volume splitbyzone: ArrayMemoryError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/20240910_Session_AllRibbon.cxs"

Log from Tue Sep 10 13:57:51 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_CryoEM_Processing_Master_Folder/Models/20240529_a2b3_Nb146_Neutral/20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb"

Chain information for 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb #1  
---  
Chain | Description  
A | No description available  
B C D E | No description available  
F | No description available  
L M N | No description available  
  

> select #1 a

Expected a keyword  

> select #1: a

Nothing selected  

> select #1/l

1820 atoms, 1844 bonds, 1 pseudobond, 120 residues, 2 models selected  

> select #1/l,m,n

5452 atoms, 5524 bonds, 3 pseudobonds, 360 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> open 6huo fromDatabase pdb format mmcif

6huo title:  
CryoEM structure of human full-length heteromeric alpha1beta3gamma2L GABA(A)R
in complex with alprazolam (Xanax), GABA and megabody Mb38. [more info...]  
  
Chain information for 6huo #2  
---  
Chain | Description | UniProt  
A D | Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN -34--8, GBRA1_HUMAN 1-429  
B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448  
C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436  
G | Megabody Mb38 |   
  
Non-standard residues in 6huo #2  
---  
08H — 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
(alprazolam)  
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25.pdb"
> models #1 relModel #2

> select #1/a,g

5437 atoms, 5511 bonds, 337 residues, 1 model selected  

> select #1/b,h

5613 atoms, 5693 bonds, 1 pseudobond, 340 residues, 2 models selected  

> select #1/a,g

5437 atoms, 5511 bonds, 337 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G.pdb"
> models #1 selectedOnly true relModel #2

> select #1/b,h

5613 atoms, 5693 bonds, 1 pseudobond, 340 residues, 2 models selected  
No model chosen to save relative to  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H.pdb"
> models #1 selectedOnly true relModel #2

> select #1/c,i

5617 atoms, 5698 bonds, 1 pseudobond, 340 residues, 2 models selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I.pdb"
> models #1 selectedOnly true relModel #2

> select #1/d,j

5617 atoms, 5699 bonds, 1 pseudobond, 340 residues, 2 models selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J.pdb"
> models #1 selectedOnly true relModel #2

> select #1/e,k

5620 atoms, 5701 bonds, 1 pseudobond, 340 residues, 2 models selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+I.pdb"
> models #1 selectedOnly true relModel #2

> select #1/f

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChF.pdb"
> models #1 selectedOnly true relModel #2

> select #1/a,f,g

7348 atoms, 7443 bonds, 463 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F.pdb"
> models #1 selectedOnly true relModel #2

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 8 8 MET B 9 LEU B 20 1 12  
Start residue of secondary structure not found: HELIX 9 9 LYS B 70 LEU B 72 1
3  
Start residue of secondary structure not found: HELIX 10 10 ASN B 85 GLN B 90
1 6  
Start residue of secondary structure not found: HELIX 11 11 GLY B 171 ALA B
174 1 4  
Start residue of secondary structure not found: HELIX 12 12 VAL B 178 ARG B
180 1 3  
79 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue ARG (192 )  
32 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChA+G+F.pdb #3  
---  
Chain | Description  
A | No description available  
F | No description available  
  

> hide #!1 models

> select add #1

29815 atoms, 30234 bonds, 4 pseudobonds, 1823 residues, 2 models selected  

> hide #3 models

> select subtract #1

Nothing selected  

> show #!1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> show #3#!1 atoms

> hide #3#!1 cartoons

> hide #!1 models

> hide #3 cartoons

> show #3 atoms

> style #3 sphere

Changed 7348 atom styles  

> hide #3 atoms

> show #3 atoms

> show #3 cartoons

> hide #3 atoms

> show #!1 models

> hide #3#!1 atoms

> show #3#!1 cartoons

> hide #!1 models

> hide #3 models

> show #3 models

> hide #3 models

> show #!1 models

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #1/C #1/D #1/E

Alignment identifier is 1  

> select clear

> select #1/B-E:220-308

5886 atoms, 5974 bonds, 356 residues, 1 model selected  

> select #1/B-E:219

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #1/B-E:219-308

5914 atoms, 6002 bonds, 360 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui mousemode right select

