id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4755 wrapped C/C++ object of type QScreen has been deleted Rebecca.Spies@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC) Description Model could not be saved. ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) Log: UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für > Chimera/ChimeraX/X AD169 und Towne model 1 mit bekannten Epitopen > markiert.cxs"" Log from Tue Jun 8 15:54:48 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" Log from Tue Jun 8 14:57:22 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" format session Log from Sat May 29 17:00:55 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X > AD169 und Towne model 1 markiert.cxs"" format session Log from Sat May 15 17:11:12 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 markiert.cxs"" Log from Sat May 15 17:06:07 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X > AD169 und Towne model 1.cxs"" format session Log from Sat May 15 16:24:00 2021UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/AD169 > model1.pdb"" ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/Towne > model1.pdb"" Chain information for AD169 model1.pdb #1 --- Chain | Description A | No description available Chain information for Towne model1.pdb #2 --- Chain | Description A | No description available > select #1 11845 atoms, 11989 bonds, 743 residues, 1 model selected Drag select of 93 residues > select #2 11848 atoms, 11988 bonds, 742 residues, 1 model selected > select #1 11845 atoms, 11989 bonds, 743 residues, 1 model selected > cofr sel > view sel > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > select #2 11848 atoms, 11988 bonds, 742 residues, 1 model selected > ~select #2 Nothing selected > select #1 11845 atoms, 11989 bonds, 743 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,77.884,0,1,0,30.214,0,0,1,-69.692 > ~select #1 Nothing selected > ui mousemode right pivot > coulombic Using Amber 20 recommended default charges and atom types for standard residues Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48, mean -1.40, maximum 9.68 Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23, mean -1.37, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1.cxs"" > 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 AD169 model1.pdb, chain A (#1) with Towne model1.pdb, chain A (#2), sequence alignment score = 3543 RMSD between 671 pruned atom pairs is 0.327 angstroms; (across all 742 pairs: 3.210) > 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 #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select #1 11845 atoms, 11989 bonds, 743 residues, 1 model selected > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > select #2 11848 atoms, 11988 bonds, 742 residues, 2 models selected > ~select #2 1 model selected > select #1 11845 atoms, 11989 bonds, 743 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-15.19,0,1,0,30.823,0,0,1,-95.799 > ~select #1 1 model selected > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1.cxs"" ——— End of log from Sat May 15 16:24:00 2021 ——— opened ChimeraX session > ui mousemode right ""rotate selected models"" > ui mousemode right pivot > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:7 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:7 14 atoms, 14 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 7 > select #1/A:10 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:10-11 30 atoms, 29 bonds, 2 residues, 1 model selected > select #1/A:10 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:10 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 10 > select #1/A:12 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:12-13 34 atoms, 34 bonds, 2 residues, 1 model selected > select #1/A:12 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:12 20 atoms, 20 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 12 > select #1/A:15 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:15 21 atoms, 21 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 15 > select #1/A:21 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:21 14 atoms, 14 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 21 > select #1/A:33 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:33 10 atoms, 9 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 33 > select #1/A:36 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:36 14 atoms, 14 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 36 > select #1/A:151 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:151 17 atoms, 16 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 151 > select #1/A:177 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:177 12 atoms, 11 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 177 > select #1/A:179 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:179-180 29 atoms, 28 bonds, 2 residues, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 179,180 > select #1/A:220 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:220 17 atoms, 16 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 220 > select #1/A:285 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:285 10 atoms, 9 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 285 > select #1/A:296 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:296 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 296 > select #1/A:360 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:360 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 360 > select #1/A:361 15 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:361-362 34 atoms, 33 bonds, 2 residues, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 360,361 > select #1/A:364 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:364 19 atoms, 18 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 364 > select #1/A:412 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:412 12 atoms, 11 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 412 > select #1/A:450 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:450 17 atoms, 16 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 450 > select #1/A:547 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:547-548 24 atoms, 23 bonds, 2 residues, 1 model selected > select #1/A:547 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:547 10 atoms, 9 bonds, 1 residue, 1 model selected > color (#!1 & sel) red > label (#!1 & sel) text 547 > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 