id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4086 MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted roberto.marotta@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-4.4.0-197-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description Performing matchmaker and then selecting chains Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > format session Log from Wed Dec 23 11:34:41 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > format session Log from Tue Dec 22 19:28:37 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > format session Log from Mon Dec 21 18:07:04 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > format session Log from Sun Dec 20 21:04:28 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > format session Log from Fri Dec 18 18:45:46 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/media/datadisk1/AnalisiGAPDH > /A8B8major/A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb"" Chain information for A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb #1 --- Chain | Description A E G I O Q | No description available B D F H J L P R | No description available C | No description available K | No description available > hide atoms > show cartoons > select #1 /Q 2740 atoms, 2789 bonds, 2 pseudobonds, 369 residues, 2 models selected > select #1 /O 2740 atoms, 2789 bonds, 2 pseudobonds, 369 residues, 2 models selected > select #1 /R 2588 atoms, 2633 bonds, 338 residues, 1 model selected > select #1 /P 2588 atoms, 2633 bonds, 338 residues, 1 model selected > color sel #1 /Q red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /Q red > select clear > color #1 /O red > color #1 /A DARK ORANGE Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /A tomato > color #1 /C tomato > color #1 /C dark orange > color #1 /A dark orange > color #1 /E crimson > color #1 /G crimson > color #1 /I K coral Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /I, K coral > color #1 /A, C crimson > color #1 /A, C tomato > color #1 /R,P,D,B,J,L,H,F BLUE Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /R,P BLUE Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /R,P blue > color #1 /R,P light blue > color #1 /R,P cyan > color #1 /R,P blue > color #1 /b,d,f,h,j,l blue > ui tool show ""Color Actions"" > set bgColor white > color #1 /A, C tomato > color #1 /A, C crimson > color #1 /A, C tomato > color #1 /I, K coral > color #1 /I, K orange > color #1 /I, K coral > color #1 /E crimson > color #1 /E red > color #1 /E crimson > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" opened ChimeraX session > lighting soft > color #1 96/O yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 .96/O yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /O:96-106 yellow > undo > color #1 /O:96-103,106,109,110 yellow > color #1 /O:96-103,106,109,110,119,121-126 yellow > color #1 > /O:96-103,106,109,110,119,121-126,141,143,148,176,179,181,183,190,191,195,215,216,219,220,222,231,341-346,349,353,356-362 > yellow > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /C: > 77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362 > yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 > /C:77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362 > yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /C: > 77,80.96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362 > yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1 /C: > 77,80,96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362 > yellow > color #1 /C: > 77,80,96,98,101-103,106,107,109,110,119,121,124,125,141-143,179,181,183,187-192,195,196,231,344,346,349,353-362 > light green > color #1 > /O:96-103,106,109,110,119,121-126,141,143,148,176,179,181,183,190,191,195,215,216,219,220,222,231,341-346,349,353,356-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" opened ChimeraX session > . Unknown command: . > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > .......................... Unknown command: .......................... > color #1 /Q: > 80,98,99,101-104,106,107,110,119,121,122-124,142,143,148,176,179,181-183,188-191,195,206,207,216,222,231,344,346,350,353,356-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /I: > 77,98,99,102,103,109,121,123-126,128,140-143,148,181,183,188-192,195,215,216,219,222,224,231,346,349,353,355-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /G: > 77,80,96-99,101-103,106,107,109,110,121,123-125,143,148,176,179-181,183,187-192,195,207,208,216,231,343-346,349,350,353,354,356-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /A: > 77,95-98,102,103,106,109,123-126,140-143,179-181,183,190-192,195,216,219,222,345,346,349,350,353,354,356-359,361,362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /K: > 