lighting full: glTexImage2D: out of memory

[andysen@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\Users\andys\OneDrive\Documents\baseplate\main_baseplate\all_base3.cxs
> format session

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Wed Dec 4 16:01:10 2024UCSF ChimeraX version: 1.8rc202406102315
(2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/full_baseplate.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Mon Dec 2 17:54:21 2024UCSF ChimeraX version: 1.8rc202406102315
(2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath4.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Mon Dec 2 16:19:56 2024UCSF ChimeraX version: 1.8rc202406102315
(2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs
> format session

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Wed Nov 27 15:30:54 2024UCSF ChimeraX version: 1.8rc202406102315
(2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/baseplate_1.cxs
> format session

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Sun Jul 9 21:19:02 2023UCSF ChimeraX version: 1.6.dev202212092052
(2022-12-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Sun Jul 9 13:23:10 2023UCSF ChimeraX version: 1.6.dev202212092052
(2022-12-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp2.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Sat Jul 8 00:54:29 2023UCSF ChimeraX version: 1.6.dev202212092052
(2022-12-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Sat Jul 8 00:43:50 2023UCSF ChimeraX version: 1.6.dev202212092052
(2022-12-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32  
Log from Sat Jul 8 00:09:27 2023UCSF ChimeraX version: 1.6.dev202212092052
(2022-12-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/UpfC_af.pdb

Chain information for UpfC_af.pdb #1  
---  
Chain | Description  
9 | No description available  
  

> open
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplAminus.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplAplus.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplB_rings.cif
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/PmgA.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/PmgG.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/Tub.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/UpfC_af.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/flip_base.mrc
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp5_af.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp6_af.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp16.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_lastring.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_onebeforelastring.pdb
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_theotherrings.cif
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp26.pdb

Summary of feedback from opening
/home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplB_rings.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Atom H is not in the residue template for MET /BA:204  
Atom 1HA is not in the residue template for GLY /BA:205  
Atom 1HB is not in the residue template for HIS /BA:206  
Atom 1HB is not in the residue template for ASN /BA:207  
Atom 1HB is not in the residue template for ASN /BA:208  
Atom 1HG2 is not in the residue template for THR /BA:209  
Atom 1HB is not in the residue template for LYS /BA:210  
Atom 1HA is not in the residue template for GLY /BA:211  
Atom 1HB is not in the residue template for ASN /BA:212  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Summary of feedback from opening
/home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_theotherrings.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Atom H is not in the residue template for MET /AA:1  
Atom 1HB is not in the residue template for SER /AA:2  
Atom 1HB is not in the residue template for GLN /AA:3  
Atom 1HB is not in the residue template for TYR /AA:4  
Atom 1HB is not in the residue template for SER /AA:5  
Atom 1HG1 is not in the residue template for ILE /AA:6  
Atom 1HB is not in the residue template for GLN /AA:7  
Atom 1HB is not in the residue template for GLN /AA:8  
Atom 1HB is not in the residue template for SER /AA:9  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for BplAminus.pdb #2  
---  
Chain | Description  
Y Z a b c d | No description available  
  
Chain information for BplAplus.pdb #3  
---  
Chain | Description  
e f g h i j | No description available  
  
Chain information for BplB_rings.cif #4  
---  
Chain | Description  
BA BB BC BD BE BF BG BH BJ BK BL BN BP BQ BR BS BT BU BV BW BY Bb Bc Bd | No description available  
  
Chain information for PmgA.pdb #5  
---  
Chain | Description  
M N O P Q R | No description available  
  
Chain information for PmgG.pdb #6  
---  
Chain | Description  
G H I J K L | No description available  
  
Chain information for Tub.pdb #7  
---  
Chain | Description  
A B C D E F | No description available  
  
Chain information for UpfC_af.pdb #8  
---  
Chain | Description  
9 | No description available  
  
Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.162, step 2, values float32  
Chain information for gp5_af.pdb #10  
---  
Chain | Description  
6 7 8 | No description available  
  
Chain information for gp6_af.pdb #11  
---  
Chain | Description  
3 4 5 | No description available  
  
Chain information for gp16.pdb #12  
---  
Chain | Description  
k l m n o p | No description available  
  
Chain information for gp22_lastring.pdb #13  
---  
Chain | Description  
q r s t u v | No description available  
  
Chain information for gp22_onebeforelastring.pdb #14  
---  
Chain | Description  
1 2 w x y z | No description available  
  
Chain information for gp22_theotherrings.cif #15  
---  
Chain | Description  
AA AB AC AD AE AF AG AH AI AJ AL AM AN AO AP AQ AS AT AV AW AZ Aa Ab Ad | No description available  
  
Chain information for gp26.pdb #16  
---  
Chain | Description  
S T U V W X | No description available  
  

> set bgColor white

> transparency 50

> show cartoons

> hide atoms

> volume #9 level 0.12

> volume #9 level 0.2

> volume #9 step 1

> volume #9 level 272

> volume #9 level 0.272

> set bgColor black

> set bgColor white

> hide #!9 models

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/baseplate.cxs

> hide #14 models

> hide #15 models

> hide #13 models

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> color sel magenta

> color sel purple

> select subtract #1

Nothing selected  

> color violet

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel violet

[Repeated 1 time(s)]

> color sel medium orchid

> color sel dark violet

> color sel medium purple

> color sel blue violet

> color sel dark violet

> select subtract #1

Nothing selected  

> select add #2

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color sel yellow

> color sel gold

> color sel yellow

> color sel gold

> color sel orange

> color sel gold

> select subtract #2

Nothing selected  

> select add #3

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color sel orange

> select add #2

89976 atoms, 90984 bonds, 5724 residues, 2 models selected  

> select subtract #3

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x1527960, name="eDP-1") screenTo: QScreen(0x1527960, name="eDP-1")
wdgScreen: QScreen(0x1527960, name="eDP-1") orgWdgScreen QScreen(0x0)  

[Repeated 25 time(s)]

> select clear

> select add #4

62808 atoms, 63336 bonds, 4056 residues, 1 model selected  

> color sel peru

> select clear

> select add #4

62808 atoms, 63336 bonds, 4056 residues, 1 model selected  

> color sel peach puff

> color sel wheat

> color sel burly wood

> select clear

> select add #5

11142 atoms, 11256 bonds, 708 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select subtract #5

Nothing selected  

> select add #5

11142 atoms, 11256 bonds, 708 residues, 1 model selected  

> color sel medium aquamarine

> color sel dodger blue

> color sel dark turquoise

> color sel medium sea green

> color sel cornflower blue

> color sel sea green

> color sel spring green

> color sel dark turquoise

> color sel medium spring green

> color sel dark cyan

> color sel steel blue

> color sel medium aquamarine

> color sel dark cyan

> color sel cornflower blue

> color sel medium turquoise

> color sel light sea green

> color sel dodger blue

> color sel medium spring green

> color sel dark turquoise

> color sel dark cyan

> color sel light sea green

> color sel teal

> color sel steel blue

> color sel cadet blue

> color sel green

> color sel light slate gray

> color sel deep sky blue

> color sel dark turquoise

> color sel medium spring green

> color sel medium turquoise

> color sel light sea green

> color sel dark cyan

> select subtract #5

Nothing selected  

> select add #6

17226 atoms, 17406 bonds, 1158 residues, 1 model selected  

> color sel green

> color sel forest green

> select clear

> color medium spring green

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark magenta

> color sel dark violet

> select subtract #1

Nothing selected  

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel dark orchid

> select add #2

46304 atoms, 46820 bonds, 2956 residues, 2 models selected  

> select subtract #1

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color sel dark orchid

[Repeated 1 time(s)]

