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#3789 closed defect (duplicate)

self._positions is None during undo

Reported by:	hrishikesh.das@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005280641 (2020-05-28 06:41:54 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005280641 (2020-05-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/1upmodandmap_new/1up_Sb23_complete-
> coot-1.pdb

Chain information for 1up_Sb23_complete-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> set bgColor white

> hide atoms

> show cartoons

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/2upmodelandmap_new/2up_Sb23_complete-
> coot-2.pdb

Chain information for 2up_Sb23_complete-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> show atoms

> show cartoons

> hide cartoons

> show cartoons

> hide atoms

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 2up_Sb23_complete-
coot-2.pdb, chain A (#2), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 90071 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #1/D#2/D

1774 atoms, 1816 bonds, 2 models selected  

> ui tool show "Color Actions"

> color sel khaki

> select #1/E#2/E

1764 atoms, 1806 bonds, 2 models selected  

> color sel khaki

> select #1/F#2/F

1774 atoms, 1816 bonds, 2 models selected  

> color sel khaki

> tile columns 2

> lighting soft

> lighting soft

> lighting full

> lighting simple

> lighting simple

> lighting soft

> lighting full

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Leo_covid/Ty1/RBDs/6lzg-1.pdb

Summary of feedback from opening
/Users/hrishikeshdas/Documents/Cororna_projects/Leo_covid/Ty1/RBDs/6lzg-1.pdb  
---  
warnings | Ignored bad PDB record found on line 704  
  
  
Ignored bad PDB record found on line 705  
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fmodern\fcharset0 Courier;}  
  
Ignored bad PDB record found on line 706  
\deftab720  
  
Ignored bad PDB record found on line 707  
\f0\fs24 \cf2 \expnd0\expndtw0\kerning0  
  
Ignored bad PDB record found on line 708  
\outl0\strokewidth0 \strokec2 HEADER VIRAL PROTEIN 19-FEB-20 6LZG \  
  
5 messages similar to the above omitted  
  
6lzg-1.pdb title:  
Structure of novel coronavirus spike receptor-binding domain complexed\ with
its receptor ACE2 \ [more info...]  
  
Chain information for 6lzg-1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in 6lzg-1.pdb #3  
---  
NAG — N-acetyl-D-glucosamine \  
ZN — zinc ion \  
  

> matchmaker #3/b to #1/a

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 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 6lzg-1.pdb, chain B
(#3), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Leo_covid/Ty1/RBDs/6lzg-2.pdb

Summary of feedback from opening
/Users/hrishikeshdas/Documents/Cororna_projects/Leo_covid/Ty1/RBDs/6lzg-2.pdb  
---  
warnings | Ignored bad PDB record found on line 704  
  
  
Ignored bad PDB record found on line 705  
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fmodern\fcharset0 Courier;}  
  
Ignored bad PDB record found on line 706  
\deftab720  
  
Ignored bad PDB record found on line 707  
\f0\fs24 \cf2 \expnd0\expndtw0\kerning0  
  
Ignored bad PDB record found on line 708  
\outl0\strokewidth0 \strokec2 HEADER VIRAL PROTEIN 19-FEB-20 6LZG \  
  
5 messages similar to the above omitted  
  
6lzg-2.pdb title:  
Structure of novel coronavirus spike receptor-binding domain complexed\ with
its receptor ACE2 \ [more info...]  
  
Chain information for 6lzg-2.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in 6lzg-2.pdb #4  
---  
NAG — N-acetyl-D-glucosamine \  
ZN — zinc ion \  
  

> matchmaker #4/b to #1/a

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 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 6lzg-2.pdb, chain B
(#4), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> matchmaker #4/b to #2/a

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 2up_Sb23_complete-coot-2.pdb, chain A (#2) with 6lzg-2.pdb, chain B
(#4), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> select #3/B

1614 atoms, 1606 bonds, 1 model selected  

> hide sel cartoons

> select #4/B

1614 atoms, 1606 bonds, 1 model selected  

> hide sel cartoons

> select #3/A

5170 atoms, 5047 bonds, 4 pseudobonds, 2 models selected  

> color (#!3 & sel) red

> select #4/A

5170 atoms, 5047 bonds, 4 pseudobonds, 2 models selected  

> color (#!4 & sel) red

> select clear

> lighting soft

> lighting simple

> set bgColor white

> set bgColor black

> set bgColor white

> lighting full

> movie record

> turn y 30 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> select #3/A

5170 atoms, 5047 bonds, 4 pseudobonds, 2 models selected  

> graphics silhouettes true

> set silhouettes true

> set silhouettesweidth 1

Expected a keyword  

> set silhouettes weidth 1

Invalid "silhouettes" argument: Expected true or false (or 1 or 0)  

> set silhouetteswidth 1

Expected a keyword  

> set silhouetteWidth 1

> select clear

> select up

Nothing selected  

> movie record

> turn y 30 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> select #1/D#2/D

1774 atoms, 1816 bonds, 2 models selected  

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P3_J257_013_volume_map_sharp.mrc

Opened cryosparc_P3_J257_013_volume_map_sharp.mrc, grid size 600,600,600,
pixel 1.02, shown at level 0.123, step 4, values float32  

> open /Users/hrishikeshdas/Downloads/cryosparc_P3_J257_013_volume_map.mrc

Opened cryosparc_P3_J257_013_volume_map.mrc, grid size 600,600,600, pixel
1.02, shown at level 0.0472, step 4, values float32  

> show sel surfaces

> show sel surfaces

> ui tool show "Color Actions"