[Repeated 1 time(s)]Drag select of 22 residues  

> delete atoms sel

> delete bonds sel

> ui mousemode right select

Drag select of 35 residues, 3 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select clear

Drag select of 1 pseudobonds  
No visible atoms or bonds selected  
Drag select of 22 residues  

> delete atoms sel

> delete bonds sel

Drag select of 36 residues, 4 pseudobonds  
Drag select of 35 residues, 4 pseudobonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> show #!1 surfaces

Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 1968 of 250302 triangles  
[Repeated 2 time(s)]

> ui mousemode right select

Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 1968 of 250302 triangles  

> select add #1

21884 atoms, 22165 bonds, 2 pseudobonds, 1349 residues, 4 models selected  

> select subtract #1

6 models selected  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 1968 of 250302 triangles  
[Repeated 1 time(s)]Drag select of
20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 1159 of 249826
triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES surface, 1968 of
250302 triangles  

> select add #1

21884 atoms, 22165 bonds, 2 pseudobonds, 1349 residues, 4 models selected  

> select subtract #1

6 models selected  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 1968 of 250302 triangles  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 991 of 250302 triangles  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1974 of 249826 triangles  
[Repeated 1 time(s)]

> select clear

Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 610
of 249826 triangles  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_A SES surface,
3624 of 393648 triangles, 2 residues  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 237
of 249826 triangles  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1019 of 249826 triangles  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface,
1151 of 249826 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 477 of 250302 triangles  

> style #!1 sphere

Changed 21884 atom styles  

> style #!1 stick

Changed 21884 atom styles  

> hide #!1 surfaces

> style #!1 sphere

Changed 21884 atom styles  

> show #!1 atoms

Drag select of 8 atoms  
Drag select of 12 atoms  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> style #!1 sphere

Changed 21870 atom styles  

> hide #!1 cartoons

> show #!1 surfaces

Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 865
of 248930 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 485 of 249436 triangles, 5 atoms  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES surface, 286
of 248988 triangles, 1 atoms  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 169
of 248160 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 481 of 248988 triangles, 2 atoms  
Drag select of 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_C SES surface, 308
of 248160 triangles, 20240529_a2b3_Mb25_Nb146_038_Model_Final.pdb_D SES
surface, 654 of 248988 triangles, 3 atoms  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> hide #!1 atoms

> show #!1 cartoons

> hide #!1 cartoons

> hide #!1 atoms

> hide #!1 surfaces

> show #!1 cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #3/A

Alignment identifier is 1  

> close #3

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:412

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:223-412

1966 atoms, 1995 bonds, 122 residues, 1 model selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select #1/a,f,g

5382 atoms, 5447 bonds, 341 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F_ECD.pdb"
> models #1 selectedOnly true relModel #2

> select #1/b,h

3627 atoms, 3673 bonds, 221 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H_ECD.pdb"
> models #1 selectedOnly true relModel #2

> select #1/c,i

3632 atoms, 3679 bonds, 221 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I_ECD.pdb"
> models #1 selectedOnly true relModel #2

> select #1/d,j

3626 atoms, 3674 bonds, 221 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb"
> models #1 selectedOnly true relModel #2

> select #1/e,k

3629 atoms, 3676 bonds, 221 residues, 1 model selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+K_ECD.pdb"
> models #1 selectedOnly true relModel #2

> hide #!1 models

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 8 8 MET B 9 LEU B 20 1 12  
Start residue of secondary structure not found: HELIX 9 9 LYS B 70 LEU B 72 1
3  
Start residue of secondary structure not found: HELIX 10 10 ASN B 85 GLN B 90
1 6  
Start residue of secondary structure not found: HELIX 11 11 GLY B 171 ALA B
174 1 4  
Start residue of secondary structure not found: HELIX 12 12 VAL B 178 ARG B
180 1 3  
90 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
33 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChA+G.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 8 8 MET B 9 LEU B 20 1 12  
Start residue of secondary structure not found: HELIX 9 9 LYS B 70 LEU B 72 1
3  
Start residue of secondary structure not found: HELIX 10 10 ASN B 85 GLN B 90
1 6  
Start residue of secondary structure not found: HELIX 11 11 GLY B 171 ALA B
174 1 4  
Start residue of secondary structure not found: HELIX 12 12 VAL B 178 ARG B
180 1 3  
79 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue ARG (192 )  
32 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChA+G+F.pdb #4  
---  
Chain | Description  
A | No description available  
F | No description available  
  