> select subtract #2

Nothing selected  

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel dark magenta

> select subtract #1

Nothing selected  

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel purple

> select add #2

46304 atoms, 46820 bonds, 2956 residues, 2 models selected  

> select subtract #1

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel dark violet

> color sel dark orchid

> color sel dark magenta

> select subtract #1

Nothing selected  

> select add #2

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color sel orange

> color sel gold

> select subtract #2

Nothing selected  

> select add #3

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color sel dark orange

> color sel orange

> select subtract #3

Nothing selected  

> select add #4

62808 atoms, 63336 bonds, 4056 residues, 1 model selected  

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x1527960, name="eDP-1") screenTo: QScreen(0x1527960, name="eDP-1")
wdgScreen: QScreen(0x1527960, name="eDP-1") orgWdgScreen QScreen(0x0)  

[Repeated 26 time(s)]

> color sel light salmon

> color sel burly wood

> select subtract #4

Nothing selected  

> select add #5

11142 atoms, 11256 bonds, 708 residues, 1 model selected  

> color sel dark turquoise

> select subtract #5

Nothing selected  

> select add #6

17226 atoms, 17406 bonds, 1158 residues, 1 model selected  

> color sel green

> color sel lawn green

> select subtract #6

Nothing selected  

> select add #6

17226 atoms, 17406 bonds, 1158 residues, 1 model selected  

> color sel green

> color sel lime green

> color sel forest green

> color sel lime green

> select subtract #6

Nothing selected  

> select add #7

16794 atoms, 16968 bonds, 1080 residues, 1 model selected  

> color sel salmon

> select subtract #7

Nothing selected  

> select add #8

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color sel dark slate blue

[Repeated 2 time(s)]

> select subtract #8

Nothing selected  

> select add #10

9078 atoms, 9180 bonds, 630 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel magenta

> color sel dark orchid

> color sel medium purple

> color sel dark orchid

> select subtract #10

Nothing selected  

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

> select add #11

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> color sel orchid

[Repeated 1 time(s)]

> color sel dark violet

> color sel slate blue

> color sel blue violet

> select subtract #11

Nothing selected  

> select add #11

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> color sel dark violet

> color sel dark orchid

> color sel medium purple

> color sel dark orchid

> color sel slate blue

> color sel dark slate blue

> color sel purple

> color sel dark orchid

> color sel dark blue

> color sel cornflower blue

> color sel dodger blue

> color sel medium slate blue

> color sel slate blue

> color sel blue violet

> select subtract #11

Nothing selected  

> select add #12

26394 atoms, 26664 bonds, 1668 residues, 1 model selected  

> color sel goldenrod

> select subtract #12

Nothing selected  

> select add #12

26394 atoms, 26664 bonds, 1668 residues, 1 model selected  

> color sel dark khaki

> select subtract #12

Nothing selected  

> select add #13

47784 atoms, 48270 bonds, 3174 residues, 1 model selected  

> color sel light steel blue

> select subtract #13

Nothing selected  

> select add #14

47784 atoms, 48270 bonds, 3174 residues, 1 model selected  

> color sel wheat

> select add #15

238920 atoms, 241350 bonds, 15870 residues, 2 models selected  

> select subtract #14

191136 atoms, 193080 bonds, 12696 residues, 1 model selected  

> color sel plum

> select add #16

203346 atoms, 205410 bonds, 13446 residues, 2 models selected  

> color sel dark sea green

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x1527960, name="eDP-1") screenTo: QScreen(0x1527960, name="eDP-1")
wdgScreen: QScreen(0x1527960, name="eDP-1") orgWdgScreen QScreen(0x0)  

[Repeated 67 time(s)]