> color sel khaki

> select #1/E#2/E

1764 atoms, 1806 bonds, 2 models selected  

> show sel surfaces

> color sel khaki

> select #1/F#2/F

1774 atoms, 1816 bonds, 2 models selected  

> show sel surfaces

> color sel khaki

> select clear

> movie record

> turn y 30 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock2.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock2.mp4  
  

> stop

> select #3/A

5170 atoms, 5047 bonds, 4 pseudobonds, 2 models selected  

> show sel surfaces

> color (#!3 & sel) red

> select #4/A

5170 atoms, 5047 bonds, 4 pseudobonds, 2 models selected  

> show sel surfaces

> color (#!4 & sel) red

> select clear

> lighting soft

> movie record

> turn z 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock3.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock3.mp4  
  

> stop

> movie record

> turn x 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock3.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock3.mp4  
  

> stop

> movie record

> turn x 70 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock4.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock4.mp4  
  

> stop

> movie record

> turn x 70 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock5.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock5.mp4  
  

> stop

> transparency #1-4 40

> lighting soft

> lighting full

> transparency #1-4 20

> transparency #1-4 60

> movie record

> turn x 90 rock 100

> turn y 70 rock 100, wait 100; movie encode
> /Users/hrishikeshdas/Desktop/rock6.mp4; stop

Invalid "rock" argument: Expected an integer  

> stop

> movie record

Already recording a movie  

> stop

> movie record

Already recording a movie  

> stop

> stop

> stop recording

Expected fewer arguments  

> stop

> stop

> movie stop

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 2up_Sb23_complete-
coot-2.pdb, chain A (#2), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> tile

> show #!2 models

> hide #!2 models

> show #!2 models

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 2up_Sb23_complete-
coot-2.pdb, chain A (#2), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> matchmaker #4/b to #1/a

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 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 6lzg-2.pdb, chain B
(#4), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> show #!3 models

> hide #!3 models

> tile coloumn 2

Expected a models specifier or a keyword  

> tile columns 2

> close #5

> close #6

> tile columns 2

> show #!3 models

> hide #!3 models

> matchmaker #4/b to #1/a

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 1up_Sb23_complete-coot-1.pdb, chain A (#1) with 6lzg-2.pdb, chain B
(#4), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> show #!4 models

> matchmaker #3/b to #2/a

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 2up_Sb23_complete-coot-2.pdb, chain A (#2) with 6lzg-1.pdb, chain B
(#3), sequence alignment score = 1010.5  
RMSD between 188 pruned atom pairs is 0.834 angstroms; (across all 193 pairs:
0.930)  
  

> show #!3 models

> movie record

> turn y 40 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock2.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock2.mp4  
  

> stop

> movie record

> turn x \- 90 rock 100; wait 100; movie encode
> /Users/hrishikeshdas/Desktop/rock2.mp4; stop

Expected a number or a keyword  

> movie record

Already recording a movie  

> movie record

Already recording a movie  

> stop movie

Expected fewer arguments  

> movie stop

> movie record

> turn y 90 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> movie record

> turn y 90 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> movie record

> turn x 90 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock2.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock2.mp4  
  

> stop

> movie record

> turn y 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock2.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock2.mp4  
  

> stop

> movie record

> turn x 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> movie record

> turn x 70 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> movie record

> turn x 80 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> dlabels text Sb23 blcks Ace2 binding; color black; size 12; xpos 0; ypos 0

Unknown command: dlabels text Sb23 blcks Ace2 binding; color black; size 12;
xpos 0; ypos 0  

> 2dlabels text Sb23 blcks Ace2 binding; color black; size 12; xpos 0; ypos 0

Expected a keyword  

> 2dlabels text Sb23 blcks Ace2 binding; color black; size 12; xpos 0; ypos 0;
> bold true; visibility true

Expected a keyword  

> 2dlabels text 'Sb23 blcks Ace2 binding'; color black; size 12; xpos 0; ypos
> 0; bold true; visibility true

Invalid "text" argument: incomplete quoted text  

> 2dlabels text "Sb23 blcks Ace2 binding" color black

> size 12; xpos 0; ypos 0; bold true; visibility true

Expected a keyword  

> 2dlabels text 'Sb23 blcks Ace2 binding'; size 12; xpos 0; ypos 0; bold true;
> visibility true

Invalid "text" argument: incomplete quoted text  

> 2dlabels text "Sb23 blcks Ace2 binding" size 12

> xpos 0; ypos 0; bold true; visibility true

Unknown command: xpos 0; ypos 0; bold true; visibility true  

> show #!3 models

> 2dlabels text "Sb23 blocks Ace2 binding" color red size 26 xpos 0.03 ypos
> 0.09

> wait 60

> hide #!5 models

> close #5

> 2dlabels text "Sb23 blocks Ace2 binding" color red size 26 xpos 0.06 ypos
> 0.09

> wait 60

> 2dlabels text "Sb23 blocks Ace2 binding" color red size 26 xpos 1 ypos 0.09

> wait 60

> close #5

> 2dlabels text "Sb23 blocks Ace2 binding" color red size 26 xpos 0.1 ypos 0.1

> wait 60

> close #5

> ui mousemode right clip

> ui mousemode right clip

> undo

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo  
inst.undo()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo  
self._update_owner(owner, attribute, old_value, option)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 417, in _update_owner  
setattr(owner, attribute, value)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 243, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 309, in _set_display  
Drawing.set_display(self, display)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 337, in set_display  
dp = self.display_positions  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
undo failed: object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> undo

> undo

> hide #!2 models

> show #!2 models

> show #!1-2 cartoons

> show #!1-2 cartoons

> hide #!2 models

> show #!2 models

> ui mousemode right clip

> ui mousemode right "clip rotate"