> close #3

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChF.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChF.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 GLY A 223 TRP A 245
1 23  
Start residue of secondary structure not found: HELIX 5 5 VAL A 251 ASN A 274
1 24  
97 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (233 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
36 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChF.pdb #3  
---  
Chain | Description  
F | No description available  
  

> close #3

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 GLY A 223 TRP A 245
1 23  
Start residue of secondary structure not found: HELIX 5 5 VAL A 251 ASN A 274
1 24  
87 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (233 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
28 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChB+H.pdb #3  
---  
Chain | Description  
B | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 GLY A 223 TRP A 245
1 23  
Start residue of secondary structure not found: HELIX 5 5 VAL A 251 ASN A 274
1 24  
87 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (233 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
28 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChC+I.pdb #5  
---  
Chain | Description  
C | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 MET B 9 LEU B 20 1
12  
Start residue of secondary structure not found: HELIX 5 5 LYS B 70 LEU B 72 1
3  
71 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
26 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb #6  
---  
Chain | Description  
D | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+I.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+I.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 GLY A 223 TRP A 245
1 23  
Start residue of secondary structure not found: HELIX 5 5 VAL A 251 ASN A 274
1 24  
87 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (233 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
28 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChE+I.pdb #7  
---  
Chain | Description  
E | No description available  
  

> close #7

> close #6

> close #3

> close #4

> close #5

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChA+G+F_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 4 4 MET B 9 LEU B 20 1 12  
Start residue of secondary structure not found: HELIX 5 5 LYS B 70 LEU B 72 1
3  
Start residue of secondary structure not found: HELIX 6 6 ASN B 85 GLN B 90 1
6  
Start residue of secondary structure not found: HELIX 7 7 GLY B 171 ALA B 174
1 4  
Start residue of secondary structure not found: HELIX 8 8 VAL B 178 ARG B 180
1 3  
63 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue ARG (192 )  
32 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChA+G+F_ECD.pdb #3  
---  
Chain | Description  
A | No description available  
F | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChB+H_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 9 9 MET C 9 LEU C 20 1
12  
Start residue of secondary structure not found: HELIX 10 10 LYS C 70 LEU C 72
1 3  
71 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
27 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChB+H_ECD.pdb #4  
---  
Chain | Description  
B | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChC+I_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 MET B 9 LEU B 20 1
12  
Start residue of secondary structure not found: HELIX 5 5 LYS B 70 LEU B 72 1
3  
71 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
27 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChC+I_ECD.pdb #5  
---  
Chain | Description  
C | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 MET B 9 LEU B 20 1
12  
Start residue of secondary structure not found: HELIX 5 5 LYS B 70 LEU B 72 1
3  
71 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
26 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChD+J_ECD.pdb #6  
---  
Chain | Description  
D | No description available  
  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+K_ECD.pdb"

Summary of feedback from opening C:/Users/jeg58/OneDrive - University of
Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ChE+K_ECD.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN A 10 LEU A 21 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 72 LEU A 74 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 87 LYS A 92 1
6  
Start residue of secondary structure not found: HELIX 4 4 MET B 9 LEU B 20 1
12  
Start residue of secondary structure not found: HELIX 5 5 LYS B 70 LEU B 72 1
3  
71 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (138 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (136 )  
Cannot find LINK/SSBOND residue CYS (22 )  
27 messages similar to the above omitted  
  
Chain information for a2b3_Nb146_038_NoMb25_ChE+K_ECD.pdb #7  
---  
Chain | Description  
E | No description available  
  

> show #!1 models

> hide #7 models

> hide #6 models

> hide #5 models

> hide #4 models

> hide #3 models

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ECD.pdb"
> models #1 relModel #2

> close #2

> close #3

> close #4

> close #5

> close #6

> close #7

> view #1

> show surfaces

> style ball

Changed 19896 atom styles  

> hide surfaces

> hide cartoons

> show atoms

> style ball

Changed 19896 atom styles  

> style sphere

Changed 19896 atom styles  

> select /F

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> select #1/f

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> color rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color fromribbons rainbow

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

> color ribbons rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 1 model selected  

