id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9167 Graphics crash, macOS 13.1, Intel Iris Plus Graphics i.lidbury@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""647682eb6bde164de156b24e"" }, ""deploymentId"" : 240000466 }, { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000288 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/bo1il/Downloads/PafA-like_Bacteroides/final.casp.pdb Chain information for final.casp.pdb #1 --- Chain | Description ? | No description available > open /Users/bo1il/Downloads/PafA-like_Bacteroides/c5tj3A_.1.pdb Chain information for c5tj3A_.1.pdb #2 --- Chain | Description ? | No description available > toolshed show > select #1/?#2/? 7994 atoms, 8186 bonds, 1000 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2 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 final.casp.pdb, chain (blank) (#1) with c5tj3A_.1.pdb, chain (blank) (#2), sequence alignment score = 2597.5 RMSD between 500 pruned atom pairs is 0.000 angstroms; (across all 500 pairs: 0.000) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/? #2/? Alignment identifier is 1 > hide #1 models > show #1 models > hide #1 models > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > open > /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_Prevotella_KCOM1933.pdb Chain information for PafA_Prevotella_KCOM1933.pdb #3 --- Chain | Description ? | No description available > hide #2 models > hide #3 models > show #3 models > show #2 models > show #1 models > hide #1 models > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > ui tool show ""Modeller Comparative"" > modeller comparative 1:1 numModels 5 fast false multichain true hetPreserve > false hydrogens false waterPreserve false No Modeller license key provided. Get a license key by registering at the Modeller web site. > ui tool show ""Show Sequence Viewer"" > sequence chain #3/? Alignment identifier is 3/ > select > #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473 1394 atoms, 1399 bonds, 175 residues, 1 model selected > select #1/*:33 #2/*:33 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:33-113 #2/*:33-113 1314 atoms, 1340 bonds, 162 residues, 2 models selected 1 [ID: 1] region 2 chains [12-92] RMSD: 0.001 > select add #3 5042 atoms, 5158 bonds, 631 residues, 3 models selected > select subtract #3 1314 atoms, 1340 bonds, 162 residues, 2 models selected > select add #2 4654 atoms, 4763 bonds, 581 residues, 2 models selected > select subtract #2 657 atoms, 670 bonds, 81 residues, 1 model selected > select add #1 3997 atoms, 4093 bonds, 500 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 3997 atoms, 4093 bonds, 500 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 3997 atoms, 4093 bonds, 500 residues, 1 model selected > select subtract #2 Nothing selected > select add #3 3728 atoms, 3818 bonds, 469 residues, 1 model selected > select subtract #3 Nothing selected > open > /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py Traceback (most recent call last): File ""/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py"", line 3, in import cPickle, base64 ModuleNotFoundError: No module named 'cPickle' Failed opening file /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py: Error opening python file /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py > open > /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py Traceback (most recent call last): File ""/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py"", line 3, in import cPickle, base64 ModuleNotFoundError: No module named 'cPickle' Failed opening file /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py: Error opening python file /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py > open > /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_mucilagnibacter.pdb Chain information for PafA_mucilagnibacter.pdb #4 --- Chain | Description ? | No description available > hide #4 models > show #4 models > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:239 #2/*:239 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:239-241 #2/*:239-241 50 atoms, 48 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [218-220] RMSD: 0.000 > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > select #3/*:156 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > hide #3 models > hide #4 models > select > #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473 1394 atoms, 1399 bonds, 175 residues, 1 model selected > hide #2 models > show #3 models > select #3/*:156 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > show sel atoms > select #3/*:155 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/*:155 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/*:239 #2/*:239 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:239-241 #2/*:239-241 50 atoms, 48 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [218-220] RMSD: 0.000 > show #2 models > select #1/*:239 #2/*:239 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:239-241 #2/*:239-241 50 atoms, 48 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [218-220] RMSD: 0.000 > select #1/*:241 #2/*:241 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:239-241 #2/*:239-241 50 atoms, 48 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [218-220] RMSD: 0.000 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:308 #2/*:308 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:306-308 #2/*:306-308 54 atoms, 52 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [285-287] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:203-204 #2/*:203-204 38 atoms, 38 bonds, 4 residues, 2 models selected > select #1/*:203-205 #2/*:203-205 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [182-184] RMSD: 0.000 > select #1/*:143 #2/*:143 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:143-162 #2/*:143-162 294 atoms, 298 bonds, 40 residues, 2 models selected 1 [ID: 1] region 2 chains [122-141] RMSD: 0.001 > select #1/*:156 #2/*:156 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:154-156 #2/*:154-156 58 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [133-135] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [134] RMSD: 0.001 > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > show sel & #2 atoms > select #1/*:156 #2/*:156 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:156 #2/*:156 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [135] RMSD: 0.001 > hide sel & #2 atoms > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > style sel & #2 ball Changed 30 atom styles > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > style sel ball Changed 28 atom styles > select #1/*:156 #2/*:156 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:156 #2/*:156 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [135] RMSD: 0.001 > style sel & #2 sphere Changed 11 atom styles > show sel & #2 atoms > style sel & #2 ball Changed 11 atom styles > select #3/*:155 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/*:155 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel atoms > hide sel atoms > show sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > select > #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473 1394 atoms, 1399 bonds, 175 residues, 1 model selected > hide #4 models > show #4 models > hide #4 models > select #1/*:316 #2/*:316 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:316-318 #2/*:316-318 50 atoms, 48 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [295-297] RMSD: 0.000 > lighting simple > lighting soft > lighting full > lighting soft > set bgColor black > set bgColor white > color bfactor sel & #2 25 atoms, 3 residues, atom bfactor range 0 to 0 > color bfactor sel & #2 25 atoms, 3 residues, atom bfactor range 0 to 0 > view sel > select #3/*:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > view sel > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #4/? Alignment identifier is 4/ > select #4/*:171 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/*:171-173 28 atoms, 27 bonds, 3 residues, 1 model selected > style #2-3 ball Changed 7725 atom styles > style #2-3 ball Changed 7725 atom styles > show #4 models > style sel ball Changed 28 atom styles > style sel ball Changed 28 atom styles > style sel ball Changed 28 atom styles > show sel atoms > hide sel atoms > show sel atoms > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > select #4/*:171 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/*:171 9 atoms, 8 bonds, 1 residue, 1 model selected > open /Users/bo1il/Downloads/5tj3.pdb 5tj3.pdb title: Crystal structure of wild type alkaline phosphatase pafa to 1.7A resolution [more info...] Chain information for 5tj3.pdb #5 --- Chain | Description | UniProt A | AP PAFA | ALPH_ELIME 21-546 Non-standard residues in 5tj3.pdb #5 --- ZN — zinc ion > style sel stick Changed 9 atom styles > style sel stick Changed 9 atom styles > select #4/*:171 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/*:171-173 28 atoms, 27 bonds, 3 residues, 1 model selected > style sel stick Changed 28 atom styles > select #3/*:156 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/*:154-156 28 atoms, 27 bonds, 3 residues, 1 model selected > style sel stick Changed 28 atom styles > select > #3/*:26-32,60-62,96-99,104-107,148-151,168-173,178-180,238-244,288-293,313-315,337-341,344-347,376-381,410-414,418-420,444-448,454-456 639 atoms, 648 bonds, 78 residues, 1 model selected > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > style sel & #2 stick Changed 30 atom styles > select #3/*:72 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/*:72 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/*:80 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/*:78-80 22 atoms, 22 bonds, 3 residues, 1 model selected > select #3/*:79-80 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3/*:79-80 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3/*:83 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/*:83 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/*:74 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/*:74 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > show sel atoms > hide #4 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162-164 28 atoms, 27 bonds, 3 residues, 1 model selected > style sel stick Changed 28 atom styles > show sel atoms > hide #2 models > show #2 models > hide #!5 models > show #!5 models > ui mousemode right select > ui mousemode right swapaa > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right swapaa > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > ui mousemode right distance > nucleotides sel & #2 tube/slab shape box > nucleotides sel & #2 atoms > style nucleic & sel & #2 stick Changed 0 atom styles > style sel & #2 ball Changed 30 atom styles > nucleotides sel & #2 atoms > style nucleic & sel & #2 stick Changed 0 atom styles > nucleotides sel & #2 ladder > nucleotides sel & #2 atoms > style nucleic & sel & #2 stick Changed 0 atom styles > style sel & #2 sphere Changed 30 atom styles > style sel & #2 sphere Changed 30 atom styles > style sel & #2 ball Changed 30 atom styles > color bfactor sel & #2 30 atoms, 3 residues, atom bfactor range 0 to 0 > color bfactor sel & #2 30 atoms, 3 residues, atom bfactor range 0 to 0 > style sel & #2 ball Changed 30 atom styles > style sel & #2 ball Changed 30 atom styles > color sel & #2 bynucleotide > color bfactor sel & #2 30 atoms, 3 residues, atom bfactor range 0 to 0 > mlp sel & #2 Map values for surface ""c5tj3A_.1.pdb_ SES surface"": minimum -27.73, mean -3.887, maximum 28.44 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel & #!2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean -1.08, maximum 15.28 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel & #!2 Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean -1.08, maximum 15.28 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel & #!2 Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean -1.08, maximum 15.28 To also show corresponding color key, enter the above coulombic command and add key true > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162-164 28 atoms, 27 bonds, 3 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue TPO (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.in.mol2 -fi mol2 -o /var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (TPO) `` (TPO) `Welcome to antechamber 20.0: molecular input file processor.` (TPO) `` (TPO) `Info: Finished reading file (/var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.in.mol2); atoms read (29), bonds read (28).