id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4573 Main graphics restricted to smaller monitor size josh.mccluskey@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description When using two monitors of different sizes (Microsoft Surface connected to a 24"" monitor) the main viewport is restricted to the size it would be on the smaller monitor. I haven't been able to find an option to manually adjust the resolution of the viewport. Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:\Users\joshm\OneDrive\PhD\Protein Models\Prefoldin Filament.cxs"" > format session Log from Mon Apr 26 13:54:12 2021UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb"" Summary of feedback from opening C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.004 0.036 13173 Ignored bad PDB record found on line 23 ANGLE : 0.888 13.546 17750 Ignored bad PDB record found on line 24 CHIRALITY : 0.051 0.283 2239 17 messages similar to the above omitted Chain information for yPFD - cryoEM.pdb #1 --- Chain | Description A B C D E F G a b c d e f g | No description available > style ball Changed 13103 atom styles > hide atoms > show cartoons > select coil 2456 atoms, 2359 bonds, 335 residues, 1 model selected > select add coil 2456 atoms, 2359 bonds, 335 residues, 1 model selected > select add helix 11290 atoms, 11235 bonds, 1441 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale goldenrod > color sel dark khaki > color sel goldenrod > color sel sandy brown > color sel dark khaki > color sel khaki > color sel moccasin > color sel navajo white > color sel peach puff > color sel cornsilk > color sel tan > color sel burly wood > select clear > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F /G /a /b /c /d /e /f /g Alignment identifier is 1 > color sel orange > color sel orange red > color sel cornflower blue > transparency 50 > transparency 50 > transparency 50 > volume showOutlineBox true No volumes specified > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting simple > lighting soft > lighting full > ui tool show ""Side View"" > ui tool show ""Side View"" > view orient > view sel > view > set bgColor white > set bgColor gray > set bgColor black > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\joshm\Desktop\movie1.mp4 Movie saved to \C:Users\\...\Desktop\movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\joshm\Desktop\movie2.mp4 Movie saved to \C:Users\\...\Desktop\movie2.mp4 > save C:\Users\joshm\Desktop\image1.png supersample 3 > view orthographic Expected an objects specifier or a view name or a keyword > ui tool show ""Side View"" > ui tool show ""Side View"" > select clear > camera mono > camera ortho > lighting shadows false > lighting simple > lighting soft > lighting full > lighting shadows false > select helix 8834 atoms, 8876 bonds, 1106 residues, 1 model selected > select add coil 11290 atoms, 11235 bonds, 1441 residues, 1 model selected > ui tool show ""Color Actions"" > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide sel atoms > show sel cartoons Drag select of 1 residues > undo > ui tool show ""Color Actions"" > color sel burly wood > color sel burly wood > transparency 10 > ~transparency Unknown command: ~transparency > transparency 80 > transparency 100 > Transparency 0 Unknown command: Transparency 0 > Transparency 10 Unknown command: Transparency 10 > transparency Missing or invalid ""percent"" argument: Expected a number > transparency 0 > hide sel cartoons > show sel atoms > transparency 80 > transparency 0 > hide sel atoms > hide sel cartoons > show sel cartoons > transparency 80,r Missing or invalid ""percent"" argument: Expected a number > transparency 80 cartoons > undo > undo > transparency 0 cartoons > show sel cartoons > transparency sel 50 cartoons > transparency sel 90 cartoons > transparency sel 80 cartoons > select clear > undo > transparency sel 95 cartoons > select clear > set bgColor white > undo > transparency sel 90 cartoons > select clear > transparency sel 80 cartoons > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > transparency sel 80 cartoons > select clear > cd C:\Users\joshm\OneDrive\PhD\Thesis\Figures Current working directory is: C:\Users\joshm\OneDrive\PhD\Thesis\Figures > save B-Barrel.png > view orient > view orient > save B-Barrel end-on.png Cannot determine format for 'B-Barrel' > save B-Barrelendon.png > transparency 0 > transparency sel 0 > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > transparency sel 0 > transparency sel c 0 Missing or invalid ""percent"" argument: Expected a number > transparency c sel 0 Missing or invalid ""percent"" argument: Expected a number > transparency sel 0 > transparency sel 0 cartoons > select clear > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > color sel bychain > undo > undo > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > color sel bychain > color sel saddle brown > color sel medium aquamarine > color sel bychain > color sel bypolymer > color sel byelement > color sel byhetero > color sel byelement > color sel bynucleotide > color sel bychain > color sel bychain > color sel bychain > color sel bychain > color sel bypolymer > color sel bychain > select /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select /B 936 atoms, 941 bonds, 121 residues, 1 model selected > select /C 936 atoms, 941 bonds, 121 residues, 1 model selected > select /g 936 atoms, 941 bonds, 121 residues, 1 model selected No target buttons for the coloring action are checked > color sel red target c > color sel alice blue target c > color sel dark sea green target c > select /f 936 atoms, 941 bonds, 121 residues, 1 model selected > select /e 936 atoms, 941 bonds, 121 residues, 1 model selected > select /d 936 atoms, 941 bonds, 121 residues, 1 model selected > select /c 936 atoms, 941 bonds, 121 residues, 1 model selected > select /A 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel dark sea green target c > select /B 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel light green target c > select /C 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel pale green target c > select /D 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel rosy brown target c > select /E 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel tan target c > select /F 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel burly wood target c > select /G 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel beige target c > color sel beige target c > color sel aquamarine target c > color sel burly wood target c > color sel light coral target c > color sel aquamarine target c > color sel sky blue target c > select /F 936 atoms, 941 bonds, 121 residues, 1 model selected > select /G 936 atoms, 941 bonds, 121 residues, 1 model selected > select /a 935 atoms, 940 bonds, 121 residues, 1 model selected > color sel sky blue target c > color sel light sky blue target c > color sel light sky blue target c Drag select of 12 residues > ui tool show ""Color Actions"" > ui tool show ""Color Actions"" > view sel > select /g 936 atoms, 941 bonds, 121 residues, 1 model selected > color sel bychain > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > color sel bychain > select /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select /B 936 atoms, 941 bonds, 121 residues, 1 model selected > select /C 936 atoms, 941 bonds, 121 residues, 1 model selected > undo > select clear > save ypfdfilamentdimer.png > select /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /a 1871 atoms, 1881 bonds, 242 residues, 1 model selected > select clear > select add /g 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /G 1872 atoms, 1882 bonds, 242 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected atoms"" > undo > undo > move x 10 > move sel x 10 Missing or invalid ""axis"" argument: Axis argument requires 2 atoms, got 1872 atoms > move x sel 10 Expected a number or a keyword > move x 10 sel Expected an integer >= 1 or a keyword > select clear > select add /f 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /f 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /F 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /e 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /E 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /e 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > select add /d 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /D 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /c 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > select add /d 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /D 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > select add /g 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /e 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /c 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select add /C 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select add /E 4680 atoms, 4705 bonds, 605 residues, 1 model selected > select add /G 5616 atoms, 5646 bonds, 726 residues, 1 model selected > select add /A 6552 atoms, 6587 bonds, 847 residues, 1 model selected > select add /a 7487 atoms, 7527 bonds, 968 residues, 1 model selected > select clear > save separateddimers.png > undo > undo > undo > undo > undo > undo > undo > undo > undo > undo > open ""C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb"" Summary of feedback from opening C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.004 0.036 13173 Ignored bad PDB record found on line 23 ANGLE : 0.888 13.546 17750 Ignored bad PDB record found on line 24 CHIRALITY : 0.051 0.283 2239 17 messages similar to the above omitted Chain information for yPFD - cryoEM.pdb #2 --- Chain | Description A B C D E F G a b c d e f g | No description available > close session > open ""C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb"" Summary of feedback from opening C:/Users/joshm/OneDrive/PhD/Protein Models/yPFD - cryoEM.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.004 0.036 13173 Ignored bad PDB record found on line 23 ANGLE : 0.888 13.546 17750 Ignored bad PDB record found on line 24 CHIRALITY : 0.051 0.283 2239 17 messages similar to the above omitted Chain information for yPFD - cryoEM.pdb #1 --- Chain | Description A B C D E F G a b c d e f g | No description available > hide atoms > show cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F /G /a /b /c /d /e /f /g Alignment identifier is 1 > undo > color sel orange red > color sel cornflower blue > select clear > select ~sel 10541 atoms, 10625 bonds, 1330 residues, 1 model selected > transparency sel 80 cartoons > transparency sel 90 cartoons > select clear > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > transparency sel 90 cartoons > select clear > save Bbarrelcoloured.png > view orient > save Bbarrelcolouredendon.png > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /a 1871 atoms, 1881 bonds, 242 residues, 1 model selected > transparency 0 cartoons > undo > select ~sel 11232 atoms, 11292 bonds, 1452 residues, 1 model selected > hide sel cartoons > ui mousemode right translate > select add /A 12168 atoms, 12233 bonds, 1573 residues, 1 model selected > ui mousemode right ""translate selected atoms"" > undo > save ypfddimerfront.png > save ypfddimertop.png > save ypfddimerseparate.png > undo > undo > select add strand 12297 atoms, 12359 bonds, 1591 residues, 1 model selected > select ~sel 806 atoms, 814 bonds, 103 residues, 1 model selected > ui tool show ""Color Actions"" > color sel burly wood > select clear > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > color sel burly wood > save ypfddimerfrontwood.png > select clear > save ypfddimerfrontwood.png > save ypfddimertopwood.png > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > save ypfddimerseparatewood.png > undo > undo > show sel cartoons > select clear > show cartoons > select clear > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /C 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /a 2807 atoms, 2822 bonds, 363 residues, 1 model selected > select add /c 3743 atoms, 3763 bonds, 484 residues, 1 model selected > undo > select ~sel 9360 atoms, 9410 bonds, 1210 residues, 1 model selected > hide sel cartoons > select add /A 10296 atoms, 10351 bonds, 1331 residues, 1 model selected > select add /a 11231 atoms, 11291 bonds, 1452 residues, 1 model selected > select clear > show cartoons > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > undo > select add strand 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > select ~sel Nothing selected > ui tool show ""Color Actions"" > color bychain > undo > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > select clear > ortho Unknown command: ortho > camera ortho > undo > select clear > select add /B 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /b 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /c 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select clear > select add /B 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /D 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /F 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select add /b 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select add /d 4680 atoms, 4705 bonds, 605 residues, 1 model selected > select add /f 5616 atoms, 5646 bonds, 726 residues, 1 model selected > select subtract /B 4680 atoms, 4705 bonds, 605 residues, 1 model selected > select subtract /b 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select subtract /F 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select add /F 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select subtract /D 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select subtract /d 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /C 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /E 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /G 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select add /c 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select add /e 4680 atoms, 4705 bonds, 605 residues, 1 model selected > select add /g 5616 atoms, 5646 bonds, 726 residues, 1 model selected > select subtract /C 4680 atoms, 4705 bonds, 605 residues, 1 model selected > select subtract /c 3744 atoms, 3764 bonds, 484 residues, 1 model selected > select subtract /E 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select subtract /e 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > save dimerseparatecoloured.png > undo > select clear > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > close session > open ""C:\Users\joshm\OneDrive\PhD\Protein Models\yPFD - cryoEM.pdb"" format > pdb Summary of feedback from opening C:\Users\joshm\OneDrive\PhD\Protein Models\yPFD - cryoEM.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.004 0.036 13173 Ignored bad PDB record found on line 23 ANGLE : 0.888 13.546 17750 Ignored bad PDB record found on line 24 CHIRALITY : 0.051 0.283 2239 17 messages similar to the above omitted Chain information for yPFD - cryoEM.pdb #1 --- Chain | Description A B C D E F G a b c d e f g | No description available > hide atoms > show cartoons > ui tool show ""Blast Protein"" > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F /G /a /b /c /d /e /f /g Alignment identifier is 1 > color sel orange red > color sel cornflower blue > select strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > ui tool show ""Color Actions"" > color sel burly wood > transparency sel 90 cartoons > select clear > select /a:58 7 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 70 residues > hbonds sel 61 hydrogen bonds found > undo Drag select of 4 residues, 1 pseudobonds > view sel Drag select of 20 residues > hbonds sel 13 hydrogen bonds found Drag select of 43 residues, 2 pseudobonds > hbonds sel 32 hydrogen bonds found > undo > select clear > select 13103 atoms, 13173 bonds, 32 pseudobonds, 1694 residues, 2 models selected > volume step 1 No volumes specified > view sel > select clear > select strand 1806 atoms, 1764 bonds, 15 pseudobonds, 252 residues, 2 models selected > hbonds sel 166 hydrogen bonds found > undo > undo > select clear Drag select of 6 residues > hbonds sel 6 hydrogen bonds found > hbonds sel 6 hydrogen bonds found Drag select of 14 residues Drag select of 12 residues Drag select of 3 residues > view sel > select /E:27 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 4 residues > select /E:67 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 7 residues > ui mousemode right select > select /C:84 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:86 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:86 9 atoms, 8 bonds, 1 residue, 1 model selected Drag select of 7 residues > hbonds sel 7 hydrogen bonds found > view sel > select clear Drag select of 3 residues > ui mousemode right zoom > ui mousemode right translate > ~hbonds > select clear > select 13103 atoms, 13173 bonds, 1694 residues, 1 model selected > view sel > select clear > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > select ~sel 11297 atoms, 11409 bonds, 1442 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > select clear > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /C 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select clear > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /B 1872 atoms, 1882 bonds, 242 residues, 1 model selected > select add /b 2808 atoms, 2823 bonds, 363 residues, 1 model selected > select add /a 3743 atoms, 3763 bonds, 484 residues, 1 model selected > select ~sel 9360 atoms, 9410 bonds, 1210 residues, 1 model selected > hide sel cartoons > select add /A 10296 atoms, 10351 bonds, 1331 residues, 1 model selected > select add /C 10296 atoms, 10351 bonds, 1331 residues, 1 model selected > select add /B 11232 atoms, 11292 bonds, 1452 residues, 1 model selected > select clear > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > select add /b 1872 atoms, 1882 bonds, 242 residues, 1 model selected > camera ortho > camera perspective Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs', 'stereo', or 'tb' or a keyword > camera perspec Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs', 'stereo', or 'tb' or a keyword > camera pers Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs', 'stereo', or 'tb' or a keyword > camera persp Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs', 'stereo', or 'tb' or a keyword > volume region all imageMode ""full region"" No volumes specified > volume planes z style image imageMode ""full region"" No volumes specified > view orient > view orient > ui mousemode right ""tape measure"" > ui mousemode right ""move planes"" > ui mousemode right ""crop volume"" > ui mousemode right ""tape measure"" > marker segment #2 position 7.785,5.321,16.41 toPosition 7.259,14.04,13.57 > color yellow radius 0.1 label 9.183 labelHeight 0.9183 labelColor yellow > marker segment #2 position 21.26,12.6,2.174 toPosition 10.97,-17.36,-9.234 > color yellow radius 0.1 label 33.67 labelHeight 3.367 labelColor yellow > marker delete #2 > ui mousemode right minimize > ui mousemode right tug > ui mousemode right ""bond rotation"" > ui mousemode right ""move planes"" > ui mousemode right ""contour level"" > select clear > save topdownBbarrel.png > select add /A 936 atoms, 941 bonds, 121 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected atoms"" > select clear > select add /a 935 atoms, 940 bonds, 121 residues, 1 model selected > select clear > select add /C 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > select add /B 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > select add /b 936 atoms, 941 bonds, 121 residues, 1 model selected > select clear > save topdownexploded Bbarrel Cannot determine format for 'topdownexploded' > save topdownexplodedBBarrel.png > close session > open ""C:\Users\joshm\OneDrive\PhD\Protein Models\yPFD - cryoEM.pdb"" format > pdb Summary of feedback from opening C:\Users\joshm\OneDrive\PhD\Protein Models\yPFD - cryoEM.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.004 0.036 13173 Ignored bad PDB record found on line 23 ANGLE : 0.888 13.546 17750 Ignored bad PDB record found on line 24 CHIRALITY : 0.051 0.283 2239 17 messages similar to the above omitted Chain information for yPFD - cryoEM.pdb #1 --- Chain | Description A B C D E F G a b c d e f g | No description available > hide atoms > show cartoons > select add strand 1806 atoms, 1764 bonds, 252 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F /G /a /b /c /d /e /f /g Alignment identifier is 1 > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C /D /E /F /G /a /b /c /d /e /f /g Alignment identifier is 2 > undo > undo > undo > undo > color sel orange red > color sel cornflower blue > select add strand 2310 atoms, 2282 bonds, 322 residues, 1 model selected > select ~sel 10793 atoms, 10891 bonds, 1372 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > transparency sel 90 cartoons > save ""C:/Users/joshm/OneDrive/PhD/Protein Models/Prefoldin Filament.cxs"" opened ChimeraX session OpenGL version: 3.3.0 - Build 24.20.100.6299 OpenGL renderer: Intel(R) HD Graphics 520 OpenGL vendor: Intel Manufacturer: Microsoft Corporation Model: Surface Pro 4 OS: Microsoft Windows 10 Pro (Build 19041) Memory: 4,212,711,424 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-6300U CPU @ 2.40GHz"" 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: 2.1.3 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: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 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 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 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+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 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 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 pywin32: 228 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 WMI: 1.5.1 File attachment: ChimeraX Screenshot.png }}} [attachment:""ChimeraX Screenshot.png""] " defect closed normal Graphics duplicate Greg Couch all ChimeraX