> select subtract #15

12210 atoms, 12330 bonds, 750 residues, 1 model selected  

> select subtract #16

Nothing selected  

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

> select add #10

9078 atoms, 9180 bonds, 630 residues, 1 model selected  

> select subtract #10

Nothing selected  

> select add #11

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark orchid

> color sel dark magenta

> color sel slate blue

> color sel dark slate blue

> color sel magenta

> color sel blue violet

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

——— End of log from Sat Jul 8 00:09:27 2023 ———

opened ChimeraX session  

> select add #1

16979 atoms, 17153 bonds, 1108 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel magenta

> color sel hot pink

> color sel medium violet red

> select subtract #1

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> select add #1

16979 atoms, 17153 bonds, 1108 residues, 2 models selected  

> color sel deep pink

> color sel purple

> color sel medium violet red

> select subtract #1

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

——— End of log from Sat Jul 8 00:43:50 2023 ———

opened ChimeraX session  

> show sel atoms

> hide sel atoms

> ui tool show "Color Actions"

> color sel slate blue

> color sel blue violet

> color sel dark orchid

> color sel blue violet

> color sel royal blue

> color sel indigo

> color sel dark blue

> color sel medium blue

> color sel cornflower blue

> color sel midnight blue

> color sel dark slate blue

> color sel medium slate blue

> color sel dark blue

> color sel navy

> color sel indigo

> color sel steel blue

> color sel navy

> color sel indigo

> color sel slate blue

> color sel medium slate blue

> color sel blue violet

> color sel dark violet

[Repeated 1 time(s)]

> color sel blue violet

> color sel slate blue

> select subtract #11

Nothing selected  

> show #1-8,10-12,16 atoms

> hide #1-8,10-12,16 cartoons

> select add #16

12210 atoms, 12330 bonds, 750 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #16

12210 atoms, 12330 bonds, 750 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #11

15663 atoms, 15825 bonds, 1014 residues, 1 model selected  

> select subtract #11

Nothing selected  

> select add #10

9078 atoms, 9180 bonds, 630 residues, 1 model selected  

> style sel sphere

Changed 9078 atom styles  

> hide sel cartoons

> select add #1

10394 atoms, 10508 bonds, 724 residues, 2 models selected  

> style sel sphere

Changed 10394 atom styles  

> select subtract #1

9078 atoms, 9180 bonds, 630 residues, 1 model selected  

> select subtract #10

Nothing selected  

> lighting soft

> select add #9

2 models selected  

> select subtract #9

Nothing selected  

> select add #5

11142 atoms, 11256 bonds, 708 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light sea green

> color sel dark cyan

> select subtract #5

Nothing selected  

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp2.cxs

——— End of log from Sat Jul 8 00:54:29 2023 ———

opened ChimeraX session  

> hide #1-8,10-12,16 atoms

> show #1-8,10-12,16 cartoons

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting simple

> graphics silhouettes true

> lighting full

> lighting soft

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs

——— End of log from Sun Jul 9 13:23:10 2023 ———

opened ChimeraX session  

> hide #2 models

> hide #4 models

> hide #3 models

> hide #5 models

> hide #6 models

> show #6 models

> hide #12 models

> hide #11 models

> show #11 models

> hide #10 models

> show #10 models

> hide #16 models

> hide #8 models

> save /home/andy/Desktop/image9.png supersample 3

> show #4 models

> hide #4 models

> show #16 models

> hide #16 models

> show #5 models

> save /home/andy/Desktop/image10.png supersample 3

> save /home/andy/Desktop/image11.png supersample 3

> turn x 90

[Repeated 2 time(s)]