> ui mousemode right pivot

> ui mousemode right pivot

> ui mousemode right pivot

> ui mousemode right "translate selected atoms"

> ui mousemode right select

> hide #!2 models

> show #!2 models

> select #2

45287 atoms, 45941 bonds, 34 pseudobonds, 4 models selected  

> ~select #2

3 models selected  

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> show #!3 models

> show #!4 models

> ui mousemode right zone

> zone #4/A:388

> zone #1/E:95

> ui mousemode right zone

> ui mousemode right zone

> ui mousemode right pivot

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/hrishikeshdas/Desktop/movie1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/movie1.mp4  
  

> hide #!1 models

> show #!1 models

> hide cartoons

> show cartoons

> close #1.1

> close

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/2upmodelandmap_new/2up_Sb23_complete-
> coot-2.pdb format pdb

Chain information for 2up_Sb23_complete-coot-2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/1upmodandmap_new/1up_Sb23_complete-
> coot-1.pdb format pdb

Chain information for 1up_Sb23_complete-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> set bgColor white

> hide atoms

> show cartoons

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2up_Sb23_complete-coot-2.pdb, chain A (#1) with 1up_Sb23_complete-
coot-1.pdb, chain A (#2), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> lighting soft

> open
> /Users/hrishikeshdas/Downloads/cryosparc_P18_J28_class_00_final_volume.mrc

Opened cryosparc_P18_J28_class_00_final_volume.mrc, grid size 256,256,256,
pixel 2.39, shown at level 0.0725, step 1, values float32  

> volume #3 level 0.1084

> volume #3 level 0.1706

> hide #!2 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> volume #3 level 0.1203

> hide #!3 target m

> show #!2 models

> show #!1 models

> show #!3 models

> hide #!3 models

> close #3

> preset cartoons/nucleotides cylinders/stubs

Changed 90071 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select #1/D#2/D

1774 atoms, 1816 bonds, 2 models selected  

> ui tool show "Color Actions"

> color sel khaki

> select #1/E#2/E

1764 atoms, 1806 bonds, 2 models selected  

> color sel khaki

> select #1/F#2/F

1774 atoms, 1816 bonds, 2 models selected  

> color sel khaki

> show sel surfaces

> color sel khaki

> select #1/E#2/E

1764 atoms, 1806 bonds, 2 models selected  

> show sel surfaces

> color sel khaki

> select #1/D#2/D

1774 atoms, 1816 bonds, 2 models selected  

> color sel khaki

> show sel surfaces

> color sel khaki

> hide sel surfaces

> surface hidePatches (#!1-2 & sel)

> select #1/E#2/E

1764 atoms, 1806 bonds, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select #1/F#2/F

1774 atoms, 1816 bonds, 2 models selected  

> hide sel surfaces

> select clear

> tile columns 2

> 2dlabels text "Blue Fluorescent Protein" color light sea green size 26 xpos
> .03 ypos .92

> wait 60

> 2dlabels text Sb23 color black bold true size 26 xpos .03 ypos .92

> wait 60

> close #3.1

> 2dlabels text Sb23 color black bold true size 26 xpos .02 ypos .92

> wait 60

> close #3.2

> 2dlabels text Sb23 color black bold true size 26 xpos .07 ypos .92

> wait 60

> select #3.1

1 model selected  

> close #3.1

> 2dlabels #1 text "'1-up" Sb23' color black bold true size 26 x .07 y .92;
> wait 60

Expected a keyword  

> 2dlabels #1:text ''1-up' Sb23' color black bold true size 26 x .07 y .92;
> wait 60

Expected a keyword  

> 2dlabels #1: text ''1-up' Sb23' color black bold true size 26 x .07 y .92;
> wait 60

Expected a keyword  

> 2dlabels #1 text "-up Sb23" color black bold true size 26 xpos .07 ypos .92

> wait 60

> hide #3.2 models

> show #3.2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> ui mousemode right "move label"

> select #3.2

1 model selected  

> 2dlabels #3.2 xpos 0.340 ypos 0.907

> ui mousemode right label

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> ui mousemode right "move label"

> 2dlabels #3.2 xpos 0.457 ypos 0.913

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/1upmodandmap_new/cryosparc_P13_J235_006_volume_map_sharp_local.mrc

Opened cryosparc_P13_J235_006_volume_map_sharp_local.mrc, grid size
600,600,600, pixel 1.02, shown at level 0.0415, step 4, values float32  

> volume #4 level 0.09506

> volume #4 step 1

> volume #4 level 0.1285

> matchmaker #1 to #2

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 1up_Sb23_complete-coot-1.pdb, chain A (#2) with 2up_Sb23_complete-
coot-2.pdb, chain A (#1), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> close #3

> close #4

> hide #!2 models

> tile

> show #!2 models

> hide #!1 models

> tile

> matchmaker #1 to #2

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 1up_Sb23_complete-coot-1.pdb, chain A (#2) with 2up_Sb23_complete-
coot-2.pdb, chain A (#1), sequence alignment score = 5571.3  
RMSD between 1072 pruned atom pairs is 0.001 angstroms; (across all 1072
pairs: 0.001)  
  

> show #!1 models

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/1upmodandmap_new/cryosparc_P13_J235_006_volume_map_sharp_local.mrc

Opened cryosparc_P13_J235_006_volume_map_sharp_local.mrc, grid size
600,600,600, pixel 1.02, shown at level 0.0415, step 4, values float32  

> select #3

2 models selected  

> ui mousemode right "translate selected models"

> volume #3 level 0.1865

> volume #3 step 1

> hide #!2 models

> hide #!1 models

> tile

> show #!2 models

> show #!1 models

> ui tool show "Fit in Map"