` (TPO) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (TPO) `` (TPO) `` (TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (TPO) `Info: Total number of electrons: 134; net charge: -2` (TPO) `` (TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (TPO) `` (TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (TPO) `` (TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (TPO) `` Charges for residue TPO determined Coulombic values for 5tj3.pdb_A SES surface #5.3: minimum, -21.27, mean -2.57, maximum 14.32 To also show corresponding color key, enter the above coulombic command and add key true > color sel byhetero > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > select #1/*:155-156 #2/*:155-156 44 atoms, 44 bonds, 4 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > hide sel & #!2 surfaces > style sel & #!2 stick Changed 30 atom styles > style sel & #!2 sphere Changed 30 atom styles > style sel & #!2 ball Changed 30 atom styles > style sel & #!2 stick Changed 30 atom styles > nucleotides sel & #!2 atoms > style nucleic & sel & #!2 stick Changed 0 atom styles > nucleotides sel & #!2 atoms > style nucleic & sel & #!2 stick Changed 0 atom styles > nucleotides sel & #!2 tube/slab shape box > hide sel & #!2 atoms > show sel & #!2 atoms > color sel & #!2 bynucleotide > color sel & #!2 bychain > color sel & #!2 byhetero > color sel & #!2 bychain > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:35-36 #2/*:35-36 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [14-15] RMSD: 0.000 > select #5/A:38-39 17 atoms, 16 bonds, 2 residues, 1 model selected > select #5/A:38-39 17 atoms, 16 bonds, 2 residues, 1 model selected > select #5/A:38 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/*:35-36 #2/*:35-36 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/*:35-36 #2/*:35-36 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [14-15] RMSD: 0.000 > select #1/*:34-35 #2/*:34-35 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:34-75 #2/*:34-75 716 atoms, 728 bonds, 84 residues, 2 models selected 1 [ID: 1] region 2 chains [13-54] RMSD: 0.001 > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [14] RMSD: 0.000 > style sel & #!2 stick Changed 8 atom styles > style sel & #!2 stick Changed 8 atom styles > show sel & #!2 atoms > select #1/*:315 #2/*:315 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:315 #2/*:315 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [294] RMSD: 0.001 > select #1/*:307 #2/*:307 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:307 #2/*:307 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [286] RMSD: 0.001 > select #5/A:353 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:352-353 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/*:342 #2/*:342 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:342-343 #2/*:342-343 32 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [321-322] RMSD: 0.000 > select #1/*:346 #2/*:346 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/*:346-347 #2/*:346-347 46 atoms, 46 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [325-326] RMSD: 0.001 > select #1/*:351 #2/*:351 8 atoms, 6 bonds, 2 residues, 2 models selected > select #1/*:351-352 #2/*:351-352 26 atoms, 24 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [330-331] RMSD: 0.000 > select #1/*:353-354 #2/*:353-354 42 atoms, 44 bonds, 4 residues, 2 models selected > select #1/*:353-355 #2/*:353-355 58 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [332-334] RMSD: 0.000 > select #1/*:364 #2/*:364 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:330-364 #2/*:330-364 524 atoms, 534 bonds, 70 residues, 2 models selected 1 [ID: 1] region 2 chains [309-343] RMSD: 0.000 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:362 #2/*:362 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:358-362 #2/*:358-362 68 atoms, 66 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [337-341] RMSD: 0.000 > select #1/*:372 #2/*:372 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:367-372 #2/*:367-372 90 atoms, 90 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [346-351] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:338-339 #2/*:338-339 30 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:338-339 #2/*:338-339 30 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [317-318] RMSD: 0.001 > select #1/*:340-341 #2/*:340-341 18 atoms, 16 bonds, 4 residues, 2 models selected > select #1/*:329-341 #2/*:329-341 174 atoms, 176 bonds, 26 residues, 2 models selected 1 [ID: 1] region 2 chains [308-320] RMSD: 0.000 > select #1/*:329-330 #2/*:329-330 28 atoms, 26 bonds, 4 residues, 2 models selected > select #1/*:329-332 #2/*:329-332 50 atoms, 48 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [308-311] RMSD: 0.000 > select #1/*:333-334 #2/*:333-334 22 atoms, 20 bonds, 4 residues, 2 models selected > select #1/*:333-335 #2/*:333-335 46 atoms, 46 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [312-314] RMSD: 0.001 > select #1/*:333 #2/*:333 14 atoms, 12 bonds, 2 residues, 2 models selected > show sel & #!2 atoms > style sel & #!2 stick Changed 7 atom styles > select #1/*:334 #2/*:334 8 atoms, 6 bonds, 2 residues, 2 models selected > select #1/*:334 #2/*:334 8 atoms, 6 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [313] RMSD: 0.001 > style sel & #!2 stick Changed 4 atom styles > show sel & #!2 atoms > style sel & #!2 stick Changed 4 atom styles > style sel & #!2 stick Changed 4 atom styles > style sel & #!2 ball Changed 4 atom styles > style sel & #!2 ball Changed 4 atom styles > show sel & #!2 atoms > hide sel & #!2 atoms > show sel & #!2 atoms > select #1/*:335 #2/*:335 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/*:335 #2/*:335 24 atoms, 24 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [314] RMSD: 0.000 > show sel & #!2 atoms > style sel & #!2 stick Changed 12 atom styles > hide sel & #!2 atoms > select #1/*:334 #2/*:334 8 atoms, 6 bonds, 2 residues, 2 models selected > select #1/*:334 #2/*:334 8 atoms, 6 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [313] RMSD: 0.001 > show sel & #!2 cartoons > hide sel & #!2 cartoons > show sel & #!2 cartoons > hide sel & #!2 atoms > show sel & #!2 atoms > show sel & #!2 cartoons > show sel & #!2 surfaces > hide sel & #!2 surfaces > show sel & #!2 atoms > hide sel & #!2 atoms > show sel & #!2 atoms > show sel & #!2 cartoons > hide sel & #!2 cartoons > show sel & #!2 cartoons > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [14] RMSD: 0.000 > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > select #1/*:34 #2/*:34 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:22-34 #2/*:22-34 192 atoms, 196 bonds, 26 residues, 2 models selected 1 [ID: 1] region 2 chains [1-13] RMSD: 0.000 > hide sel & #!2 cartoons > hide sel & #!2 atoms > hide sel & #!2 surfaces > select #1/*:37 #2/*:37 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:37-44 #2/*:37-44 136 atoms, 136 bonds, 16 residues, 2 models selected 1 [ID: 1] region 2 chains [16-23] RMSD: 0.001 > hide sel & #!2 cartoons > show sel & #!2 cartoons > hide sel & #!2 cartoons > select #5/A:37 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:24-37 102 atoms, 103 bonds, 14 residues, 1 model selected > hide sel cartoons > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #5/A:309 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:309 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/*:361 #2/*:361 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:356-361 #2/*:356-361 90 atoms, 88 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [335-340] RMSD: 0.000 > select #1/*:274-317 #2/*:274-317 706 atoms, 714 bonds, 88 residues, 2 models selected > select #1/*:274-318 #2/*:274-318 724 atoms, 732 bonds, 90 residues, 2 models selected 1 [ID: 1] region 2 chains [253-297] RMSD: 0.000 > select #1/*:306-307 #2/*:306-307 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:306-316 #2/*:306-316 172 atoms, 170 bonds, 22 residues, 2 models selected 1 [ID: 1] region 2 chains [285-295] RMSD: 0.000 > select #1/*:328-329 #2/*:328-329 28 atoms, 26 bonds, 4 residues, 2 models selected > select #1/*:321-329 #2/*:321-329 130 atoms, 128 bonds, 18 residues, 2 models selected 1 [ID: 1] region 2 chains [300-308] RMSD: 0.000 > select #1/*:321 #2/*:321 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:302-321 #2/*:302-321 330 atoms, 330 bonds, 40 residues, 2 models selected 1 [ID: 1] region 2 chains [281-300] RMSD: 0.000 > select #1/*:342 #2/*:342 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:342-353 #2/*:342-353 188 atoms, 192 bonds, 24 residues, 2 models selected 1 [ID: 1] region 2 chains [321-332] RMSD: 0.000 > select #1/*:305 #2/*:305 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:305-385 #2/*:305-385 1280 atoms, 1302 bonds, 162 residues, 2 models selected 1 [ID: 1] region 2 chains [284-364] RMSD: 0.000 > select #1/*:264 #2/*:264 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:264-286 #2/*:264-286 352 atoms, 354 bonds, 46 residues, 2 models selected 1 [ID: 1] region 2 chains [243-265] RMSD: 0.001 > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [268] RMSD: 0.001 > style sel & #!2 stick Changed 10 atom styles > show sel & #!2 atoms > select #1/*:290 #2/*:290 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:290 #2/*:290 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [269] RMSD: 0.000 > show sel & #!2 atoms > style sel & #!2 stick Changed 11 atom styles > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [268] RMSD: 0.001 > hide sel & #!2 atoms > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid Missing or invalid ""chains"" argument: only initial part ""#1"" of atom specifier valid > select #5/A:84-85 13 atoms, 12 bonds, 2 residues, 1 model selected > select #5/A:84 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:88 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:78-88 84 atoms, 85 bonds, 11 residues, 1 model selected > select #5/A:79 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:79 11 atoms, 10 bonds, 1 residue, 1 model selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:85 #2/*:85 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:78 #2/*:78 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/*:78 #2/*:78 12 atoms, 10 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [57] RMSD: 0.000 > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [53] RMSD: 0.001 > select #1/*:75 #2/*:75 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:75-76 #2/*:75-76 38 atoms, 36 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [54-55] RMSD: 0.001 > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [55] RMSD: 0.000 > style sel & #!2 stick Changed 11 atom styles > show sel & #!2 atoms > view sel > view > view sel > select #1/*:203-204 #2/*:203-204 38 atoms, 38 bonds, 4 residues, 2 models selected > select #1/*:203-205 #2/*:203-205 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [182-184] RMSD: 0.000 > select #1/*:243 #2/*:243 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:243-244 #2/*:243-244 44 atoms, 44 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [222-223] RMSD: 0.000 > select #1/*:113-114 #2/*:113-114 28 atoms, 26 bonds, 4 residues, 2 models selected > select #1/*:113-119 #2/*:113-119 100 atoms, 100 bonds, 14 residues, 2 models selected 1 [ID: 1] region 2 chains [92-98] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:126-157 #2/*:126-157 486 atoms, 494 bonds, 64 residues, 2 models selected > select #1/*:126-156 #2/*:126-156 470 atoms, 478 bonds, 62 residues, 2 models selected 1 [ID: 1] region 2 chains [105-135] RMSD: 0.000 > select #1/*:154 #2/*:154 14 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:154-157 #2/*:154-157 74 atoms, 76 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [133-136] RMSD: 0.001 > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:155-157 #2/*:155-157 60 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [134-136] RMSD: 0.001 > rainbow sel & #!2 > color sel & #!2 byhetero > color sel & #!2 bychain > color sel & #!2 byhetero > color sel & #!2 bychain > color sel & #!2 bypolymer > color sel & #!2 byhetero > select #5/A:100 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:100 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show sel atoms > select #1/*:72 #2/*:72 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:72 #2/*:72 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [51] RMSD: 0.001 > select #1/*:66-67 #2/*:66-67 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/*:66-73 #2/*:66-73 140 atoms, 142 bonds, 16 residues, 2 models selected 1 [ID: 1] region 2 chains [45-52] RMSD: 0.001 > select #1/*:92-93 #2/*:92-93 24 atoms, 22 bonds, 4 residues, 2 models selected > select #1/*:91-93 #2/*:91-93 40 atoms, 38 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [70-72] RMSD: 0.001 > select #1/*:98 #2/*:98 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:98-101 #2/*:98-101 88 atoms, 92 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [77-80] RMSD: 0.000 > select #1/*:102 #2/*:102 14 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:102-112 #2/*:102-112 174 atoms, 176 bonds, 22 residues, 2 models selected 1 [ID: 1] region 