> select subtract #1

6 models selected  

> show cartoons

> hide atoms

> color fromribbons rainbow

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

> color fromribbons cartoons rainbow

Expected ',' or a keyword  

> color fromribbons cartoons, rainbow

Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'  

> color #1/f #rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1/f fromcartoons, rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1/f fromcartoons, red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #1/f fromcartoons blue

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

> color #1/f fromcartoons All blue

Expected ',' or a keyword  

> color #1/f fromcartoons all, blue

Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'  

> color #1/f fromcartoons all,blue

Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'  

> color #1/f fromribbons all,blue

Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'  

> color #1/f fromribbons byhet

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

> color #d9d9d9ff

> color #c3c3c3ff

> color #b9b9b9ff

> color #b8b8b8ff

> color #9e9e9eff

> color #7f7f7fff

> color #6a6a6aff

> color #686868ff

> color #565656ff

> color #707070ff

> color #848484ff

> color #9a9a9aff

> color #b9b9b9ff

> color #bcbcbcff

> color #cfcfcfff

> color #1/a #cfcfcf

> color #d9d9d9ff

> color #d8d8d8ff

> color #d5d5d5ff

> color #d1d1d1ff

> color #cfcfcfff

> color #ccccccff

> color #c7c7c7ff

> color #b5b5b5ff

> color #abababff

> color #a5a5a5ff

> color #a2a2a2ff

> color #919191ff

> color #909090ff

> color #8d8d8dff

> color #8c8c8cff

> color #8d8d8dff

> color #8f8f8fff

> color #919191ff

> color #949494ff

> color #959595ff

> color #969696ff

> color #989898ff

> color #999999ff

> color #9c9c9cff

> color #9d9d9dff

> color #1/a #cfcfcf

> color #1/b-e #d9d9d9

> select #1/b-e

13771 atoms, 13926 bonds, 852 residues, 1 model selected  

> color (#!1 & sel) dark gray

> color (#!1 & sel) dim gray

> color (#!1 & sel) gray

> select #1/a

3417 atoms, 3459 bonds, 213 residues, 1 model selected  

> color (#!1 & sel) light gray

> select /F

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> color (#!1 & sel) purple

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> select #1/f

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> rainbow sel

[Repeated 1 time(s)]

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> view #1

> style sphere

Changed 19896 atom styles  

> view #1

> open 6huo fromDatabase pdb format mmcif

6huo title:  
CryoEM structure of human full-length heteromeric alpha1beta3gamma2L GABA(A)R
in complex with alprazolam (Xanax), GABA and megabody Mb38. [more info...]  
  
Chain information for 6huo #2  
---  
Chain | Description | UniProt  
A D | Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 | GBRA1_BOVIN -34--8, GBRA1_HUMAN 1-429  
B E | Gamma-aminobutyric acid receptor subunit beta-3 | GBRB3_HUMAN -24-448  
C | Gamma-aminobutyric acid receptor subunit gamma-2 | GBRG2_HUMAN -38-436  
G | Megabody Mb38 |   
  
Non-standard residues in 6huo #2  
---  
08H — 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
(alprazolam)  
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide #!2 models

No model chosen to save relative to  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/a2b3_Nb146_038_NoMb25_ECD_a2LG_b3DG_NbRBow_AllRibbon.pdb"
> models #1 relModel #2

> view #1

[Repeated 3 time(s)]

> style #!1 ball

Changed 19896 atom styles  

> style #!1 sphere

Changed 19896 atom styles  

> style #!1 stick

Changed 19896 atom styles  

> style #!1 sphere

Changed 19896 atom styles  

> show #!1 atoms

> hide #!1 surfaces

> show #!1 surfaces

> hide #!1 surfaces

> hide #!1 cartoons

> style #!1 ball

Changed 19896 atom styles  

> show #!1 cartoons

> hide #!1 atoms

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/20240910_Example1_TopView.jpg"
> width 1128 height 772 supersample 3