Fit molecule 1up_Sb23_complete-coot-1.pdb (#2) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 47232 atoms  
average map value = 0.003865, steps = 116  
shifted from previous position = 8.41  
rotated from previous position = 3.09 degrees  
atoms outside contour = 47232, contour level = 0.18647  
  
Position of 1up_Sb23_complete-coot-1.pdb (#2) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99899932 0.02146099 0.03924000 -4.21252113  
-0.02165787 0.99975486 0.00459893 -189.61255966  
-0.03913168 -0.00544418 0.99921923 176.07148963  
Axis -0.11157476 0.87067712 -0.47903279  
Axis point 1434.74121412 -0.00000000 851.84707138  
Rotation angle (degrees) 2.57953486  
Shift along axis -248.96532490  
  
Fit molecule 1up_Sb23_complete-coot-1.pdb (#2) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 47232 atoms  
average map value = 0.003865, steps = 48  
shifted from previous position = 0.0033  
rotated from previous position = 0.00182 degrees  
atoms outside contour = 47232, contour level = 0.18647  
  
Position of 1up_Sb23_complete-coot-1.pdb (#2) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99899970 0.02146529 0.03922811 -4.21207769  
-0.02166324 0.99975461 0.00462780 -189.61993316  
-0.03911914 -0.00547298 0.99921957 176.07368437  
Axis -0.11222814 0.87050419 -0.47919443  
Axis point 1434.14329989 0.00000000 856.21306562  
Rotation angle (degrees) 2.57924280  
Shift along axis -248.96576168  
  

> select #2

47232 atoms, 47882 bonds, 38 pseudobonds, 2 models selected  
Fit molecule 1up_Sb23_complete-coot-1.pdb (#2) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 47232 atoms  
average map value = 0.3043, steps = 112  
shifted from previous position = 8.35  
rotated from previous position = 2.57 degrees  
atoms outside contour = 13449, contour level = 0.18647  
  
Position of 1up_Sb23_complete-coot-1.pdb (#2) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99998762 0.00454379 -0.00203022 -0.81700408  
-0.00454282 0.99998957 0.00048104 1.34106598  
0.00203239 -0.00047181 0.99999782 -0.40720791  
Axis -0.09529482 -0.40630332 -0.90875547  
Axis point 286.11298064 182.62020088 0.00000000  
Rotation angle (degrees) 0.28645048  
Shift along axis -0.09697089  
  

> ~select #2

3 models selected  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/2upmodelandmap_new/cryosparc_P13_J233_008_volume_map_sharp_local.mrc

Opened cryosparc_P13_J233_008_volume_map_sharp_local.mrc, grid size
600,600,600, pixel 1.02, shown at level 0.059, step 4, values float32  

> select #4

2 models selected  

> volume #4 level 0.1768

> volume #4 step 1

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> hide #!1 models

> hide #!2 models

> volume #4 color #b2b2b2

> volume #3 color #ffb2b2

> volume #3 color #b2b2b2

> lighting soft

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

Fit map cryosparc_P13_J235_006_volume_map_sharp_local.mrc in map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc using 265166 points  
correlation = 0.2931, correlation about mean = 0.01436, overlap = 474.2  
steps = 300, shift = 20, angle = 9.95 degrees  
  
Position of cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98495350 -0.08739179 -0.14909489 -84.24310528  
0.08804613 0.99611393 -0.00221895 -41.93874386  
0.14870941 -0.01094166 0.98882040 -70.61585078  
Axis -0.02522850 -0.86133242 0.50741500  
Axis point 437.34022369 0.00000000 -608.75709414  
Rotation angle (degrees) 9.95497301  
Shift along axis 2.41698511  
  

> tile columns 2

> hide #!4 models

> tile

> show #!4 models

> tile columns 2

> ~select #1

3 models selected  

> tile columns 2

> tile columns 2

> ui tool show "Volume Viewer"

> tile columns 2

> tile columns 2

> tile

> tile

> show #!2 models

> hide #!4 models

> tile

> show #!1 models

> show #!3 models

> show #!4 models

> hide #!2 models

> hide #!1 models

> tile columns 2

> tile columns 2

> dust hide #1 size 5

Unknown command: dust hide #1 size 5  

> dust #3 size 5

Unknown command: dust #3 size 5  

> dust hide #3 size 5

Unknown command: dust hide #3 size 5  

> hide dust #3 size 5

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> surface dust #3 size 5

> surface dust #4 size 5

> tile columns 2

> volume #3 level 0.1601

> volume #4 level 0.1513

> volume #4 level 0.1641

> show #!2 models

> hide #!2 models

> show #!2 models

> select #2

47232 atoms, 47882 bonds, 38 pseudobonds, 2 models selected  

> ui tool show "Fit in Map"

Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 45287 atoms  
average map value = 0.004506, steps = 88  
shifted from previous position = 2.34  
rotated from previous position = 1.7 degrees  
atoms outside contour = 45287, contour level = 0.16009  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.98932386 0.07308802 0.12608107 -65.59327107  
-0.07398033 0.99725681 0.00240302 19.11470867  
-0.12555957 -0.01170489 0.99201703 246.99595612  
Axis -0.04834676 0.86235391 -0.50399238  
Axis point 1502.65779920 0.00000000 687.68457882  
Rotation angle (degrees) 8.38959322  
Shift along axis -104.82921456  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 45287 atoms  
average map value = 0.004506, steps = 60  
shifted from previous position = 0.00303  
rotated from previous position = 0.00301 degrees  
atoms outside contour = 45287, contour level = 0.16009  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.98932990 0.07305572 0.12605241 -65.57549822  
-0.07395164 0.99725885 0.00243630 19.09448576  
-0.12552890 -0.01173209 0.99202059 246.99089258  
Axis -0.04856716 0.86238396 -0.50391976  
Axis point 1503.12375346 0.00000000 687.84404652  
Rotation angle (degrees) 8.38730660  
Shift along axis -104.81199799  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 45287 atoms  
average map value = 0.004508, steps = 48  
shifted from previous position = 0.021  
rotated from previous position = 0.00472 degrees  
atoms outside contour = 45287, contour level = 0.16009  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.98933987 0.07298332 0.12601607 -65.56391224  
-0.07387799 0.99726432 0.00243446 19.07930254  
-0.12549366 -0.01171833 0.99202521 246.97461896  
Axis -0.04853634 0.86254093 -0.50365402  
Axis point 1503.90854258 0.00000000 687.84868295  
Rotation angle (degrees) 8.38336641  
Shift along axis -104.75084829  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 45287 atoms  
average map value = 0.004505, steps = 48  
shifted from previous position = 0.0232  
rotated from previous position = 0.0105 degrees  
atoms outside contour = 45287, contour level = 0.16009  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.98931613 0.07312993 0.12611746 -65.61287428  
-0.07401995 0.99725392 0.00237889 19.13471244  
-0.12559717 -0.01168869 0.99201246 247.00578107  
Axis -0.04819156 0.86230324 -0.50409394  
Axis point 1502.09172001 0.00000000 687.56555324  
Rotation angle (degrees) 8.39257466  
Shift along axis -104.85220710  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 45287 atoms  
average map value = 0.004506, steps = 48  
shifted from previous position = 0.00873  
rotated from previous position = 0.00333 degrees  
atoms outside contour = 45287, contour level = 0.16009  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.98932196 0.07307662 0.12610257 -65.60161097  
-0.07396902 0.99725765 0.00240251 19.11357033  
-0.12558119 -0.01170454 0.99201430 247.00415195  
Axis -0.04833958 0.86242573 -0.50387017  
Axis point 1502.66011378 0.00000000 687.64016998  
Rotation angle (degrees) 8.39033754  
Shift along axis -104.80283506  
  
Fit molecule 1up_Sb23_complete-coot-1.pdb (#2) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 47232 atoms  
average map value = 0.3043, steps = 176  
shifted from previous position = 20  
rotated from previous position = 9.96 degrees  
atoms outside contour = 9733, contour level = 0.16009  
  
Position of 1up_Sb23_complete-coot-1.pdb (#2) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99998757 0.00453951 -0.00206105 -0.80073434  
-0.00453850 0.99998958 0.00049217 1.33389877  
0.00206326 -0.00048281 0.99999775 -0.41776512  
Axis -0.09731705 -0.41166849 -0.90612275  
Axis point 285.09177328 179.15906755 0.00000000  
Rotation angle (degrees) 0.28701071  
Shift along axis -0.09265250  
  

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> show #!1 models

Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.1004, steps = 160  
shifted from previous position = 13  
rotated from previous position = 9.59 degrees  
atoms outside contour = 36960, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98706610 -0.15010453 0.05629513 39.46826206  
0.15235792 0.98759023 -0.03811294 -38.43388276  
-0.04987559 0.04619700 0.99768645 -50.32100584  
Axis 0.25436141 0.32031496 0.91252320  
Axis point 177.76542501 329.28353305 0.00000000  
Rotation angle (degrees) 9.53956496  
Shift along axis -48.19083059  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.3732, steps = 128  
shifted from previous position = 5.96  
rotated from previous position = 9.58 degrees  
atoms outside contour = 10029, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999743 0.00135555 0.00181534 -0.92476119  
-0.00135518 0.99999906 -0.00020156 0.41963921  
-0.00181561 0.00019910 0.99999833 0.62384702  
Axis 0.08807679 0.79820625 -0.59591045  
Axis point 304.32790814 0.00000000 504.10840738  
Rotation angle (degrees) 0.13031606  
Shift along axis -0.11824832  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.3732, steps = 96  
shifted from previous position = 0.00692  
rotated from previous position = 0.00247 degrees  
atoms outside contour = 10017, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999738 0.00133853 0.00185488 -0.93645389  
-0.00133816 0.99999908 -0.00020145 0.41010385  
-0.00185514 0.00019897 0.99999826 0.63904049  
Axis 0.08719319 0.80787790 -0.58286417  
Axis point 305.41469338 0.00000000 499.51838829  
Rotation angle (degrees) 0.13155987  
Shift along axis -0.12281237  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.3732, steps = 44  
shifted from previous position = 0.0103  
rotated from previous position = 0.00402 degrees  
atoms outside contour = 10024, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999724 0.00134739 0.00192285 -0.95256285  
-0.00134704 0.99999908 -0.00018660 0.40515370  
-0.00192310 0.00018401 0.99999813 0.67046722  
Axis 0.07867866 0.81646672 -0.57200678  
Axis point 310.19010080 0.00000000 490.61147963  
Rotation angle (degrees) 0.13494559  
Shift along axis -0.12766366  
  

> tile columns 2

> hide #!1 models

> hide #!2 models

> tile columns 2

> 2dlabels text Sb23 color black bold true size 26 xpos .07 ypos .92

> wait 60

> 2dlabels text "'1-up" conformation' color black bold true size 26 x .07 y
> .92; wait 60

Expected a keyword  

> 2dlabels text "1-up conformation" color black bold true size 26 xpos .07
> ypos .92

> wait 60

> close #5.1

> ui mousemode right "move label"

> 2dlabels #5.2 xpos 0.142 ypos 0.808

> 2dlabels #5.2 xpos 0.142 ypos 0.808

> 2dlabels text "2-up conformation" color black bold true size 26 xpos .07
> ypos .92

