id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7427 QMainWindowLayout::tabPosition called with out-of-bounds value chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/chrismuriel/Desktop/modified_aligned/VasH_VFischeri_model_iTasser_T_newfit_02-coot-0.pdb > format pdb Chain information for VasH_VFischeri_model_iTasser_T_newfit_02-coot-0.pdb #1 --- Chain | Description T | No description available > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. Alignment identifier is 1/T > select > /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select > /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > cartoon sel Alignment identifier is 1/T > select /T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /T:1-181 1334 atoms, 1349 bonds, 181 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light coral > color sel peach puff > color sel navajo white > color sel light pink > select > /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select > /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select /T:334 7 atoms, 6 bonds, 1 residue, 1 model selected > select /T:334-346 106 atoms, 109 bonds, 13 residues, 1 model selected > select /T:442 7 atoms, 6 bonds, 1 residue, 1 model selected > select /T:321-442 945 atoms, 961 bonds, 122 residues, 1 model selected > select /T:297-298 13 atoms, 12 bonds, 2 residues, 1 model selected > select /T:297-442 1136 atoms, 1155 bonds, 146 residues, 1 model selected > color sel light green > color sel dark sea green > color sel aquamarine > color sel dark sea green > select > /T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select > /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select /T:1-5 34 atoms, 33 bonds, 5 residues, 1 model selected > select /T:1-180 1328 atoms, 1343 bonds, 180 residues, 1 model selected > color sel pink [Repeated 1 time(s)] > select > /T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > open > /Users/chrismuriel/Desktop/modified_aligned/VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb > format pdb VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb title: Alphafold monomer V2.0 prediction for transcriptional regulator vash (Q9KN48) [more info...] Chain information for VasH_VCholerae_model_iTasser_newfit_01-coot-0.pdb #2 --- Chain | Description | UniProt A | transcriptional regulator vash | VASH_VIBCH Destroying pre-existing alignment with identifier 1/T Alignment identifier is 1/T > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-180 1328 atoms, 1343 bonds, 180 residues, 1 model selected > color sel salmon > undo Destroying pre-existing alignment with identifier 1/T Alignment identifier is 1/T QMainWindowLayout::tabPosition called with out-of-bounds value '0' > hide #1 models > show #1 models > hide #1 models > ui tool show ""Color Actions"" QMainWindowLayout::tabPosition called with out-of-bounds value '0' [Repeated 2 time(s)]Alignment identifier is 1/T > select #2 4173 atoms, 4251 bonds, 530 residues, 1 model selected Alignment identifier is 2/A > ~select #2 Nothing selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-180 1459 atoms, 1492 bonds, 180 residues, 1 model selected > color sel salmon > color sel misty rose > color sel bisque > color sel blanched almond [Repeated 3 time(s)] > select #2/A:181 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:181-191 82 atoms, 81 bonds, 11 residues, 1 model selected > color sel blanched almond > select #2/A:192 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:192-212 154 atoms, 153 bonds, 21 residues, 1 model selected > color sel blanched almond > select #2/A:212-213 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:212-213 14 atoms, 13 bonds, 2 residues, 1 model selected > color sel blanched almond [Repeated 1 time(s)] > select #2/A:214-215 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:214-422 1655 atoms, 1685 bonds, 209 residues, 1 model selected > select #2/A:421-423 20 atoms, 19 bonds, 3 residues, 1 model selected > select #2/A:410-423 114 atoms, 115 bonds, 14 residues, 1 model selected > select #2/A:214 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:214-389 1385 atoms, 1409 bonds, 176 residues, 1 model selected > select #2/A:214 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:214-359 1132 atoms, 1151 bonds, 146 residues, 1 model selected > color sel azure > select > #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524 2124 atoms, 2136 bonds, 261 residues, 1 model selected > select > #2/A:36-42,49-51,79-82,106-113,122-129,217-220,245-249,288-292,328-333,357-360 424 atoms, 424 bonds, 54 residues, 1 model selected > show #1 models > select #2 4173 atoms, 4251 bonds, 530 residues, 1 model selected > ~select #2 Nothing selected > hide #2 models > hide #1 models > show #1 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > hide #1 models > show #2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models Alignment identifier is 1/T Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > select > #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524 2124 atoms, 2136 bonds, 261 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select #1/T:1-2 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/T:1-180 1328 atoms, 1343 bonds, 180 residues, 1 model selected > color sel cornflower blue > color sel crimson > color sel gray > color sel saddle brown > color sel chocolate > color sel tomato > color sel orange red > color sel light sea green > color sel orange red > color sel violet > select #1/T:442 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:296-442 1143 atoms, 1163 bonds, 147 residues, 1 model selected > color sel light sea green [Repeated 1 time(s)] > select #1/T:301 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/T:301-442 