markiert.cxs"" > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:7 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:7 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 7 > select #2/A:10 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:10 19 atoms, 18 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 10 > select #2/A:12 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:12 19 atoms, 18 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 12 > select #2/A:15 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:15 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 15 > select #2/A:21 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:21 19 atoms, 18 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 21 > select #2/A:33 14 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:33 14 atoms, 14 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 33 > select #2/A:36 22 atoms, 21 bonds, 1 residue, 1 model selected > select #2/A:36-37 32 atoms, 31 bonds, 2 residues, 1 model selected > select #2/A:36 22 atoms, 21 bonds, 1 residue, 1 model selected > select #2/A:36 22 atoms, 21 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 36 > select #2/A:150 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:150 15 atoms, 14 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 150 > select #2/A:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:176 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 176 > select #2/A:178 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:178 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 178 > select #2/A:179 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:179 15 atoms, 14 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > view sel > label (#!2 & sel) text 179 > select #2/A:219 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:219 19 atoms, 18 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 219 > select #2/A:295 14 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:295 14 atoms, 14 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 295 > select #2/A:284 12 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:284 12 atoms, 11 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 284 > select #2/A:359 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:359 10 atoms, 9 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 359 > select #2/A:360 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:360 17 atoms, 16 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 360 > select #2/A:361 16 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:361 16 atoms, 15 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 361 > select #2/A:363 16 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:363 16 atoms, 15 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 363 > select #2/A:411 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:411 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 411 > select #2/A:449 22 atoms, 21 bonds, 1 residue, 1 model selected > select #2/A:449 22 atoms, 21 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text 449 > select #2/A:546 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:546 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > label (#!2 & sel) text ""546 bei Merlin ein A"" > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 markiert.cxs"" ——— End of log from Sat May 15 17:06:07 2021 ——— opened ChimeraX session > ui mousemode right pivot > ui mousemode right ""rotate selected models"" > coulombic sel Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23, mean -1.37, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23, mean -1.37, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > rainbow sel > mlp sel Map values for surface ""Towne model1.pdb_A SES surface"": minimum -28.54, mean -2.275, maximum 25.31 To also show corresponding color key, enter the above mlp command and add key true > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > coulombic sel Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48, mean -1.40, maximum 9.68 To also show corresponding color key, enter the above coulombic command and add key true > select #2 11848 atoms, 11988 bonds, 742 residues, 3 models selected > ~select #2 Nothing selected > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > select #2 11848 atoms, 11988 bonds, 742 residues, 3 models selected > mlp sel Map values for surface ""Towne model1.pdb_A SES surface"": minimum -28.54, mean -2.275, maximum 25.31 To also show corresponding color key, enter the above mlp command and add key true > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > mlp sel Map values for surface ""AD169 model1.pdb_A SES surface"": minimum -29.15, mean -2.437, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > select #2 11848 atoms, 11988 bonds, 742 residues, 3 models selected > coulombic sel Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23, mean -1.37, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > ~select #1 Nothing selected > hide surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:546 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:546-547 28 atoms, 27 bonds, 2 residues, 1 model selected > select #2/A:546 14 atoms, 13 bonds, 1 residue, 1 model selected > select #2/A:546 14 atoms, 13 bonds, 1 residue, 1 model selected > color (#!2 & sel) red > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 markiert.cxs"" ——— End of log from Sat May 15 17:11:12 2021 ——— opened ChimeraX session > select clear > select #2/A:677 20 atoms, 20 bonds, 1 residue, 1 model selected > select #2/A:677-684 125 atoms, 127 bonds, 8 residues, 1 model selected > color (#!2 & sel) purple > label (#!2 & sel) text ""3G11 AS 677-684"" > select #2/A:705 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:705-708 57 atoms, 56 bonds, 4 residues, 1 model selected > color (#!2 & sel) purple > label (#!2 & sel) text ""3G11 AS 705-708"" > select #2/A:238-239 27 atoms, 26 bonds, 2 residues, 1 model selected > select #2/A:238-247 146 atoms, 146 bonds, 10 residues, 1 model selected > color (#!2 & sel) orange > label (#!2 & sel) text ""13H11 AS 238-247"" > select #2/A:442 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:442-446 78 atoms, 78 bonds, 5 residues, 1 model selected > color (#!2 & sel) forest green > label (#!2 & sel) text ""MSL-109 AS 442-446"" > select #2/A:403 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:403-419 276 atoms, 278 bonds, 