2 chains [81-91] RMSD: 0.000 > select #1/*:48 #2/*:48 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:48-54 #2/*:48-54 118 atoms, 120 bonds, 14 residues, 2 models selected 1 [ID: 1] region 2 chains [27-33] RMSD: 0.001 > select #1/*:84-85 #2/*:84-85 38 atoms, 38 bonds, 4 residues, 2 models selected > select #1/*:62-85 #2/*:62-85 390 atoms, 396 bonds, 48 residues, 2 models selected 1 [ID: 1] region 2 chains [41-64] RMSD: 0.000 > select #1/*:110-111 #2/*:110-111 26 atoms, 24 bonds, 4 residues, 2 models selected > select #1/*:110-121 #2/*:110-121 180 atoms, 182 bonds, 24 residues, 2 models selected 1 [ID: 1] region 2 chains [89-100] RMSD: 0.000 > select #1/*:96 #2/*:96 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:96-97 #2/*:96-97 28 atoms, 26 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [75-76] RMSD: 0.000 > select #1/*:97-98 #2/*:97-98 40 atoms, 38 bonds, 4 residues, 2 models selected > select #1/*:97-98 #2/*:97-98 40 atoms, 38 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [76-77] RMSD: 0.000 > select #1/*:97 #2/*:97 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:97 #2/*:97 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [76] RMSD: 0.000 > style sel & #!2 stick Changed 9 atom styles > show sel & #!2 atoms > rainbow sel & #!2 > color sel & #!2 bychain > color sel & #!2 byhetero > select > #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473 1394 atoms, 1399 bonds, 175 residues, 1 model selected > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select > #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 > #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490 1192 atoms, 1194 bonds, 144 residues, 2 models selected > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:22 #2/*:22 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/* #2/* 7994 atoms, 8186 bonds, 1000 residues, 2 models selected 1 [ID: 1] region 2 chains [1-500] RMSD: 0.000 > hide sel & #!2 cartoons > hide sel & #!2 atoms > show sel & #!2 atoms > hide sel & #!2 atoms > show sel & #!2 cartoons > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #4/*:171-173 28 atoms, 27 bonds, 3 residues, 1 model selected > select #4/*:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/*:172 8 atoms, 7 bonds, 1 residue, 1 model selected > open /Users/bo1il/Downloads/pdb2rh6.ent pdb2rh6.ent title: Structure of xac NPP for evaluation of refinement methodology [more info...] Chain information for pdb2rh6.ent #6 --- Chain | Description | UniProt A B | phosphodiesterase-nucleotide pyrophosphatase | Q8PIS1_XANAC 40-432 Non-standard residues in pdb2rh6.ent #6 --- AMP — adenosine monophosphate ZN — zinc ion > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > color #6 #7adb89ff > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A #6/B Alignment identifier is 2 > select > #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423 2654 atoms, 2678 bonds, 342 residues, 1 model selected > select #6/A-B:91 22 atoms, 22 bonds, 2 residues, 1 model selected > select #6/A-B:90-91 36 atoms, 36 bonds, 4 residues, 1 model selected > style sel stick Changed 36 atom styles > show sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > color sel bychain > hide #!5 models > show #!5 models > hide #!5 models > hide #!2 models > hide #!6 models > show #!6 models > select add #6 6624 atoms, 6129 bonds, 19 pseudobonds, 1440 residues, 2 models selected > select subtract #6 Nothing selected > show #!6 atoms > hide #!6 models > show #!6 models > show #!5 models > ui tool show Matchmaker > matchmaker #3-4#!5-6 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 final.casp.pdb, chain (blank) (#1) with PafA_Prevotella_KCOM1933.pdb, chain (blank) (#3), sequence alignment score = 850.4 RMSD between 381 pruned atom pairs is 0.221 angstroms; (across all 457 pairs: 2.586) Matchmaker final.casp.pdb, chain (blank) (#1) with PafA_mucilagnibacter.pdb, chain (blank) (#4), sequence alignment score = 1009.3 RMSD between 425 pruned atom pairs is 0.220 angstroms; (across all 495 pairs: 2.942) Matchmaker final.casp.pdb, chain (blank) (#1) with 5tj3.pdb, chain A (#5), sequence alignment score = 1086.3 RMSD between 442 pruned atom pairs is 0.213 angstroms; (across all 495 pairs: 1.602) Matchmaker final.casp.pdb, chain (blank) (#1) with pdb2rh6.ent, chain A (#6), sequence alignment score = 221.9 RMSD between 140 pruned atom pairs is 0.988 angstroms; (across all 348 pairs: 11.374) > show #1 models > ui tool show ""Side View"" > lighting flat > graphics silhouettes false > lighting shadows true intensity 0.5 > graphics silhouettes true > lighting soft > lighting full > lighting flat > lighting simple > graphics silhouettes false > view > select #6/A 3293 atoms, 3052 bonds, 10 pseudobonds, 712 residues, 2 models selected > select #6/B 3331 atoms, 3077 bonds, 9 pseudobonds, 728 residues, 2 models selected > hide sel cartoons > hide sel surfaces > hide sel atoms > select #6/B 3331 atoms, 3077 bonds, 9 pseudobonds, 728 residues, 2 models selected > select #6/A 3293 atoms, 3052 bonds, 10 pseudobonds, 712 residues, 2 models selected > hide sel atoms > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select > #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423 2654 atoms, 2678 bonds, 342 residues, 1 model selected > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:161-171 79 atoms, 79 bonds, 11 residues, 1 model selected > select #6/A-B:125-126 30 atoms, 28 bonds, 4 residues, 1 model selected > select #6/A-B:125-133 128 atoms, 126 bonds, 18 residues, 1 model selected > select #6/A-B:139 14 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:139-149 166 atoms, 170 bonds, 22 residues, 1 model selected > select #6/A-B:134-162 450 atoms, 474 bonds, 58 residues, 1 model selected > select #6/A-B:134-161 440 atoms, 464 bonds, 56 residues, 1 model selected > select #6/A-B:82 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:82-99 286 atoms, 298 bonds, 36 residues, 1 model selected > select #6/A-B:91 22 atoms, 22 bonds, 2 residues, 1 model selected > select #6/A-B:90-91 36 atoms, 36 bonds, 4 residues, 1 model selected > style sel stick Changed 36 atom styles > show sel atoms > select #6/A-B:111 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:111 16 atoms, 14 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > show sel atoms > hide sel atoms > show sel atoms > color sel byhetero > select #6/A-B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > select #6/A-B:90-91 