1113 atoms, 1132 bonds, 142 residues, 1 model selected > color sel turquoise > select #1/T:290-296 51 atoms, 52 bonds, 7 residues, 1 model selected > select #1/T:290-300 74 atoms, 75 bonds, 11 residues, 1 model selected > color sel navajo white > undo [Repeated 7 time(s)] > select #1/T:299-300 10 atoms, 9 bonds, 2 residues, 1 model selected > select #1/T:299-442 1123 atoms, 1142 bonds, 144 residues, 1 model selected > color sel turquoise > color sel light sea green [Repeated 2 time(s)] > color sel dodger blue > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select #1/T:296 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:296-300 30 atoms, 30 bonds, 5 residues, 1 model selected > select #1/T:298 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:298-300 18 atoms, 17 bonds, 3 residues, 1 model selected > color sel dodger blue > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select #1/T:287 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/T:287-290 32 atoms, 31 bonds, 4 residues, 1 model selected > select #1/T:295 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:295-298 27 atoms, 27 bonds, 4 residues, 1 model selected > select #1/T:293-294 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/T:293-295 23 atoms, 22 bonds, 3 residues, 1 model selected > select #1/T:296 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:296-297 12 atoms, 12 bonds, 2 residues, 1 model selected > color sel peach puff > color sel navajo white > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select #1/T:296-297 12 atoms, 12 bonds, 2 residues, 1 model selected > select #1/T:296-298 20 atoms, 20 bonds, 3 residues, 1 model selected > select #1/T:296-442 1143 atoms, 1163 bonds, 147 residues, 1 model selected > color sel dodger blue [Repeated 1 time(s)] > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select #1/T:296-442 1143 atoms, 1163 bonds, 147 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected Alignment identifier is 1/T > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select > #1/T:12-25,35-44,63-73,89-96,109-132,141-153,170-180,198-206,214-217,228-230,233-245,271-276,282-288,298-320,329-337,343-357,369-371,374-379,389-392,396-414,419-426,430-440 1818 atoms, 1810 bonds, 231 residues, 1 model selected > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-180 1328 atoms, 1343 bonds, 180 residues, 1 model selected > label sel attribute label_specifier > redo > label sel attribute label_specifier > ~label sel atoms [Repeated 2 time(s)] > ~label sel residues > select strand 871 atoms, 865 bonds, 110 residues, 2 models selected > undo > select coil 2713 atoms, 2708 bonds, 370 residues, 2 models selected > select #1/T:287-288 19 atoms, 18 bonds, 2 residues, 1 model selected > select #1/T:287-300 99 atoms, 100 bonds, 14 residues, 1 model selected > select #1/T:292 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:292-300 60 atoms, 61 bonds, 9 residues, 1 model selected > select #1/T:296 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:296-300 30 atoms, 30 bonds, 5 residues, 1 model selected > select #1/T:291-292 14 atoms, 14 bonds, 2 residues, 1 model selected > select #1/T:291-300 67 atoms, 68 bonds, 10 residues, 1 model selected > select #1/T:291 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:291-298 57 atoms, 58 bonds, 8 residues, 1 model selected > select #1/T:292-293 14 atoms, 14 bonds, 2 residues, 1 model selected > select #1/T:292-300 60 atoms, 61 bonds, 9 residues, 1 model selected > select #1/T:294 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/T:294-300 46 atoms, 46 bonds, 7 residues, 1 model selected > select #1/T:291 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:291-296 44 atoms, 45 bonds, 6 residues, 1 model selected > select #1/T:291 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:291-298 57 atoms, 58 bonds, 8 residues, 1 model selected > select #1/T:290-291 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/T:290-297 56 atoms, 57 bonds, 8 residues, 1 model selected > select #1/T:290 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/T:290-295 44 atoms, 44 bonds, 6 residues, 1 model selected > select #1/T:296 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:296-300 30 atoms, 30 bonds, 5 residues, 1 model selected > color sel dodger blue [Repeated 1 time(s)] > select > #1/T:4-8,28-32,49-53,79-84,101-105,160-163,188-192,222-226,247-249,256-258,262-267,291-294 447 atoms, 441 bonds, 56 residues, 1 model selected > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-221 1616 atoms, 1636 bonds, 221 residues, 1 model selected > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-119 873 atoms, 885 bonds, 119 residues, 1 model selected > select #1/T:1-5 34 atoms, 33 bonds, 5 residues, 1 model selected > select #1/T:1-180 1328 atoms, 1343 bonds, 180 residues, 1 model selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > label sel atoms attribute alt_loc > show #2 models > hide #!1 models > select #1/T:9-10 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/T:9-10 16 atoms, 15 bonds, 2 residues, 1 model selected Destroying pre-existing alignment with identifier 1/T Alignment identifier is 1/T > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-132 978 atoms, 990 bonds, 132 residues, 1 model selected > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-132 978 atoms, 990 bonds, 132 residues, 1 model selected > select #1/T:1-130 962 atoms, 974 bonds, 130 residues, 1 model selected > select #1/T:1-134 988 atoms, 1000 bonds, 134 residues, 1 model selected > select #1/T:1-22 156 atoms, 155 bonds, 22 residues, 1 model selected > select #1/T:1-22 156 atoms, 155 bonds, 22 residues, 1 model selected > select #1/T:1-126 929 atoms, 941 bonds, 126 residues, 1 model selected > select #1/T:1-126 929 atoms, 941 bonds, 126 residues, 1 model selected > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-132 978 atoms, 990 bonds, 132 residues, 1 model selected Window position QRect(1497,-531 100x30) outside any known screen, using primary screen Height must be a number [Repeated 4 time(s)] > hide #2 models > show #!1 models > show #2 models > hide #!1 models Destroying pre-existing alignment with identifier 1/T Alignment identifier is 1/T QMainWindowLayout::tabPosition called with out-of-bounds value '0' [Repeated 1 time(s)] > select #1/T:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/T:1-132 978 atoms, 990 bonds, 132 residues, 1 model selected Destroying pre-existing alignment with identifier 1/T Alignment identifier is 1/T > ui tool show ""Color Actions"" > color #2 darkgrey transparency 0 > select #2 4173 atoms, 4251 bonds, 530 residues, 1 model selected Alignment identifier is 2/A > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-111 890 atoms, 913 bonds, 111 residues, 1 model selected > select #2/A:1-2 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:1-113 905 atoms, 929 bonds, 113 residues, 1 model selected > select #2/A:1-3 23 atoms, 22 bonds, 3 residues, 1 model selected > select #2/A:1-192 1548 atoms, 1581 bonds, 192 residues, 1 model selected > color sel dark turquoise > color sel cornflower blue > select #2/A:193-195 20 atoms, 19 bonds, 3 residues, 1 model selected > select #2/A:193-212 147 atoms, 146 bonds, 20 residues, 1 model selected > color sel cornflower blue > select > #2/A:3-11,17-32,68-75,85-89,93-99,130-137,140-191,198-212,227-236,255-263,280-283,294-296,299-311,337-342,348-354,364-386,395-403,409-422,432-435,475-477,481-499,504-510,515-524 2124 atoms, 2136 bonds, 261 residues, 1 model selected > select #2/A:193-212 147 atoms, 146 bonds, 20 residues, 1 model selected > select #2/A:193-194 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:193-387 1520 atoms, 1544 bonds, 195 residues, 1 model selected > color sel plum [Repeated 1 time(s)] > select #2/A:395-396 23 atoms, 23 bonds, 2 residues, 1 model selected > select #2/A:395-530 1048 atoms, 1067 bonds, 136 residues, 1 model selected > color sel pale green [Repeated 1 time(s)] > color sel spring green > color sel lime green > select > #2/A:36-42,49-51,79-82,106-113,122-129,217-220,245-249,288-292,328-333,357-360 424 atoms, 424 bonds, 54 residues, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > select #2 4173 atoms, 4251 bonds, 530 residues, 1 model selected > ~select #2 Nothing selected > hide #!1 models > show #!1 models > hide #!1 models > select #2/A:395-530 1048 atoms, 1067 bonds, 136 residues, 1 model selected > select #2/A:393-394 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:193-394 1577 atoms, 1601 bonds, 202 residues, 1 model selected > color sel blue violet [Repeated 1 time(s)] > show #!1 models > hide #2 models > hide #!1 models > show #2 models > show #!1 models > hide #2 models > hide #!1 models > show #2 models > select #2 4173 atoms, 4251 bonds, 530 residues, 1 model selected > ~select #2 Nothing selected > show #!1 models > hide #!1 models > view > label #2 atoms attribute alt_loc > label #2 atoms attribute num_alt_locs > label #2 atoms attribute alt_loc [Repeated 1 time(s)] > show #!1 models > label #1-2 atoms attribute alt_loc > hide #!2 models Window position QRect(1229,-751 654x459) outside any known screen, using primary screen > save /Users/chrismuriel/Desktop/2022_vasHmodel_VF.tif width 1358 height 824 > supersample 3 transparentBackground true > show #!2 models > hide #!1 models Window position QRect(1229,-751 654x459) outside any known screen, using primary screen > save /Users/chrismuriel/Desktop/2022_vasHmodel_VC.tif width 1358 height 824 > supersample 3 transparentBackground true > show #!1 models Window position QRect(1229,-751 654x459) outside any known screen, using primary screen > save /Users/chrismuriel/Desktop/2022_alignment_vasHmodel_VC_VF.tif width > 1358 height 824 supersample 3 transparentBackground true Window position QRect(1177,-756 654x459) outside any known screen, using primary screen Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 2251, in dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 648, in close_request all_windows = self.tool_instance_to_windows[tool_instance] KeyError: KeyError: File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 648, in close_request all_windows = self.tool_instance_to_windows[tool_instance] See log for complete Python traceback. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60000feb38a0> contents scale of 1 - updating layer to match. [Repeated 3 time(s)] OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) HD Graphics 615 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Model Identifier: MacBook10,1 Processor Name: Dual-Core Intel Core m3 Processor Speed: 1.2 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 451.120.7.0.0 OS Loader Version: 540.120.3~6 SMC Version (system): 2.42f13 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 58 days 46 minutes Graphics/Displays: Intel HD Graphics 615: Chipset Model: Intel HD Graphics 615 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591e Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2304 x 1440 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP V21: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 1CR042225R Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Apple TV: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 63.00Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Connection Type: AirPlay Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX