![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#4573 closed defect (duplicate)
Main graphics restricted to smaller monitor size
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Attachments (1)
Change History (4)
by , 4 years ago
| Attachment: | ChimeraX Screenshot.png added |
|---|
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Main graphics restricted to smaller monitor size |
comment:2 by , 4 years ago
I think what is going on is that ChimeraX is only displaying graphics in the lower-left quadrant of the window (exactly half the width and height). This is because the Qt window toolkit incorrectly reports the display pixel scale. I believe that display pixel scale comes from the Windows display scaling which you probably have set to 175% or 200% on one display and 125% or similar on the other display. This happens when one display is a high DPI (dots per inch) display and the other is not. ChimeraX has no way to override what the Qt window toolkit tells it, and so it uses incorrect graphics size by a factor of 2.
comment:3 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Same bug was reported before #3675 and supposedly it is fixed in the ChimeraX daily build or the ChimeraX 1.2 release candidate. Update ChimeraX and it should work.
Note:
See TracTickets
for help on using tickets.
Added by email2trac