag select of P53_1.pdb_B SES surface, 166298 of 169976 triangles, P53_1.pdb_B SES surface, 996 atoms, 205 residues, 4 pseudobonds, 843 bonds > color (#!1.5,7 & sel) orange > transparency (#!1.5,7 & sel) 90 > transparency (#!1.5,7 & sel) 80 Drag select of P53_1.pdb_B SES surface, 163549 of 170260 triangles, P53_1.pdb_B SES surface, 983 atoms, 205 residues, 4 pseudobonds, 832 bonds > color (#!1.3-4 & sel) orange > transparency (#!1.3-4 & sel) 80 Drag select of P53_1.pdb_B SES surface, 146878 of 170986 triangles, P53_1.pdb_B SES surface, 16241 of 17442 triangles, 915 atoms, 191 residues, 776 bonds > color (#!1.1-2 & sel) orange > transparency (#!1.1-2 & sel) 80 > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 81532 of 170986 triangles, 536 atoms, 114 residues, 4 pseudobonds, 455 bonds > color (#!1.1 & sel) orange > select clear > save /Users/bioinformatica/Downloads/Propuesta_1_P53.cxs > save /Users/bioinformatica/Downloads/Propuesta_1.1_P53.bmp width 15360 > height 8640 supersample 3 > open /Users/bioinformatica/Downloads/DNA_1.pdb Summary of feedback from opening /Users/bioinformatica/Downloads/DNA_1.pdb --- warning | Ignored bad PDB record found on line 1036 END DNA_1.pdb title: Structure of A B-DNA dodecamer. Conformation and dynamics [more info...] Chain information for DNA_1.pdb #2 --- Chain | Description A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*CP*GP*CP*G)- 3') > ui mousemode right select > select #2/A#2/B 566 atoms, 544 bonds, 104 residues, 1 model selected > ui mousemode right ""translate selected models"" > select #2/A#2/B 566 atoms, 544 bonds, 104 residues, 1 model selected > delete atoms sel > delete bonds sel > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 5696 of 170986 triangles, 11 atoms, 6 residues, 9 bonds > color (#!1.1 & sel) orange > save ""/Users/bioinformatica/Downloads/Proyecto Chimera P53.cxs"" > ui mousemode right select > select clear > save /Users/bioinformatica/Downloads/Proyecto_Chimera_P53.cxs ——— End of log from Wed Apr 26 14:37:38 2023 ——— opened ChimeraX session > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""rotate selected models"" > view matrix models > #1.4,0.21777,0.63544,-0.74081,150.09,-0.94711,-0.045726,-0.31763,-20.993,-0.23571,0.7708,0.59187,110.3 > turn > view matrix models > #1.4,-0.25362,0.91819,-0.30431,164.34,-0.9151,-0.12579,0.38311,-70.637,0.31349,0.37564,0.87214,41.134 > turn [Repeated 2 time(s)] > view matrix models > #1.4,-0.22288,0.94334,-0.24584,162.26,-0.92377,-0.12382,0.36239,-68.973,0.31142,0.30786,0.89902,33.409 > view matrix models > #1.4,-0.11878,0.95433,-0.27413,161.82,-0.90546,0.00919,0.42434,-61.01,0.40748,0.29862,0.86301,31.806 > view matrix models > #1.4,-0.13675,0.87202,-0.46999,166.38,-0.90689,0.080688,0.41357,-53.791,0.39856,0.48278,0.77979,53.834 > turn > view matrix models > #1.4,0.13162,0.71036,-0.69142,156.61,-0.91267,0.35907,0.19518,-15.259,0.38692,0.60535,0.69559,70.367 > turn [Repeated 2 time(s)] > view matrix models > #1.4,-0.35364,0.67537,-0.64716,165.36,-0.93272,-0.30678,0.18953,-75.241,-0.070533,0.67065,0.73842,87.535 > turn > view matrix models > #1.4,-0.5234,0.73904,-0.42412,163.11,-0.83183,-0.33528,0.44233,-95.795,0.1847,0.58431,0.79023,68.922 > view matrix models > #1.4,-0.41781,0.74042,-0.52651,166.11,-0.89806,-0.24883,0.36273,-81.202,0.13756,0.62439,0.7689,75.262 > view matrix models > #1.4,-0.46459,0.66994,-0.57908,164.17,-0.87354,-0.23951,0.42374,-84.685,0.14518,0.70271,0.6965,86.472 > turn [Repeated 4 time(s)] > view matrix models > #1.4,-0.62347,0.44884,-0.64017,152.31,-0.76185,-0.16477,0.62645,-93.163,0.17569,0.87829,0.44468,116.48 > turn [Repeated 3 time(s)] > view matrix models > #1.4,-0.67921,0.34193,-0.64944,144.75,-0.71724,-0.12146,0.68616,-94.063,0.15573,0.93184,0.32774,128.88 > turn [Repeated 1 time(s)] > view matrix models > #1.4,-0.72798,0.3215,-0.60554,141.76,-0.67772,-0.20399,0.70646,-104,0.1036,0.92467,0.36639,127.51 > ui mousemode right ""move picked models"" > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""move picked models"" > view matrix models > #1.2,0.37199,0.64796,-0.66466,-16.104,-0.92254,0.17887,-0.34195,-7.8912,-0.10268,0.74038,0.6643,-5.0434 > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 17428 of 17430 triangles, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""move picked models"" > view matrix models > #1.8,-0.12284,-0.52283,0.84354,89.023,0.062133,0.84426,0.53233,102.77,-0.99048,0.1178,-0.071224,56.197 > ui mousemode right select Drag select of P53_1.pdb_B SES surface, 17586 of 17612 triangles, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""move picked