> hide #10 models

> show #10 models

> hide #11 models

> show #11 models

> hide #10 models

> show #10 models

> hide #5 models

> show #5 models

> hide #5 models

> turn x -90

> save /home/andy/Desktop/image9.png supersample 3

> turn x 90

> save /home/andy/Desktop/image10.png supersample 3

> show #5 models

> save /home/andy/Desktop/image11.png supersample 3

> turn x -90

> save /home/andy/Desktop/image12.png supersample 3

> turn x 90

> show #12 models

> hide #12 models

> show #16 models

> save /home/andy/Desktop/image13.png supersample 3

> turn x -90

> save /home/andy/Desktop/image14.png supersample 3

> turn x 90

> show #12 models

> save /home/andy/Desktop/image15.png supersample 3

> turn x -90

> save /home/andy/Desktop/image16.png supersample 3

> turn x 90

> show #2 models

> save /home/andy/Desktop/image17.png supersample 3

> turn x -90

> save /home/andy/Desktop/image18.png supersample 3

> turn x 90

> show #3 models

> save /home/andy/Desktop/image19.png supersample 3

> turn x -90

> save /home/andy/Desktop/image20.png supersample 3

> turn x 90

> show #4 models

> save /home/andy/Desktop/image21.png supersample 3

> hide #4 models

> save
> /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/baseplate.cxs

——— End of log from Sun Jul 9 21:19:02 2023 ———

opened ChimeraX session  

> color #2 #ffd70011

> color #2 #ffd70012

> color #3 #ffa50011

> color #3 #ffa50012

> color #12 #bdb76b14

> select add #16

12210 atoms, 12330 bonds, 750 residues, 1 model selected  

> select add #6

29436 atoms, 29736 bonds, 1908 residues, 2 models selected  

> select subtract #6

12210 atoms, 12330 bonds, 750 residues, 1 model selected  

> select add #5

23352 atoms, 23586 bonds, 1458 residues, 2 models selected  

> show sel surfaces

> lighting simple

> lighting full

> sel: #5/Q

Unknown command: sel: #5/Q  

> transparency sel 50

> show sel surfaces

> transparency sel 0

> select clear

> sel: #5/Q

Unknown command: sel: #5/Q  

> select #5/Q

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> transparency sel 50

> select #16/V

2035 atoms, 2055 bonds, 125 residues, 1 model selected  

> transparency sel 50

> select #16/V

2035 atoms, 2055 bonds, 125 residues, 1 model selected  

> hide sel cartoons

> show sel surfaces

> transparency sel 0

> select #5/Q

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> transparency sel 0

> select #16/X

2035 atoms, 2055 bonds, 125 residues, 1 model selected  

> surface hidePatches (#!16 & sel)

> save /Users/aninditosen/Documents/P1/baseplate/full_fig.cxs

> hide (#!16 & sel) target a

> delete atoms (#!16 & sel)

> delete bonds (#!16 & sel)

> color #2 gold

> color #3 orange

> select add #2

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> select add #3

89976 atoms, 90984 bonds, 5724 residues, 2 models selected  

> select add #12

116370 atoms, 117648 bonds, 7392 residues, 3 models selected  

> show sel cartoons

> show sel surfaces

> select subtract #12

89976 atoms, 90984 bonds, 5724 residues, 20 models selected  

> select subtract #3

44988 atoms, 45492 bonds, 2862 residues, 13 models selected  

> color #2 gold

> color #2 #ffd700d3

> color #2 gold

> color #2 #ffd70021

> color #2 gold

> hide sel surfaces

> select subtract #2

6 models selected  

> select add #3

44988 atoms, 45492 bonds, 2862 residues, 1 model selected  

> color #3 orange

> hide sel surfaces

> color #12 darkkhaki

> hide sel surfaces

> select add #12

71382 atoms, 72156 bonds, 4530 residues, 8 models selected  

> hide sel surfaces

> select clear

> select #2/d

7498 atoms, 7582 bonds, 477 residues, 1 model selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #12/p

4399 atoms, 4444 bonds, 278 residues, 1 model selected  

> delete atoms (#!12 & sel)

> delete bonds (#!12 & sel)

> select #3/j

7498 atoms, 7582 bonds, 477 residues, 1 model selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> save
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs

> select #5/P

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> surface hidePatches (#!5 & sel)

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #2/c

7498 atoms, 7582 bonds, 477 residues, 1 model selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> show #4 models