> wait 60

> 2dlabels #5.1 xpos 0.593 ypos 0.811

> 2dlabels #5.1 xpos 0.592 ypos 0.813

> ui mousemode right "tape measure"

> ui mousemode right "move label"

> 2dlabels #5.1 xpos 0.610 ypos 0.813

> 2dlabels #5.2 xpos 0.138 ypos 0.810

> show #!2 models

> select #2

47232 atoms, 47882 bonds, 38 pseudobonds, 2 models selected  

> ui mousemode right "translate selected atoms"

Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.001696, steps = 120  
shifted from previous position = 4.77  
rotated from previous position = 4.37 degrees  
atoms outside contour = 45287, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99979881 -0.00128998 0.02001698 -36.23807238  
0.00277200 0.99724042 -0.07418797 232.26855734  
-0.01986605 0.07422853 0.99704336 187.40577035  
Axis 0.96540142 0.25942625 0.02642187  
Axis point 0.00000000 -2389.91903298 3114.02061629  
Rotation angle (degrees) 4.40854700  
Shift along axis 30.22388374  
  
Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.002567, steps = 212  
shifted from previous position = 15  
rotated from previous position = 4.34 degrees  
atoms outside contour = 45287, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99741832 0.05398250 0.04735585 -63.61392462  
-0.04798278 0.99164019 -0.11978060 250.98899302  
-0.05342602 0.11719910 0.99167032 178.94867642  
Axis 0.85561002 0.36387075 -0.36814341  
Axis point 0.00000000 -1274.34177924 2272.38142407  
Rotation angle (degrees) 7.96023601  
Shift along axis -28.97993388  
  

> ui mousemode right "rotate selected models"

Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.002542, steps = 120  
shifted from previous position = 0.632  
rotated from previous position = 1.18 degrees  
atoms outside contour = 45287, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99806544 0.04976873 0.03726186 -59.65996139  
-0.04572795 0.99369250 -0.10239228 244.14175117  
-0.04212277 0.10049029 0.99404596 179.35911299  
Axis 0.85290809 0.33372899 -0.40146326  
Axis point 0.00000000 -1464.77414249 2609.58797904  
Rotation angle (degrees) 6.83068712  
Shift along axis -41.41337914  
  

> show #!1 models

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> ui mousemode right "translate selected atoms"

> 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 mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

Fit molecule 2up_Sb23_complete-coot-2.pdb (#1) to map
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) using 45287 atoms  
average map value = 0.3732, steps = 284  
shifted from previous position = 22.4  
rotated from previous position = 13.5 degrees  
atoms outside contour = 10032, contour level = 0.16406  
  
Position of 2up_Sb23_complete-coot-2.pdb (#1) relative to
cryosparc_P13_J233_008_volume_map_sharp_local.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999720 0.00133250 0.00192459 -3.34039511  
-0.00133230 0.99999904 -0.00010228 144.16921566  
-0.00192471 0.00009972 0.99999802 -118.61226365  
Axis 0.04310678 0.82143773 -0.56866674  
Axis point -6755.83808752 0.00000000 5886.07137485  
Rotation angle (degrees) 0.13424564  
Shift along axis 185.73288885  
  

> select #2

47232 atoms, 47882 bonds, 38 pseudobonds, 2 models selected  
Fit molecule 1up_Sb23_complete-coot-1.pdb (#2) to map
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) using 47232 atoms  
average map value = 0.3043, steps = 132  
shifted from previous position = 13.4  
rotated from previous position = 13 degrees  
atoms outside contour = 9745, contour level = 0.16009  
  
Position of 1up_Sb23_complete-coot-1.pdb (#2) relative to
cryosparc_P13_J235_006_volume_map_sharp_local.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99998745 0.00455767 -0.00207978 18.19385008  
-0.00455691 0.99998955 0.00037141 -1.35990596  
0.00208145 -0.00036193 0.99999777 198.74501778  
Axis -0.07299496 -0.41420362 -0.90725250  
Axis point -16754.91580342 -1137.95416461 0.00000000  
Rotation angle (degrees) 0.28780812  
Shift along axis -181.07669535  
  

> volume #4 level 0.1598

> volume #4 level 0.1342

> volume #3 level 0.1454

> ui mousemode right "move label"

> select #5.1

1 model selected  

> 2dlabels #5.1 xpos 0.622 ypos 0.844

> color sel red

> color sel purple

> color sel black

> 2dlabels #5.1 xpos 0.626 ypos 0.863

> select #5.2

1 model selected  

> 2dlabels #5.2 xpos 0.140 ypos 0.864

> 2dlabels #5.2 xpos 0.139 ypos 0.861

> hide #!1 models

> hide #!2 models

> ui mousemode right pivot

> ui mousemode right pivot

> ui mousemode right distance

> ui mousemode right label

> label delete residues

> label delete residues

> ui mousemode right label

> ui mousemode right "move label"

> ui mousemode right clip

> ui mousemode right "move label"

> 2dlabels #5.1 xpos 0.626 ypos 0.863

> ~select #5.2

Nothing selected  

> select #5

3 models selected  

> 2dlabels #5.1 xpos 0.626 ypos 0.863

> ~select #5

Nothing selected  

> select #5.1

1 model selected  

> ~select #5.1

Nothing selected  

> select #5.1

1 model selected  

> ~select #5.1

Nothing selected  

> movie record

> turn y 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> select #5.1

1 model selected  

> ui mousemode right "clip rotate"

> select #5

3 models selected  

> movie record

> turn y 50 rock 100

> wait 100

> movie encode /Users/hrishikeshdas/Desktop/rock1.mp4

Movie saved to /Users/hrishikeshdas/Desktop/rock1.mp4  
  

> stop

> show #!1 models

> select #1:d

Nothing selected  

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> label sel text "2-up conformation" color black bold true size 26 x .07 y
> .92; wait 60