models"" > view matrix models > #1.4,-0.72798,0.3215,-0.60554,139.19,-0.67772,-0.20399,0.70646,-133.31,0.1036,0.92467,0.36639,129.41 > ui mousemode right select [Repeated 2 time(s)]Drag select of P53_1.pdb_B SES surface, 17172 of 17450 triangles, 63 atoms, 11 residues, 56 bonds > ui mousemode right ""move picked models"" > view matrix models > #1.7,0.96201,0.097447,-0.25504,41.81,-0.22282,-0.25963,-0.93965,144.45,-0.15778,0.96078,-0.22805,81.968 > ui mousemode right ""move picked models"" > view matrix models > #1.1,-0.048666,0.98891,0.14029,5.0729,-0.4281,-0.14756,0.8916,-10.185,0.90242,-0.016669,0.43054,7.4088 > view matrix models > #1.6,0.3285,0.77755,0.53619,-53.155,-0.29045,-0.45703,0.84069,67.865,0.89874,-0.4319,0.07571,26.047 > view matrix models > #1.5,-0.27196,-0.81489,0.51184,90.332,0.71162,0.18774,0.67701,-64.658,-0.64779,0.54836,0.52884,96.243 > view matrix models > #1.3,-0.85829,0.20075,0.47227,35.275,-0.29483,0.56036,-0.774,49.642,-0.42002,-0.80355,-0.42176,54.996 > view matrix models > #1.2,0.37199,0.64796,-0.66466,0.90387,-0.92254,0.17887,-0.34195,-6.0687,-0.10268,0.74038,0.6643,10.22 > view matrix models > #1.8,-0.12284,-0.52283,0.84354,90.726,0.062133,0.84426,0.53233,76.405,-0.99048,0.1178,-0.071224,59.133 > view matrix models > #1.7,0.96201,0.097447,-0.25504,20.169,-0.22282,-0.25963,-0.93965,140.02,-0.15778,0.96078,-0.22805,62.659 > view matrix models > #1.4,-0.72798,0.3215,-0.60554,134.43,-0.67772,-0.20399,0.70646,-104.46,0.1036,0.92467,0.36639,123.58 > ui mousemode right ""rotate selected models"" > view matrix models > #1.7,0.94308,0.14177,-0.30084,22.979,-0.26471,-0.2276,-0.93708,142.4,-0.20132,0.96338,-0.17712,63.349 > view matrix models > #1.7,0.93793,0.15481,-0.31035,23.441,-0.27313,-0.22178,-0.93606,142.88,-0.21374,0.96273,-0.16573,63.891 > ui mousemode right select Drag select of P53_1.pdb_A SES surface, 87866 of 88382 triangles, P53_1.pdb_B SES surface, 86145 of 88366 triangles, P53_1.pdb_C SES surface, 87038 of 88170 triangles, P53_1.pdb_D SES surface, 88157 of 88172 triangles, 1911 atoms, 168 residues, 1787 bonds > ui mousemode right ""rotate selected models"" > view matrix models > #1.9,-0.96104,0.031717,-0.27459,83.957,0.27578,0.17725,-0.94474,48.542,0.018706,-0.98366,-0.17909,49.057 > ui mousemode right select > save C:/Users/manu_/Documents/1_IMAG.cxs ——— End of log from Thu Apr 27 09:24:57 2023 ——— opened ChimeraX session > select ::name=""HOH"" 300 atoms, 300 residues, 8 models selected > show sel atoms > delete atoms sel > delete bonds sel > save > /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/China_hCoV-19_phylo_20230307.cxs > save /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/p53_alone.x3d Traceback (most recent call last): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 109, in save return save_x3d(session, path, **kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1042, in save_x3d m.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1381, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 750, in x3d_needs super().x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1381, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1388, in x3d_needs if any_transp and self.vertex_colors: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1388, in x3d_needs if any_transp and self.vertex_colors: See log for complete Python traceback. > select 9264 atoms, 9432 bonds, 16 pseudobonds, 992 residues, 14 models selected > hide sel atoms > save /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/p53_alone.x3d Traceback (most recent call last): File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 109, in save return save_x3d(session, path, **kw) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1042, in save_x3d m.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1381, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 750, in x3d_needs super().x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1381, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1388, in x3d_needs if any_transp and self.vertex_colors: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() File ""/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/drawing.py"", line 1388, in x3d_needs if any_transp and self.vertex_colors: See log for complete Python traceback. OpenGL version: 4.1 INTEL-18.8.6 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini8,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 2:44 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202304252053 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal 1.6 Input/Output fixed chimera-programmers all ChimeraX