> show #13 models

> save
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs

——— End of log from Wed Nov 27 15:30:54 2024 ———

opened ChimeraX session  

> show #1,4,6-7,10-11,13#!2-3,5,12,16 surfaces

> select add #7

16794 atoms, 16968 bonds, 1080 residues, 1 model selected  

> select add #4

79602 atoms, 80304 bonds, 5136 residues, 8 models selected  

> hide sel cartoons

> transparency sel 50

> color #7 #fa807236

> color #4 #b2b2b235

> color #4 #b2b2b236

> select subtract #7

62808 atoms, 63336 bonds, 4056 residues, 31 models selected  

> select subtract #4

24 models selected  

> graphics silhouettes false

> select #13/u :1-100

1463 atoms, 1478 bonds, 100 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark turquoise

> select #13/u :101-240

2103 atoms, 2119 bonds, 140 residues, 1 model selected  

> color sel salmon

> select #13/u :241-400

2401 atoms, 2428 bonds, 160 residues, 1 model selected  

> color sel cornflower blue

> select #13/u :401-530

1997 atoms, 2017 bonds, 129 residues, 1 model selected  

> color sel fire brick

> select add #13

47784 atoms, 48270 bonds, 3174 residues, 2 models selected  

> select subtract #13

6 models selected  

> cd /Users/aninditosen/Documents/P1/baseplate/main_baseplate

Current working directory is:
/Users/aninditosen/Documents/P1/baseplate/main_baseplate  

> save
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath4.cxs

——— End of log from Mon Dec 2 16:19:56 2024 ———

opened ChimeraX session  

> color #1 #c715850a

> color #1 #c715853d

> color #1 #c7158516

> color #1 #c715850b

> color #2 #ffd7000c

> hide #!2 models

> color #2 #ffd7000d

> show #!2 models

> color #2 #ffd700fb

> hide #!2 models

> show #!2 models

> color #2 #ffd70021

> color #2 #ffd700fd

> hide #2.1 models

> show #2.1 models

> hide #2.2 models

> show #2.2 models

> hide #2.3 models

> show #2.3 models

> select add #2.3

7498 atoms, 477 residues, 1 model selected  

> select add #2

29992 atoms, 30328 bonds, 1908 residues, 2 models selected  

> select subtract #2

4 models selected  

> color #2 #ffd70013

> color #2 #ffd70014

> color #2.3 #ffd700fd

> color #2.3 #ffd700fc

> color #12 #bdb76b08

> color #12 darkkhaki

> select add #12.5

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.5

1 model selected  

> select add #12.4

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.4

1 model selected  

> select add #12.3

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.3

1 model selected  

> select add #12.2

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.2

1 model selected  

> select add #12.3

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.3

1 model selected  

> select add #12.3

4399 atoms, 278 residues, 1 model selected  

> select subtract #12.3

1 model selected  

> color #12 darkkhaki

> color #12 #bdb76b09

> color #12 #bdb76b14

> color #12 #bdb76b2a

> color #12 #bdb76b1a

> color #12.4 darkkhaki

> color #12.4 #bdb76b16

> hide #12.3 models

> color #12.4 #bdb76b17

> show #12.3 models

> color #12.3 #bdb76bfd

> color #12.3 darkkhaki

> save
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/full_baseplate.cxs

——— End of log from Mon Dec 2 17:54:21 2024 ———

opened ChimeraX session  

> show #!1-7,10-13,16 cartoons

> hide #!1-7,10-13,16 surfaces

> color #1 mediumvioletred

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> color #1 mediumvioletred

> select subtract #1

1 model selected  

> select add #1

1316 atoms, 1328 bonds, 94 residues, 1 model selected  

> show sel cartoons

[Repeated 1 time(s)]