36 atoms, 36 bonds, 4 residues, 1 model selected > style sel stick Changed 36 atom styles > style sel stick Changed 36 atom styles > select #1/* #2/* 7994 atoms, 8186 bonds, 1000 residues, 2 models selected > select #1/*:69 #2/*:69 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/*:69-71 #2/*:69-71 58 atoms, 60 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [48-50] RMSD: 0.000 > select #1/*:74-75 #2/*:74-75 30 atoms, 28 bonds, 4 residues, 2 models selected > select #1/*:74-75 #2/*:74-75 30 atoms, 28 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [53-54] RMSD: 0.001 > select #1/*:106 #2/*:106 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:106-109 #2/*:106-109 70 atoms, 70 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [85-88] RMSD: 0.001 > select #1/*:66-67 #2/*:66-67 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/*:66-75 #2/*:66-75 170 atoms, 172 bonds, 20 residues, 2 models selected 1 [ID: 1] region 2 chains [45-54] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:90-91 #2/*:90-91 28 atoms, 26 bonds, 4 residues, 2 models selected > select #1/*:81-91 #2/*:81-91 152 atoms, 154 bonds, 22 residues, 2 models selected 1 [ID: 1] region 2 chains [60-70] RMSD: 0.000 > select #6/A-B:107 8 atoms, 6 bonds, 2 residues, 1 model selected > select #6/A-B:102-107 100 atoms, 104 bonds, 12 residues, 1 model selected > hide #1 models > show #1 models > hide #!5 models > select #6/A-B:96-97 30 atoms, 28 bonds, 4 residues, 1 model selected > select #6/A-B:96-102 104 atoms, 102 bonds, 14 residues, 1 model selected > select #1/*:75-76 #2/*:75-76 38 atoms, 36 bonds, 4 residues, 2 models selected > select #1/*:75-80 #2/*:75-80 86 atoms, 84 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [54-59] RMSD: 0.000 > select #1/*:58-59 #2/*:58-59 38 atoms, 36 bonds, 4 residues, 2 models selected > select #1/*:54-59 #2/*:54-59 116 atoms, 116 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [33-38] RMSD: 0.000 > select #1/*:51 #2/*:51 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:51-91 #2/*:51-91 658 atoms, 668 bonds, 82 residues, 2 models selected 1 [ID: 1] region 2 chains [30-70] RMSD: 0.001 > select #1/*:62-63 #2/*:62-63 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:62-67 #2/*:62-67 110 atoms, 110 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [41-46] RMSD: 0.001 > select #1/*:100 #2/*:100 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:93-100 #2/*:93-100 140 atoms, 144 bonds, 16 residues, 2 models selected 1 [ID: 1] region 2 chains [72-79] RMSD: 0.000 > select #1/*:102 #2/*:102 14 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:102-107 #2/*:102-107 98 atoms, 100 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [81-86] RMSD: 0.000 > select #1/*:98-99 #2/*:98-99 50 atoms, 52 bonds, 4 residues, 2 models selected > select #1/*:77-99 #2/*:77-99 334 atoms, 340 bonds, 46 residues, 2 models selected 1 [ID: 1] region 2 chains [56-78] RMSD: 0.000 > select #1/*:83-84 #2/*:83-84 40 atoms, 40 bonds, 4 residues, 2 models selected > select #1/*:83-88 #2/*:83-88 90 atoms, 90 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [62-67] RMSD: 0.000 > select #1/*:88 #2/*:88 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:87-88 #2/*:87-88 28 atoms, 26 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [66-67] RMSD: 0.000 > select #1/*:84 #2/*:84 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/*:84-85 #2/*:84-85 38 atoms, 38 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [63-64] RMSD: 0.000 > select #1/*:87-88 #2/*:87-88 28 atoms, 26 bonds, 4 residues, 2 models selected > select #1/*:87-89 #2/*:87-89 42 atoms, 42 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [66-68] RMSD: 0.001 > select #1/*:79 #2/*:79 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:79-81 #2/*:79-81 36 atoms, 34 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [58-60] RMSD: 0.000 > select #1/*:81 #2/*:81 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:81-85 #2/*:81-85 74 atoms, 74 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [60-64] RMSD: 0.000 > select #1/*:85 #2/*:85 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:85-89 #2/*:85-89 64 atoms, 64 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [64-68] RMSD: 0.000 > select #1/*:76-77 #2/*:76-77 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:76-92 #2/*:76-92 238 atoms, 240 bonds, 34 residues, 2 models selected 1 [ID: 1] region 2 chains [55-71] RMSD: 0.000 > hide #!6 models > select #1/*:93-94 #2/*:93-94 24 atoms, 22 bonds, 4 residues, 2 models selected > select #1/*:84-94 #2/*:84-94 156 atoms, 158 bonds, 22 residues, 2 models selected 1 [ID: 1] region 2 chains [63-73] RMSD: 0.001 > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:76-81 #2/*:76-81 80 atoms, 78 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [55-60] RMSD: 0.000 > select #1/*:74-75 #2/*:74-75 30 atoms, 28 bonds, 4 residues, 2 models selected > select #1/*:74-83 #2/*:74-83 136 atoms, 134 bonds, 20 residues, 2 models selected 1 [ID: 1] region 2 chains [53-62] RMSD: 0.000 > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!5 models > show #!6 models > hide #!5 models > select #6/A-B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > select #6/A-B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > select #5/A:63 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:63 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:79 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:79 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > select #1/*:85 #2/*:85 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:85 #2/*:85 14 atoms, 12 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [64] RMSD: 0.000 > hide #1 models > show #1 models > hide #!6 models > show #!6 models > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #5/A:84 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:84-85 13 atoms, 12 bonds, 2 residues, 1 model selected > select #5/A:80 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/A:79-80 16 atoms, 15 bonds, 2 residues, 1 model selected > hide #!6 models > show #!6 models > select #1/*:85 #2/*:85 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:85-88 #2/*:85-88 50 atoms, 48 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [64-67] RMSD: 0.000 > select #1/*:81 #2/*:81 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:81-82 #2/*:81-82 20 atoms, 18 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [60-61] RMSD: 