17 residues, 1 model selected > select #2/A:410-411 28 atoms, 28 bonds, 2 residues, 1 model selected > select #2/A:410-411 28 atoms, 28 bonds, 2 residues, 1 model selected > select #2/A:403 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:403-410 137 atoms, 139 bonds, 8 residues, 1 model selected > color (#!2 & sel) forest green > label (#!2 & sel) text ""MSL-109 AS 403-410"" > select #2/A:412 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:412-419 125 atoms, 124 bonds, 8 residues, 1 model selected > color (#!2 & sel) forest green > label (#!2 & sel) text ""MSL-109 AS 412-419"" > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select #1/A:678 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:678-684 110 atoms, 112 bonds, 7 residues, 1 model selected > view sel > color (#!1 & sel) forest green > color (#!1 & sel) purple > undo > undo > select #1/A:678 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:678-685 125 atoms, 127 bonds, 8 residues, 1 model selected > color (#!1 & sel) purple > label (#!1 & sel) text ""3G16 AS 678-685"" > select #1/A:706-707 31 atoms, 30 bonds, 2 residues, 1 model selected > select #1/A:706-709 57 atoms, 56 bonds, 4 residues, 1 model selected > color (#!1 & sel) purple > label (#!1 & sel) text ""3G16 AS706-709"" > select #1/A:239 16 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:239-248 146 atoms, 146 bonds, 10 residues, 1 model selected > view sel > color (#!1 & sel) orange > label (#!1 & sel) text ""13H11 AS 239-248"" > select #1/A:443 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:443-447 78 atoms, 78 bonds, 5 residues, 1 model selected > view sel > color (#!1 & sel) forest green > label (#!1 & sel) text ""MSL-109 AS 443-447"" > select #1/A:403 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:403 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:404 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:404-410 123 atoms, 124 bonds, 7 residues, 1 model selected > view sel > select #1/A:404-407 66 atoms, 65 bonds, 4 residues, 1 model selected > select #1/A:404-411 137 atoms, 139 bonds, 8 residues, 1 model selected > color (#!1 & sel) forest green > label (#!1 & sel) text ""MSL-109 AS404-411"" > select #1/A:413 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:413-420 125 atoms, 124 bonds, 8 residues, 1 model selected > color (#!1 & sel) forest green > label (#!1 & sel) text ""MSL-109 AS 413-420"" > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" ——— End of log from Sat May 29 17:00:55 2021 ——— opened ChimeraX session > select 23693 atoms, 23977 bonds, 1485 residues, 7 models selected > view sel > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" ——— End of log from Tue Jun 8 14:57:22 2021 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > select ~sel 11848 atoms, 11988 bonds, 742 residues, 3 models selected > select #1/A:34 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:34-43 166 atoms, 169 bonds, 10 residues, 1 model selected > select #1/A:34 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:34-36 45 atoms, 45 bonds, 3 residues, 1 model selected > select #1/A:34 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:34-35 31 atoms, 30 bonds, 2 residues, 1 model selected > color (#!1 & sel) yellow > label (#!1 & sel) text ""AP86 AS34-35"" > select #1/A:37 17 atoms, 17 bonds, 1 residue, 1 model selected > select #1/A:37-43 121 atoms, 123 bonds, 7 residues, 1 model selected > color (#!1 & sel) yellow > label (#!1 & sel) text ""AP86 AS37-43"" > select #2/A:34 19 atoms, 18 bonds, 1 residue, 1 model selected > select #2/A:34-35 31 atoms, 30 bonds, 2 residues, 1 model selected > color (#!2 & sel) yellow > label (#!2 & sel) text ""AP86 AS34-35"" > select #2/A:37 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:37-42 104 atoms, 105 bonds, 6 residues, 1 model selected > color (#!2 & sel) yellow > label (#!2 & sel) text ""AP86 AS37-42"" > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" > select 23693 atoms, 23977 bonds, 1485 residues, 7 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 AD169 model1.pdb, chain A (#1) with Towne model1.pdb, chain A (#2), sequence alignment score = 3543 RMSD between 671 pruned atom pairs is 0.327 angstroms; (across all 742 pairs: 3.210) > select 23693 atoms, 23977 bonds, 1485 residues, 7 models selected > select clear > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select #1 11845 atoms, 11989 bonds, 743 residues, 4 models selected > ui mousemode right ""move picked models"" > view matrix models #1,1,0,0,-43.571,0,1,0,-31.003,0,0,1,-98.711 > ~select #1 1 model selected > ui mousemode right rotate > ui mousemode right clip > ui mousemode right ""rotate selected models"" > view > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X > AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"" ——— End of log from Tue Jun 8 15:54:48 2021 ——— opened ChimeraX session > hide surfaces > show surfaces > select 23693 atoms, 23977 bonds, 1485 residues, 6 models selected > coulombic sel Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48, mean -1.40, maximum 9.68 Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23, mean -1.37, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > select clear > hide #!1 models > select #2/A:359 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:359-363 70 atoms, 69 bonds, 5 residues, 1 model selected > close session Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 932, in close_action.triggered.connect(lambda *, s=self, sess=session: s.file_close_cb(sess)) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 652, in file_close_cb run(session, 'close session') File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\std_commands\close.py"", line 60, in close_session session.reset() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 529, in reset sm.reset_state(container, self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 252, in reset_state alignment._destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 603, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq- view\tool.py"", line 474, in alignment_notification self.delete() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq- view\tool.py"", line 512, in delete ToolInstance.delete(self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\tools.py"", line 154, in delete self.session.ui.remove_tool(self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 345, in remove_tool self.main_window.remove_tool(tool_instance) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 725, in remove_tool tw._destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 2049, in _destroy self.