77,80,96-98,101-103,106,107,109,110,121,122,123-125,141-143,148,179,181,183,188-191,195,346,347,350,354-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > color #1 /E: > 96,98,99,102,103,106,109,110,121,122-126,141,143,179-181,183,188-191,195,216,219,222,231,343-346,348-350,352,353,355-362 > light green > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > open ""/media/datadisk1/AnalisiGAPDH > /A8B8major/A8B8GAPDH2Job303PostProcFlipped.ccp4"" Opened A8B8GAPDH2Job303PostProcFlipped.ccp4, grid size 300,300,300, pixel 1.21, shown at level 0.0145, step 2, values float32 > volume #2 step 1 > volume #2 level 0.008939 > volume appearance initial > vop gaussian #2 sdev 3.63 > close #3 > show #!2 models > transparency 50 > transparency 0 > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > graphics silhouettes true > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting flat > lighting flat > lighting soft > graphics silhouettes false > transparency #2 40 > transparency #2 30 > transparency #2 20 > graphics silhouettes true > graphics silhouettes false > transparency #2 10 > transparency #2 5 > transparency #2 5 > transparency #2 0 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" opened ChimeraX session > transparency #2 5 > transparency #2 10 > transparency #2 15 > transparency #2 20 > hide #!2 models > show #!2 models > color sel #2 /Q: 333-343 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel #2 /Q: 333-343 yellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > select clear > hide #!2 models > show #!2 models > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel red > select clear > color zone #2 near #1 /Q: 333-343 distance 3 > undo > color zone #2 near #1 /Q: 333-343 distance 3 yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3 palette yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3 spec yellow Expected a keyword > color spec yellow zone #2 near #1 /Q: 333-343 dist 3 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color yellow > undo > color zone #2 near #1 /Q: 333-343 distance 3 > undo > color zone #2 near #1 /Q: 333-343 distance 3 palette yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3 palette: yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3 colorname yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3 color name yellow Expected a keyword > color zone #2 near #1 /Q: 333-343 distance 3, yellow Invalid ""distance"" argument: Expected a number > color zone #2 near #1 /Q: 333-343 distance 3 yellow Expected a keyword > color yellow > undo > color zone yellow #2 near #1 /Q: 333-343 dist 3 Missing or invalid ""surfaces"" argument: invalid surfaces specifier > color yellow zone #2 near #1 /Q: 333-343 dist 3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color zone #2 near #1 /Q: 333-343 distance 3 > undo > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > transparency #2 0 > select clear > color zone #2 near #1 /Q: 333-343 distance 2 > undo > color zone #2 near #1 /Q: 333-343 distance 2.5 > undo > color zone #2 near #1 /Q: 333-343 distance 3 > transparency #2 20 > undo > transparency #2 0 > transparency #2 0 > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > hide #!2 models > show #!2 models > color zone #2 near #1 /Q: 333-343 distance 2.8 > undo > toolshed show > ui tool show ""Show Volume Menu"" > volume gaussian #2 1 Expected a keyword > volume gaussian #2 sDev 1 > volume #2 level 0.008211 > hide #!2 models > volume #2 level 0.007605 > hide #!2 models > hide #!2 models > select #3 2 models selected > volume #2 level 0.008333 > hide #!2 models > select clear > volume #3 sdLevel 1 > volume #3 sdLevel 2 > volume #3 sdLevel 3 > hide #!3 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!3 models > lighting soft > lighting soft > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > color zone #3 near #1 /Q: 333-343 distance 2.8 > select #1 /O: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > hide #!3 models > color sel yellow > show #!3 models > color zone #3 near #1 /O: 333-343 distance 2.8 > hide #!3 models > select #1 /C: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > select clear > select #1 /A: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > select #1 /G: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > select clear > select #1 /E: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > select #1 /K: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel yellow > select clear > color zone #3 near #1 /O: 333-343,/C:333-343,/G:333-343,/K:333-343 dist 2.8 Expected a keyword > show #!3 models > color zone #3 near #1 /O: 333-343 /C:333-343 /G:333-343 /K:333-343 distance > 2.8 > color zone #3 near #1 /Q: 333-343 /C:333-343 /G:333-343 /K:333-343 distance > 2.8 > transparency #3 20 > transparency #3 10 > transparency #3 5 > transparency #3 0 > save /home/roberto/Desktop/image1.png supersample 3 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_1.tif"" width > 1299 height 880 supersample 4 > transparency #3 25 > transparency #3 50 > transparency #3 65 > ui tool show ""Side View"" > transparency #3 75 > transparency #3 85 > color zone #3 near #2 /O: 333-343 /C:333-343 /G:333-343 /K:333-343 distance > 2.8 > transparency #3 85 > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > select #1 /O: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel RED Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel red > select clear > select clear > select clear > hide #!3 models > select #1 /C: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel tomato > select clear > show #!3 models > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_2.tif"" width > 1299 height 880 supersample 4 > select #1 /I: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > select clear > select #1 /Q: 333-343 56 atoms, 56 bonds, 11 residues, 1 model selected > color sel red > select clear > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_3.tif"" width > 1299 height 880 supersample 3 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_5.tif"" width > 1299 height 880 supersample 4 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_4.tif"" width > 1299 height 880 supersample 4 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > transparency #3 75 > transparency #3 85 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig4EM_6.tif"" width > 1299 height 880 supersample 3 > hide #!3 models > select /Q:349 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > style sel ball Changed 12 atom styles > show sel atoms > style sel stick Changed 12 atom styles > select #1 NAD\ Expected a keyword > select #1 NAD Expected a keyword > select #1 /NAD Nothing selected > show atoms > hide atoms > select /Q:349 6 atoms, 5 bonds, 1 residue, 1 model selected > select /Q:355 5 atoms, 4 bonds, 1 residue, 1 model selected > select /Q:354 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select /Q:355 5 atoms, 4 bonds, 1 residue, 1 model selected > select /Q:358 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 12 atom styles > show sel atoms > color sel yellow > select clear > color sel red > select clear > select /Q:346 5 atoms, 4 bonds, 1 residue, 1 model selected > select /Q:349 6 atoms, 5 bonds, 1 residue, 1 model selected > select /Q:346 5 atoms, 4 bonds, 1 residue, 1 model selected > ui tool show ""Build Structure"" > select #1 /I: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > select #1 /I: 349,358 /Q: 349,358 24 atoms, 22 bonds, 4 residues, 1 model selected > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C 2778 atoms, 2825 bonds, 375 residues, 1 model selected > 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 > style sel stick Changed 2778 atom styles > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C 2778 atoms, 2825 bonds, 375 residues, 1 model selected > 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 > select #1 /I: 349,358, /Q: 349,358 /O: 349,358 /C;349,358 /A:349,358 > /G:349,358 /E:349,358 /K:349,358 Expected a keyword > select #1 /I: 349,358, /Q: 349,358, /O: 349,358, /C;349,358, /A:349,358, > /G:349,358, /E:349,358, /K:349,358 Expected a keyword > select #1 /I: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > style sel stick Changed 12 atom styles > show sel cartoons > show sel cartoons > show sel atoms > select #1 /I: 349,358 /Q: 349,358 24 atoms, 22 bonds, 4 residues, 1 model selected > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C 2778 atoms, 2825 bonds, 375 residues, 1 model selected > 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 > show sel atoms > style sel stick Changed 2778 atom styles > color sel yellow > undo > select clear > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C 2778 atoms, 2825 bonds, 375 residues, 1 model selected > 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 > hide sel atoms > select clear > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C:349,358 /A:349,358 > /G:349,358 /E:349,358 /K:349,358 96 atoms, 88 bonds, 16 residues, 1 model selected > show sel atoms > style sel stick Changed 96 atom styles > color sel yellow > select clear > color byhetero > color bynucleotide > select ligand 704 atoms, 768 bonds, 16 residues, 1 model selected > show sel > select clear > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > setattr Missing or invalid ""target"" argument: Expected a text string > setattr #1 /I: 346-352 res ss_type 1 Assigning ss_type attribute to 7 items > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" opened ChimeraX session > show #!2 models > volume #!2 appearance initial > volume #2 level 0.01655 > transparency #2 50 > transparency #2 35 > volume #2 level 0.02001 > ui tool show ""Side View"" > volume #2 level 0.02013 > setattr #1 /G: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > select #1 /G: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel crimson > select clear > select #1 /G: 191,77,183 33 atoms, 30 bonds, 3 residues, 1 model selected > select clear > select #1 /D: 191,77,183 33 atoms, 30 bonds, 3 residues, 1 model selected > select clear > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C 2778 atoms, 2825 bonds, 375 residues, 1 model selected > 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 Unknown command: 349,358 /A:349,358 /G:349,358 /E:349,358 /K:349,358 > select #1 /I: 349,358 /Q: 349,358 /O: 349,358 /C:349,358 /A:349,358 > /G:349,358 /E:349,358 /K:349,358 96 atoms, 88 bonds, 16 residues, 1 model selected > color sel yellow > select clear > select #1 /G:NAD 44 atoms, 48 bonds, 1 residue, 1 model selected > hide #!2 models > show #!2 models > select clear > select #1 /A:NAD 44 atoms, 48 bonds, 1 residue, 1 model selected > color sel byhetero > color sel byhetero > select clear > transparency #2 25 > transparency #2 15 > transparency #2 35 > transparency #2 50 > setattr #1 /O: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > select #1 /O: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel red > select #1 /O: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > volume #2 level 0.02086 > setattr #1 /C: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > select #1 /C: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel tomato > select #1 /C: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > select #1 /K: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel coral > setattr #1 /K: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > volume #2 level 0.01964 > select #1 /K: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > select #1 /E: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel crimson > select clear > setattr #1 /E: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > select #1 /E: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > setattr #1 /Q: 344-352 res ss_type 1 Assigning ss_type attribute to 9 items > select #1 /Q: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel red > select clear > select #1 /Q: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > volume #2 level 0.01443 > volume #2 level 0.01661 > volume #2 level 0.02061 > hide #!3 models > volume #2 level 0.01528 > select #1 /I: 333-362 154 atoms, 155 bonds, 30 residues, 1 model selected > color sel coral > select clear > select #1 /I: 349,358 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel yellow > select clear > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > ui tool show ""Build Structure"" > volume #2 level 0.01588 > volume #2 level 0.0177 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" > volume #2 sdLevel 3 > volume #2 sdLevel 2 > volume #2 sdLevel 4 > volume #2 sdLevel 5 > volume #2 sdLevel 6 > volume #2 sdLevel 7 > volume #2 sdLevel 6 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_1.tif"" width > 1299 height 880 supersample 4 > volume #2 level 0.02053 > volume #2 sdLevel 6 > volume #2 sdLevel 7 > volume #2 sdLevel 7 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_2.tif"" width > 1299 height 880 supersample 3 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_2.tif"" width > 1299 height 880 supersample 3 > volume #2 sdLevel 7 > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/Fig5EM_1.tif"" width > 1299 height 880 supersample 3 > hide #!2 models > open ""/media/datadisk1/AnalisiGAPDH /A2B2/chimeraA2B2GAPDH0Job614/2PKQ.pdb"" Summary of feedback from opening /media/datadisk1/AnalisiGAPDH /A2B2/chimeraA2B2GAPDH0Job614/2PKQ.pdb --- warning | Cannot find LINK/SSBOND residue CYS (349 ) 2PKQ.pdb title: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3- phosphate dehydrogenase, complexed with nadp [more info...] Chain information for 2PKQ.pdb #4 --- Chain | Description O Q | NADP-dependent glyceraldehydephosphate dehydrogenase subunit B P R | NADP-dependent glyceraldehydephosphate dehydrogenase subunit A Non-standard residues in 2PKQ.pdb #4 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotidephosphate SO4 — sulfate ion > select #4 10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected > ~select #4 Nothing selected > hide #!1 models > show #!1 models > select #4 10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected > select #1 42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected > select #4 10561 atoms, 10739 bonds, 6 pseudobonds, 1382 residues, 2 models selected > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui tool show Matchmaker > matchmaker #!4 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain I (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1593.2 RMSD between 298 pruned atom pairs is 1.024 angstroms; (across all 346 pairs: 6.754) > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui tool show Matchmaker No reference and/or match structure/chain chosen > matchmaker #4/R#4/Q#4/P#4/O & sel to #1/R#1/Q#1/P#1/O & sel pairing ss No 'to' chains specified > matchmaker #4/R#4/Q#4/P#4/O to #1/R#1/Q#1/P#1/O pairing ss Parameters --- Chain pairing | ss 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain R (#1) with 2PKQ.pdb, chain R (#4), sequence alignment score = 1538.1 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain Q (#1) with 2PKQ.pdb, chain Q (#4), sequence alignment score = 1525.4 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain P (#1) with 2PKQ.pdb, chain P (#4), sequence alignment score = 1527.3 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain O (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1506.5 RMSD between 1252 pruned atom pairs is 1.154 angstroms; (across all 1367 pairs: 4.335) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > ui mousemode right ""translate selected models"" > ui tool show Matchmaker > matchmaker #4/O#4/P#4/Q#4/R to #1/A#1/B#1/C#1/D pairing ss Parameters --- Chain pairing | ss 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain A (#1) with 2PKQ.pdb, chain O (#4), sequence alignment score = 1578.8 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain B (#1) with 2PKQ.pdb, chain P (#4), sequence alignment score = 1500.3 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain C (#1) with 2PKQ.pdb, chain Q (#4), sequence alignment score = 1528.4 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain D (#1) with 2PKQ.pdb, chain R (#4), sequence alignment score = 1505.1 RMSD between 1252 pruned atom pairs is 1.144 angstroms; (across all 1367 pairs: 4.422) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > ~select #4 Nothing selected Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!2 models > hide #!2 models > close #4 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > close #3 > open 2PK1 Summary of feedback from opening 2PK1 fetched from pdb --- warning | PDB entry 2PK1 has been replaced by 3EKA notes | Fetching compressed mmCIF 2pk1 from http://files.rcsb.org/download/2pk1.cif Fetching CCD ASC from http://ligand-expo.rcsb.org/reports/A/ASC/ASC.cif 2pk1 title: Crystal Structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites [more info...] Chain information for 2pk1 #3 --- Chain | Description A | Hyaluronidase, phage associated Non-standard residues in 2pk1 #3 --- ASC — ascorbic acid 2pk1 mmCIF Assemblies --- 1| author_defined_assembly Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > open 2PKQ Summary of feedback from opening 2PKQ fetched from pdb --- notes | Fetching compressed mmCIF 2pkq from http://files.rcsb.org/download/2pkq.cif Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif Fetching CCD NDP from http://ligand-expo.rcsb.org/reports/N/NDP/NDP.cif 2pkq title: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP [more info...] Chain information for 2pkq #4 --- Chain | Description O Q T | Glyceraldehyde-3-phosphate dehydrogenase B P R S | Glyceraldehyde-3-phosphate dehydrogenase A Non-standard residues in 2pkq #4 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate SO4 — sulfate ion 2pkq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""add models"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > save ""/media/datadisk1/AnalisiGAPDH /A8B8major/A8B8Major/ForFigureDec20.cxs"" opened ChimeraX session > open 2PKQ 2pkq title: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP [more info...] Chain information for 2pkq #5 --- Chain | Description O Q T | Glyceraldehyde-3-phosphate dehydrogenase B P R S | Glyceraldehyde-3-phosphate dehydrogenase A Non-standard residues in 2pkq #5 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate SO4 — sulfate ion 2pkq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select #5 15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected > close #5 > close #4 > close #3 > open 2PKQ 2pkq title: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP [more info...] Chain information for 2pkq #3 --- Chain | Description O Q T | Glyceraldehyde-3-phosphate dehydrogenase B P R S | Glyceraldehyde-3-phosphate dehydrogenase A Non-standard residues in 2pkq #3 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate SO4 — sulfate ion 2pkq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select #3 15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected > hide #!1 models > ui mousemode right ""translate selected models"" > hide sel atoms > show sel cartoons > select clear > select #3/S:333 