0.000 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:78 #2/*:78 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/*:78-79 #2/*:78-79 22 atoms, 20 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [57-58] RMSD: 0.001 > select #1/*:77 #2/*:77 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:74-77 #2/*:74-77 62 atoms, 60 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [53-56] RMSD: 0.001 > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [53] RMSD: 0.001 > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:76 #2/*:76 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [55] RMSD: 0.000 > style sel & #1 stick Changed 11 atom styles > show sel & #1 atoms > select #1/*:75 #2/*:75 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:75 #2/*:75 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [54] RMSD: 0.001 > style sel & #1 stick Changed 8 atom styles > show sel & #1 atoms > hide sel & #1 atoms > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > select #1/*:119 #2/*:119 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:119 #2/*:119 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [98] RMSD: 0.000 > select #1/*:109 #2/*:109 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:108-109 #2/*:108-109 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [87-88] RMSD: 0.001 > select #1/*:112 #2/*:112 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:105-112 #2/*:105-112 128 atoms, 128 bonds, 16 residues, 2 models selected 1 [ID: 1] region 2 chains [84-91] RMSD: 0.001 > select #1/*:100-101 #2/*:100-101 38 atoms, 38 bonds, 4 residues, 2 models selected > select #1/*:98-101 #2/*:98-101 88 atoms, 92 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [77-80] RMSD: 0.000 > select #1/*:93 #2/*:93 8 atoms, 6 bonds, 2 residues, 2 models selected > select #1/*:93-97 #2/*:93-97 68 atoms, 66 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [72-76] RMSD: 0.000 > select #1/*:92 #2/*:92 16 atoms, 14 bonds, 2 residues, 2 models selected > hide #!5 models > select #1/*:94-95 #2/*:94-95 32 atoms, 30 bonds, 4 residues, 2 models selected > select #1/*:94-97 #2/*:94-97 60 atoms, 58 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [73-76] RMSD: 0.000 > select #1/*:97 #2/*:97 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/*:97 #2/*:97 18 atoms, 16 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [76] RMSD: 0.000 > style sel & #1 stick Changed 9 atom styles > show sel & #1 atoms > show #!5 models > hide #!5 models > show #!5 models > select #6/A-B:179 22 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:179-184 104 atoms, 102 bonds, 12 residues, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162-164 28 atoms, 27 bonds, 3 residues, 1 model selected > hide #1 models > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162-164 28 atoms, 27 bonds, 3 residues, 1 model selected > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #1 models > hide #1 models > show #1 models > hide #1 models > select #6/A-B:139 14 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:139-147 140 atoms, 144 bonds, 18 residues, 1 model selected > hide #!5 models > show #!5 models > hide #!5 models > select #6/A-B:90-91 36 atoms, 36 bonds, 4 residues, 1 model selected > select #6/A-B:90-91 36 atoms, 36 bonds, 4 residues, 1 model selected > color sel byhetero > color sel byelement > color sel #a9ffbdff > color sel byhetero > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > style sel stick Changed 24 atom styles > show sel atoms > select #6/A-B:123 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:123 16 atoms, 14 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > show sel atoms > color sel byhetero > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > color sel byhetero > select > #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423 2654 atoms, 2678 bonds, 342 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > show sel atoms > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected > style #!6 stick Changed 6624 atom styles > show #!6 atoms > hide #!6 atoms > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #6/A-B:54-55 24 atoms, 22 bonds, 4 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:54-55 24 atoms, 22 bonds, 4 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:55 8 atoms, 6 bonds, 2 residues, 1 model selected > select #6/A-B:54-55 24 atoms, 22 bonds, 4 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:35 #2/*:35 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [14] RMSD: 0.000 > show #!6 atoms > hide #!6 atoms > show #!5 models > hide #!5 models > show #!5 models > select #6/A-B:54-55 24 atoms, 22 bonds, 4 residues, 1 model selected > select #6/A-B:54 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > hide #!6 models > select #6/A-B:257 16 atoms, 14 bonds, 2 residues, 1 model selected > select #5/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!6 models > select #6/A-B:257 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:257 16 atoms, 14 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > show sel atoms > color sel byhetero > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select #6/A-B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > select #6/A-B:90 14 atoms, 12 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > color sel byhetero > select > #5/A:31-37,65-67,70-71,101-104,109-112,121-122,156-159,176-180,187-190,295-301,345-350,370-371,394-398,401-404,433-438,467-471,475-476,495-496,498-502,508-510,514-515 682 atoms, 685 bonds, 84 residues, 1 model selected > select #5/A:353 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:353 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #6/A-B:246 14 atoms, 12 bonds, 2 residues, 1 model selected > select #6/A-B:246-247 36 atoms, 34 bonds, 4 residues, 1 model selected > select #6/A-B:257 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:257-258 36 atoms, 36 bonds, 4 residues, 1 model selected > select #6/A-B:259-260 24 atoms, 22 bonds, 4 residues, 1 model selected > select #6/A-B:259-260 24 atoms, 22 bonds, 4 residues, 1 model selected > select #6/A-B:258 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:258 20 atoms, 20 bonds, 2 residues, 1 model selected > style sel stick Changed 20 atom styles > show sel atoms > color sel byhetero > select #6/A-B:340-341 38 atoms, 38 bonds, 4 residues, 1 model selected > select #6/A-B:340 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:309 