Expected a keyword  

> label sel text "2-up conformation" color black bold true size 26 x .07 y .92

Expected a keyword  

> Place label here (at center of rotation)

Unknown command: Place label here (at center of rotation)  

> Place label here

Unknown command: Place label here  

> ui mousemode right label

> label delete residues

> label delete residues

> Place label here

Unknown command: Place label here  

> ui mousemode right label

> label delete residues

> label delete residues

> label delete residues

> label #1/F:94

> ui mousemode right "move label"

> ui mousemode right label

> label #1/F:117

> label_here ‘2-up conformation’color black bold true size 26

Unknown command: label_here ‘2-up conformation’color black bold true size 26  

> label_here ‘2-up conformation’ color black bold true size 26

Unknown command: label_here ‘2-up conformation’ color black bold true size 26  

> ui mousemode right label

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 3 models selected  

> ~select #1

3 models selected  

> ui mousemode right select

> select #1/F:119

5 atoms, 4 bonds, 1 model selected  

> label_here ‘2-up conformation’ color black bold true size 26

Unknown command: label_here ‘2-up conformation’ color black bold true size 26  

> Place label here

Unknown command: Place label here  

> ui mousemode right label

> label #1/F:119

> place label here

Unknown command: place label here  

> label_here ‘2-up conformation’ color black bold true size 26

Unknown command: label_here ‘2-up conformation’ color black bold true size 26  

> label sel ‘2-up conformation’ color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label here

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label delete residues

> label sel

> label_here ‘2-up conformation’color black bold true size 26

Unknown command: label_here ‘2-up conformation’color black bold true size 26  

> label here ‘2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> show (#!1 & sel) target ab

> cartoon hide (#!1 & sel)

> select #1

45287 atoms, 45941 bonds, 34 pseudobonds, 3 models selected  

> ~select #1

3 models selected  

> ui mousemode right select

> select clear

> label here ‘2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel ‘2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label ‘2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label ‘sel here 2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel here ' 2-up conformation’color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label_here ~sel ' 2-up conformation’color black bold true size 26

Unknown command: label_here ~sel ' 2-up conformation’color black bold true
size 26  

> label_here sel ' 2-up conformation’color black bold true size 26

Unknown command: label_here sel ' 2-up conformation’color black bold true size
26  

> label_sel ' 2-up conformation’color black bold true size 26

Unknown command: label_sel ' 2-up conformation’color black bold true size 26  

> label_sel '2-up conformation’color black bold true size 26

Unknown command: label_sel '2-up conformation’color black bold true size 26  

> label_sel '2-up conformation’ color black bold true size 26

Unknown command: label_sel '2-up conformation’ color black bold true size 26  

> label_sel '2-up conformation’

Unknown command: label_sel '2-up conformation’  

> label_here '2-up conformation’

Unknown command: label_here '2-up conformation’  
incomplete quoted text  

> label here

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label_here

Unknown command: label_here  

> label_here

Unknown command: label_here  

> ui mousemode right label

> label delete residues

> label #1/F:119

> label_here

Unknown command: label_here  

> label

> hide #!3 models

> hide #!4 models

> show #!4 models

> show #!3 models

> 2dlabels text "2-up conformation" color black bold true size 26 xpos .07
> ypos .92

> wait 60

> 2dlabels here text '2-up conformation' color black bold true size 26 x .07 y
> .92; wait 60

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlab_here text '2-up conformation' color black bold true size 26 x .07 y
> .92; wait 60

Unknown command: 2dlab_here text '2-up conformation' color black bold true
size 26 x .07 y .92; wait 60  

> label_here text '2-up conformation' color black bold true size 26 x .07 y
> .92; wait 60

Unknown command: label_here text '2-up conformation' color black bold true
size 26 x .07 y .92; wait 60  

> label text "2-up conformation" color black bold true size 26 x .07 y .92;
> wait 60

Expected a keyword  

> label sel text "2-up conformation" color black bold true size 26 x .07 y
> .92; wait 60

Expected a keyword  

> label_sel text '2-up conformation' color black bold true size 26 x .07 y
> .92; wait 60

Unknown command: label_sel text '2-up conformation' color black bold true size
26 x .07 y .92; wait 60  

> label_sel

Unknown command: label_sel  

> label sel

> label sel atoms

> label_here ‘text 2-up conformation’ color black bold true size 26

Unknown command: label_here ‘text 2-up conformation’ color black bold true
size 26  

> label here ‘text 2-up conformation’ color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel ‘text 2-up conformation’ color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel text '2-up conformation’ color black bold true size 26

Invalid "text" argument: Expected 'default' or a text string  

> label label sel atoms text '2-up conformation’ color black bold true size 26

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> ui mousemode right select

> select clear

> label sel atoms text '2-up conformation’ color black bold true size 26

Invalid "text" argument: Expected 'default' or a text string  
incomplete quoted text  

> label sel atoms "2-up conformation" color black bold true size 26

Expected a keyword  

> label sel atoms "2-up conformation" color black

Expected a keyword  

> label sel atoms "2-up conformation" color black

Expected a keyword  

> label sel atoms:"2-up conformation" color black

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel atoms: "2-up conformation" color black

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label sel atoms

> "2-up conformation" color black

Unknown command: "2-up conformation" color black  

> label sel atoms "2-up conformation" color black

Expected a keyword  

> label sel atoms '2-up conformation' color black

Expected a keyword  

> label ligand atoms text "2-up conformation" color black

> hide #5.3 models

> show #5.3 models

> close

> undo

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo  
inst.undo()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo  
self._update_owner(owner, attribute, old_value, option)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 417, in _update_owner  
setattr(owner, attribute, value)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 243, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 309, in _set_display  
Drawing.set_display(self, display)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 337, in set_display  
dp = self.display_positions  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
undo failed: object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 350, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> close #