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 32 atoms, 33 bonds, 3 residues, 1 model selected > select up 2601 atoms, 2643 bonds, 340 residues, 1 model selected > delete atoms sel > delete bonds sel > select up 50 atoms, 50 bonds, 6 residues, 1 model selected > select up 2688 atoms, 2734 bonds, 353 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected > show #!1 models > open 2PKQ 2pkq title: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP [more info...] Chain information for 2pkq #4 --- Chain | Description O Q T | Glyceraldehyde-3-phosphate dehydrogenase B P R S | Glyceraldehyde-3-phosphate dehydrogenase A Non-standard residues in 2pkq #4 --- NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate SO4 — sulfate ion 2pkq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select #4 15840 atoms, 16108 bonds, 5 pseudobonds, 2073 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > select clear > select clear > select clear > select up 37 atoms, 37 bonds, 5 residues, 1 model selected > select up 2601 atoms, 2643 bonds, 340 residues, 1 model selected > delete atoms sel > delete bonds sel > select up 31 atoms, 31 bonds, 4 residues, 1 model selected > select up 2688 atoms, 2734 bonds, 353 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected > select #3 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected > select #1 42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected > select #2 2 models selected > select #1 42627 atoms, 43384 bonds, 6 pseudobonds, 5656 residues, 2 models selected > select #4 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected > select #3 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected > ui tool show Matchmaker > matchmaker #3/R#3/Q#3/P#3/O to #1/R#1/Q#1/P#1/O pairing ss Parameters --- Chain pairing | ss 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain R (#1) with 2pkq, chain R (#3), sequence alignment score = 1538.1 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain Q (#1) with 2pkq, chain Q (#3), sequence alignment score = 1525.4 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain P (#1) with 2pkq, chain P (#3), sequence alignment score = 1527.3 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain O (#1) with 2pkq, chain O (#3), sequence alignment score = 1500.5 RMSD between 1252 pruned atom pairs is 1.154 angstroms; (across all 1367 pairs: 4.269) > matchmaker #4/O#4/P#4/Q#4/R to #1/A#1/B#1/C#1/D pairing ss Parameters --- Chain pairing | ss 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 A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain A (#1) with 2pkq, chain O (#4), sequence alignment score = 1572.8 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain B (#1) with 2pkq, chain P (#4), sequence alignment score = 1500.3 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain C (#1) with 2pkq, chain Q (#4), sequence alignment score = 1528.4 Matchmaker A8B8GAPD_major_RealspaceRefined_Dic20_25macrocycles_ren_final.pdb, chain D (#1) with 2pkq, chain R (#4), sequence alignment score = 1505.1 RMSD between 1252 pruned atom pairs is 1.144 angstroms; (across all 1367 pairs: 4.366) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > select clear Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. > hide #!1 models > select clear > select #3 /NADP Nothing selected > nucleotides #!3-4 fill > style nucleic & #!3-4 stick Changed 0 atom styles > color #!3-4 bynucleotide > show #!1 models > hide #!1 models > select #3 10551 atoms, 10731 bonds, 3 pseudobonds, 1380 residues, 2 models selected Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted Error processing trigger ""changes"": RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 305, in _items_change if not hasattr(self, '_recursion'): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Hewlett-Packard Model: HP Z800 Workstation OS: Ubuntu 16.04 xenial Architecture: 64bit ELF CPU: 16 Intel(R) Xeon(R) CPU X5570 @ 2.93GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 94G 2.2G 86G 47M 6.0G 91G Swap: 13G 0B 13G Graphics: 0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1) Subsystem: NVIDIA Corporation Device [10de:119e] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 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: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 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: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 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: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 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: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 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: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Structure Comparison fixed all ChimeraX