__toolkit.destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 2189, in destroy sbar.destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\statusbar.py"", line 51, in destroy v.delete() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 438, in delete self.make_current() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 99, in make_current qc = self._initialize_context() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted RuntimeError: wrapped C/C++ object of type QScreen has been deleted File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 635, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 392, in disassociate self.session.alignments.destroy_alignment(self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\manager.py"", line 108, in destroy_alignment alignment._destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 603, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\seqalign\alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq- view\tool.py"", line 474, in alignment_notification self.delete() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq- view\tool.py"", line 512, in delete ToolInstance.delete(self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\tools.py"", line 154, in delete self.session.ui.remove_tool(self) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 345, in remove_tool self.main_window.remove_tool(tool_instance) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 725, in remove_tool tw._destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 2049, in _destroy self.__toolkit.destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\gui.py"", line 2189, in destroy sbar.destroy() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\ui\statusbar.py"", line 51, in destroy v.delete() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 438, in delete self.make_current() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 99, in make_current qc = self._initialize_context() File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted Error processing trigger ""modified"": RuntimeError: wrapped C/C++ object of type QScreen has been deleted File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) See log for complete Python traceback. > open ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/Models/AD169 > model1.pdb"" Chain information for AD169 model1.pdb #1 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select /A:678 20 atoms, 20 bonds, 1 residue, 1 model selected > select /A:678-685 125 atoms, 127 bonds, 8 residues, 1 model selected > color sel purple > label sel atoms text 3G16 > open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup > show sel atoms > hide sel atoms > label sel text 3G16 > select /A:706 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:706-709 57 atoms, 56 bonds, 4 residues, 1 model selected > color sel purple > label sel text 3G16 > select /A:239 16 atoms, 15 bonds, 1 residue, 1 model selected > select /A:239-248 146 atoms, 146 bonds, 10 residues, 1 model selected > color sel orange > label sel text 13H11 > select /A:443 17 atoms, 16 bonds, 1 residue, 1 model selected > select /A:443-447 78 atoms, 78 bonds, 5 residues, 1 model selected > color sel lime > label sel text MSL-109 > select /A:407-408 29 atoms, 28 bonds, 2 residues, 1 model selected > select /A:407-409 53 atoms, 54 bonds, 3 residues, 1 model selected > select > /A:20-23,95-98,103-109,116-123,129-132,265-268,285-288,291-294,300-303,310-328,336-353,357-359,364-385,389-392,398-408,417-429,433-435,438-455,462-476,482-495,498-508,516-519,522-524,533-538,548-559,646-648,673-680,708-714 3825 atoms, 3830 bonds, 237 residues, 1 model selected > select /A:404 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:404-420 274 atoms, 276 bonds, 17 residues, 1 model selected > color sel lime > label sel text MSL-109 > select /A:34 19 atoms, 18 bonds, 1 residue, 1 model selected > select /A:34-43 166 atoms, 169 bonds, 10 residues, 1 model selected > color sel yellow > label sel text AP86 > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für > Chimera/ChimeraX/AD169 model 1 markiert.cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > select clear > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für > Chimera/ChimeraX/AD169 model 1 markiert.cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save ""C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für > Chimera/ChimeraX/AD169 model 1 markiert.cxs"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1143, in take_snapshot 'structure': self.structure, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\atomic\molc.py"", line 78, in get_prop cget(self._c_pointer_ref, 1, v_ref) RuntimeError: Access violation - no RTTI data! The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> -> 'chain A' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 162, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 379, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1285, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\toolbar\\__init__.py"", line 37, in run_provider providers.run_provider(session, name) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\toolbar\providers.py"", line 45, in run_provider what(session) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\toolbar\providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 87, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 877, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 607, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A' File ""C:\Program Files\ChimeraX 1.2.2\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 21.20.16.4727 OpenGL renderer: Intel(R) HD Graphics 520 OpenGL vendor: Intel Manufacturer: HP Model: HP Spectre x360 Convertible OS: Microsoft Windows 10 Home (Build 19042) Memory: 8,496,566,272 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz OSLanguage: de-DE Locale: ('de_DE', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.3 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.2 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.2 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.4 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.7 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Graphics duplicate chimera-programmers all ChimeraX