Expected a models specifier or a keyword  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/1upmodandmap_new/1up_Sb23_complete-
> coot-1.pdb format pdb

Chain information for 1up_Sb23_complete-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> open
> /Users/hrishikeshdas/Documents/Cororna_projects/Covid_chirsitisan/Sb23/2upmodelandmap_new/2up_Sb23_complete-
> coot-2.pdb format pdb

Chain information for 2up_Sb23_complete-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D F | No description available  
E | No description available  
  

> show atoms

> hide atoms

> show cartoons

> select clear

> ui mousemode right zoom

> ui mousemode right select

> select #2/F:119

5 atoms, 4 bonds, 1 model selected  

> show sel target ab

> cartoon hide sel

> select #2

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> ui mousemode right select

> ui mousemode right select

> select #2/F:119@O

1 atom, 1 model selected  

> label ligand atoms text "2-up conformation" color black

> select #1.2

1 model selected  

> ~select #1.2

Nothing selected  

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> label ligand atoms text "2-up conformation" color light sea green size 26 x
> .03 y .92; wait 60

Expected a keyword  

> select #1.2

1 model selected  

> hide #1.1 models

> hide #!1 models

> hide #!2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #1.1 models

> close #1

> close #2.2

> select /F:119@O

1 atom, 1 model selected  

> label ligand atoms text "2-up conformation" color light sea green size 26

> hide #2.2 models

> show #2.2 models

> select #2.2

1 model selected  

> label ligand atoms text "2-up conformation" color light sea green size 111

> ~select #2.2

Nothing selected  

> select #2.2

1 model selected  

> hide #2.2 models

> show #2.2 models

> ui mousemode right label

> label #2/F:119

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 248, in _draw_scene  
pixel_width = self._highlight_width)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1494, in draw_highlight_outline  
_draw_multiple(drawings, r, Drawing.HIGHLIGHT_DRAW_PASS)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1438, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 716, in draw  
self.draw_self(renderer, draw_pass)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 730, in draw_self  
self._draw_geometry(renderer, highlighted_only = True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 762, in _draw_geometry  
t.bind_texture()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2892, in bind_texture  
self.fill_opengl_texture()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2927, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2829, in initialize_texture  
tdtype, data)  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1281,  
description = b'invalid value',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
2048,  
75888,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
2048,  
75888,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
2048,  
75888,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
)  
)  
  

> label ligand atoms text "2-up conformation" color light sea green size 50

> label #2/F:119

> ui mousemode right select

> select /F:119@O

1 atom, 1 model selected  

> select /F:119@O

1 atom, 1 model selected  

> select /F:119@N

1 atom, 1 model selected  

> close #2.2

> close #

Expected a models specifier or a keyword  

> ~select #

> select subtract #

Expected an objects specifier or a keyword  

> select #

Expected an objects specifier or a keyword  

> hide # models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select /F:119@N

1 atom, 1 model selected  

> select #2

45287 atoms, 45941 bonds, 34 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> select /F:119@N

1 atom, 1 model selected  

> label sel atoms text 2-up

> show # models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> close #

Expected a models specifier or a keyword  

> ~select #

> select subtract #

Expected an objects specifier or a keyword  

> select #

Expected an objects specifier or a keyword  

> close #

Expected a models specifier or a keyword  

> select /F:119@CB

1 atom, 1 model selected  

> select #2

45287 atoms, 45941 bonds, 34 pseudobonds, 3 models selected  

> ~select #2

Nothing selected  

> close #

Expected a models specifier or a keyword  

> select /F:119@N

1 atom, 1 model selected  

> select #2

45287 atoms, 45941 bonds, 34 pseudobonds, 3 models selected  

> ~select #2

Nothing selected  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Drag select of 3 atoms  

> select clear

> select /F:119@N

1 atom, 1 model selected  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 476, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 45, in mouse_drag  
self._draw_drag_rectangle(event)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 118, in _draw_drag_rectangle  
v.draw_xor_rectangle(dx, h-dy, x, h-y, self.drag_color)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 310, in draw_xor_rectangle  
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1534, in draw_xor_rectangle  
r.draw_front_buffer(True)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.0-rc-2020.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1151, in draw_front_buffer  
GL.glDrawBuffer(GL.GL_FRONT if front else GL.GL_BACK)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_FRONT,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Drag select of  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2,6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 3 days 12:11

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → self._positions is None during undo

There were various errors, including the one in the summary.

comment:2 by Tom Goddard, 5 years ago

Resolution:	→ duplicate
Status:	assigned → closed

There were 3 different errors in this report. I think all of them are fixed in ChimeraX 1.1. Bug report was for a pre-1.0 version of ChimeraX.

First was caused by using Undo to undo an operation on a closed model. Code was fixed to avoid attempting undo on a deleted object back in June (in ChimeraX 1.1).

Second error was trying to create a texture of size 2048 x 75888 which is larger than the OpenGL size limit. There were labels on atoms, usually it takes thousands of labels to produce this error. This was fixed a few months ago (in ChimeraX 1.1) so that it just gives a warning that too many labels were shown, and only shows as many as allowed by the OpenGL texture size limit.

Third error was drag selected could not draw to the front buffer. Possibly that was a consequence of the previous error. It seems the framebuffer stack had an extra framebuffer on it so the outline attempted to draw to an off-screen buffer instead of the window framebuffer. This error should be rereported if drag select normally produces this error on this machine.

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