> transparency sel 50

> transparency sel 0

> color #1 #c7158500

> color #1 #c715857c

> color #1 #c71585fc

> select subtract #1

1 model selected  

> color #12 darkkhaki

> color #2 gold

> color #3 #ffa500f7

> lighting soft

> lighting full

> graphics silhouettes true

> ui tool show "Side View"

> save /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_base2.cxs

> lighting full

> lighting soft

> lighting full

> lighting flat

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> color #7 salmon

[Repeated 1 time(s)]

> color #7 #fa8072aa

> color #7 #fa80727b

> color #7 #fa807260

> color #7 #fa807280

> save /Users/aninditosen/Desktop/image9.png supersample 3

> hide #!16 models

> hide #!2 models

> hide #!3 models

> hide #!7 models

> hide #!6 models

> hide #!11 models

> hide #!12 models

> ui windowfill toggle

[Repeated 1 time(s)]

> select add #5

9285 atoms, 9380 bonds, 590 residues, 1 model selected  

> show sel surfaces

> select #13/t

7964 atoms, 8045 bonds, 529 residues, 1 model selected  

> hide (#!13 & sel) target a

> delete atoms (#!13 & sel)

> delete bonds (#!13 & sel)

> select #5/n

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> select #5/N

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hbonds sel reveal true

83 hydrogen bonds found  

> select clear

> ~hbonds

> select #13/u #5/O

9821 atoms, 9921 bonds, 647 residues, 2 models selected  

> hbonds sel reveal true

537 hydrogen bonds found  

> style sel stick

Changed 9821 atom styles  

> ~hbonds

> select clear

> hide #!1,4-5,10,13 atoms

> show #!12 models

> show #!2 models

> show #!3 models

> lighting full

> lighting soft

> lighting simple

> select #5/M

1857 atoms, 1876 bonds, 118 residues, 1 model selected  

> hide sel surfaces

> select up

9285 atoms, 9380 bonds, 590 residues, 2 models selected  

> ~hbonds

> select clear

> ~hbonds

[Repeated 1 time(s)]

> select

511878 atoms, 517059 bonds, 33539 residues, 26 models selected  

> ~hbonds

> style sel & #!1-5,10,12-13 stick

Changed 211784 atom styles  

> select clear

> hide #!2 models

> select #13/s

7964 atoms, 8045 bonds, 529 residues, 1 model selected  

> hide sel cartoons

> select #14?BN

Expected an objects specifier or a keyword  

> select #14/BN

Nothing selected  

> select #14/BN

Nothing selected  

> select #4/BN:178

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

55 atoms, 54 bonds, 4 residues, 2 models selected  

> select up

2617 atoms, 2639 bonds, 169 residues, 2 models selected  

> select up

62808 atoms, 63336 bonds, 4056 residues, 2 models selected  

> hide sel cartoons

> select #13/v

7964 atoms, 8045 bonds, 529 residues, 1 model selected  

> hide sel cartoons

> select #12/m #3.g

Expected a keyword  

> select #12/m #3/g

11897 atoms, 12026 bonds, 755 residues, 2 models selected  

> hide sel cartoons

> select #12/m #3/f

11897 atoms, 12026 bonds, 755 residues, 2 models selected  

> hide sel cartoons

> select #12/o #13/i

4399 atoms, 4444 bonds, 278 residues, 1 model selected  

> hide sel cartoons

> select #12/o #3/i

11897 atoms, 12026 bonds, 755 residues, 2 models selected  

> hide sel cartoons

> show #!2 models

> select #12/o #3/i #2/a

19395 atoms, 19608 bonds, 1232 residues, 3 models selected  

> hide sel cartoons

> select #12/o #3/i #2/Z

19395 atoms, 19608 bonds, 1232 residues, 3 models selected  

> hide sel cartoons

> hide #!10 models

> hide sel atoms

> select clear

> hide #!1-5,12-13 atoms

> select add #3

37490 atoms, 37910 bonds, 2385 residues, 1 model selected  

> select subtract #3

5 models selected  

> show #!7 models

> hide #!7 models

> select #13/u :516 #5/O :61

21 atoms, 19 bonds, 2 residues, 2 models selected  

> hbonds sel reveal true

1 hydrogen bonds found  

> select clear

> select #13/u :522 #5/O :114

34 atoms, 32 bonds, 2 residues, 2 models selected  

> hbonds sel reveal true

3 hydrogen bonds found  

> select clear

> select #13/u :522 :516 #5/O :114 :61

55 atoms, 51 bonds, 4 residues, 2 models selected  

> hbonds sel reveal true

4 hydrogen bonds found  

> hide sel surfaces

[Repeated 1 time(s)]

> show sel surfaces

> hide sel surfaces

> select clear

> color #17 #00bfff00 models

> color #17 deepskyblue models

> color #17 #fa0908ff models

> color #17 #fa8b87ff models

> save /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_base3.cxs

——— End of log from Wed Dec 4 16:01:10 2024 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Side View"

> show #!16 models

> select add #16

10175 atoms, 10275 bonds, 625 residues, 1 model selected  

> show sel surfaces

> graphics silhouettes false

> select add #13

49995 atoms, 50500 bonds, 3270 residues, 7 models selected  

> show sel surfaces

> lighting soft

[Repeated 1 time(s)]

> lighting full

[Repeated 1 time(s)]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.  
  
GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\view.py", line 227, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\view.py", line 631, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1551, in use_shadow_map  
self._start_rendering_shadowmap(center, radius, size)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1583, in
_start_rendering_shadowmap  
fb = r.start_depth_render(self._shadow_map_framebuffer,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1372, in start_depth_render  
dt.initialize_depth((size, size))  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3071, in initialize_depth  
self.initialize_texture(size, format, iformat, tdtype, ncomp,  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
2048,  
2048,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Exception ignored in: <function Texture.__del__ at 0x000002BD3EFD5260>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3165, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

> lighting soft

> lighting simple

> lighting soft

> lighting full

> select add #13

49995 atoms, 50500 bonds, 3270 residues, 15 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 480, in _tree_change_cb  
run(self.session, "select " + mode + " #" + model.id_string)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\std_commands\select.py", line 120, in select_add  
report_selection(session)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\std_commands\select.py", line 192, in report_selection  
session.logger.status(', '.join(lines) + ' selected', log = True)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\logger.py", line 522, in status  
StatusLogger.status(self, msg, **kw)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\logger.py", line 220, in status  
if l.status(msg, color, secondary) and getattr(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1133, in status  
sbar.status(msg, color, secondary)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 165, in status  
self._draw_text(msg, color, secondary)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 175, in _draw_text  
draw_overlays(dlist, self._renderer)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry  
t.bind_texture()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3177, in bind_texture  
self.fill_opengl_texture()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3220, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
811,  
46,  
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,  
811,  
46,  
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,  
811,  
46,  
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...,  
)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
811,  
46,  
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,  
811,  
46,  
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,  
811,  
46,  
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...,  
)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 26.1.0-devel (git-219807d38d)
OpenGL renderer: D3D12 (Qualcomm(R) Adreno(TM) X1-45 GPU)
OpenGL vendor: Microsoft Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Pro 12in 1st Ed with Snapdragon
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,756,944,896
MaxProcessMemory: 137,438,953,344
CPU: 8 Snapdragon X Plus (8-core) @ 3.30 GHz
OSLanguage: en-US

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.11.12
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0

[Eric Pettersen]

Reported by Andy Sen

[Tom Goddard]

The error says that OpenGL graphics ran out of memory. It was trying to allocate a rather small 12 Mbyte texture for rendering. This was probably caused by having large models open on a machine with only 16 GB of memory. The Windows operating system is particularly prone to running out of memory. We almost never see this on Mac or Linux. Only solution on Windows is to have more memory.