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:309 20 atoms, 20 bonds, 2 residues, 1 model selected > style sel stick Changed 20 atom styles > show sel atoms > color sel byhetero > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > select #6/A-B:309 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:309-311 56 atoms, 58 bonds, 6 residues, 1 model selected > hide #!5 models > select > #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423 2654 atoms, 2678 bonds, 342 residues, 1 model selected > select #6/A-B:309 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:309 20 atoms, 20 bonds, 2 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > show #!5 models > select #6/A-B:363 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:363 20 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 20 atom styles > color sel byhetero > select #6/A-B:208 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:208-214 106 atoms, 108 bonds, 14 residues, 1 model selected > select #6/A-B:214 20 atoms, 20 bonds, 2 residues, 1 model selected > select #6/A-B:214 20 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 20 atom styles > color sel byhetero > hide #!6 models > show #1 models > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [268] RMSD: 0.001 > select #1/*:288 #2/*:288 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:288 #2/*:288 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [267] RMSD: 0.001 > select #1/*:290-291 #2/*:290-291 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/*:290 #2/*:290 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [269] RMSD: 0.000 > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [268] RMSD: 0.001 > show sel & #1 atoms > select #1/*:291 #2/*:291 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/*:290-291 #2/*:290-291 34 atoms, 32 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [269-270] RMSD: 0.000 > select #1/*:290 #2/*:290 22 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:290 #2/*:290 22 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [269] RMSD: 0.000 > show sel & #1 atoms > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected > select #1/*:289 #2/*:289 20 atoms, 20 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [268] RMSD: 0.001 > hide sel & #1 atoms > select #1/*:466 #2/*:466 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:466 #2/*:466 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [445] RMSD: 0.000 > show sel & #1 atoms > color sel & #1 byhetero > select #1/*:146 #2/*:146 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:146-147 #2/*:146-147 20 atoms, 18 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [125-126] RMSD: 0.001 > select #1/*:151 #2/*:151 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:151 #2/*:151 10 atoms, 8 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [130] RMSD: 0.000 > select #1/*:151 #2/*:151 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:146-151 #2/*:146-151 84 atoms, 84 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [125-130] RMSD: 0.001 > select #1/*:158 #2/*:158 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/*:158-159 #2/*:158-159 20 atoms, 18 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [137-138] RMSD: 0.001 > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:157-159 #2/*:157-159 36 atoms, 34 bonds, 6 residues, 2 models selected 1 [ID: 1] region 2 chains [136-138] RMSD: 0.000 > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:157 #2/*:157 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [136] RMSD: 0.000 > style sel & #1 stick Changed 8 atom styles > show sel & #1 atoms > color sel & #1 byhetero > select > #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528 1781 atoms, 1797 bonds, 228 residues, 1 model selected > select #5/A:163 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:163 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:164 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:164 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/*:75 #2/*:75 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/*:75 #2/*:75 16 atoms, 14 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [54] RMSD: 0.001 > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/*:74 #2/*:74 14 atoms, 12 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [53] RMSD: 0.001 > select #1/*:74-75 #2/*:74-75 30 atoms, 28 bonds, 4 residues, 2 models selected > select #1/*:74-77 #2/*:74-77 62 atoms, 60 bonds, 8 residues, 2 models selected 1 [ID: 1] region 2 chains [53-56] RMSD: 0.001 > select > #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 > #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507 2818 atoms, 2820 bonds, 352 residues, 2 models selected > select #1/*:77-78 #2/*:77-78 22 atoms, 20 bonds, 4 residues, 2 models selected > select #1/*:74-78 #2/*:74-78 74 atoms, 72 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [53-57] RMSD: 0.001 > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected > select #1/*:155 #2/*:155 22 atoms, 22 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [134] RMSD: 0.001 > show sel & #1 atoms > color sel & #1 byhetero > style sel & #1 stick Changed 11 atom styles > show #!6 models > hide #!5 models > hide #!6 models > show #!6 models > hide #1 models > select #6/A-B:123 16 atoms, 14 bonds, 2 residues, 1 model selected > select #6/A-B:123 16 atoms, 14 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > color sel byhetero > show sel atoms > color sel byhetero > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > select #6/A-B:205 24 atoms, 24 bonds, 2 residues, 1 model selected > show sel atoms > show #1 models > show #!5 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.2.48 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine 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: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0) OS Loader Version: 564.40.4~55 Software: System Software Overview: System Version: macOS 13.1 (22C65) Kernel Version: Darwin 22.2.0 Time since boot: 31 days, 21 hours, 18 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2719HC: 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: 5VCLY13 Mirror: Off Online: Yes Rotation: Supported 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: 2.2.5 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: 1.6.1 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 Graphics nonchimerax all ChimeraX