> color ligand orange

> show #!1 atoms

> style #!1 sphere

Changed 19896 atom styles  

> color ligand byhetero

> hide #!1 atoms

> show #!1 atoms

> style #!1 sphere

Changed 19896 atom styles  

> hide #!1 cartoons

> view #1

> hide #!1 atoms

> show #!1 cartoons

> show #!1 atoms

> hide #!1 atoms

> hide #1:a-f

> show #!1 atoms

> hide #1:a-f

> hide #!1 cartoons

> hide #!1 atoms

> show #!1 atoms

> select #1:a-e,g-i

6904 atoms, 6617 bonds, 488 residues, 1 model selected  

> hide sel surfaces

> hide sel atoms

> select #1:a-e

4660 atoms, 4438 bonds, 301 residues, 1 model selected  

> select #1/a-e

17188 atoms, 17385 bonds, 1065 residues, 1 model selected  

> select #1/a-e,g-i

17614 atoms, 17829 bonds, 1083 residues, 1 model selected  

> hide sel atoms

> select #1/f

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> show #!1 atoms

> hide #!1 cartoons

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example1_a2LG_b3DG_NbRbow_AllSphere.jpg"
> width 1128 height 772 supersample 3

> select #1/f

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 2 models selected  

> select subtract #1

6 models selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example2_a2LG_b3DG_NbRbow_GABRSphere_NbRibbon.jpg"
> width 1128 height 772 supersample 3

> hide #!1 atoms

> show #!1 cartoons

> select #1/g-i

426 atoms, 438 bonds, 18 residues, 1 model selected  

> show #1/g-i

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 1 model selected  

> select subtract #1

6 models selected  

> show ligands

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

> color #1/b:501 magenta

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example3_a2LG_b3DG_NbRbow_AllRibbon.jpg"
> width 1128 height 772 supersample 3

> view #1

[Repeated 1 time(s)]

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example3_a2LG_b3DG_NbRbow_AllRibbon_Side.jpg"
> width 1128 height 772 supersample 3

> select #1/F

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> select ~sel & ##selected

17985 atoms, 18217 bonds, 1099 residues, 1 model selected  

> style sel sphere

Changed 17985 atom styles  

> show sel atoms

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 6 models selected  

> select subtract #1

6 models selected  

> view #1

> hide #!1 cartoons

> show #!1 cartoons

> select #1/F

1911 atoms, 1932 bonds, 126 residues, 1 model selected  

> select ~sel & ##selected

17985 atoms, 18217 bonds, 1099 residues, 1 model selected  

> hide sel cartoons

> select add #1

19896 atoms, 20149 bonds, 1225 residues, 6 models selected  

> select subtract #1

6 models selected  

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example2_a2LG_b3DG_NbRbow_GABRSphere_NbRibbon_Side.jpg"
> width 1128 height 772 supersample 3

> style #!1 sphere

Changed 19896 atom styles  

> hide #!1 cartoons

> style #!1 sphere

Changed 19896 atom styles  

> show #!1 atoms

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/Example1_a2LG_b3DG_NbRbow_AllSphere_Side.jpg"
> width 1128 height 772 supersample 3

> select #1/a-e

17188 atoms, 17385 bonds, 1065 residues, 1 model selected  

> display #1/a-e@Ca

> hide sel surfaces

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide sel atoms

> hide sel surfaces

> hide sel cartoons

> display #1/a-e@Ca

> show sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> show sel surfaces

> hide sel surfaces

> display #1/a-e@Ca

> show sel atoms

> display #1/a-e@Ca

> show sel cartoons

> hide sel atoms

> display #1/a-e@Ca

[Repeated 1 time(s)]

> hide sel cartoons

> hide sel atoms

> show sel atoms

> display #1/a-e@Ca

> style sel stick

Changed 17188 atom styles  

> display #1/a-e@Ca

> ~display #1/a-e ribbon

> ~display #1/a-e sphere

> hide #1/a-e sphere

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

> ~display #1/a-e atoms

> display #1/a-e@ca

> select add #1

19896 atoms, 20149 bonds, 1056 pseudobonds, 1225 residues, 7 models selected  

> select subtract #1

6 models selected  

> show #!1 atoms

> show #!1 cartoons

> hide #!1 atoms

> save "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/20240910_Session_AllRibbon.cxs"

——— End of log from Tue Sep 10 13:57:51 2024 ———

opened ChimeraX session  

> open "C:/Users/jeg58/OneDrive - University of
> Cambridge/JEGP_a2a3_Paper_Figures/20240909_Initial_Proposals/20240910_Nb146_ChimeraX/20240529_a2b3_Mb25_Nb146_Map_J483_2.67A.mrc"

Opened 20240529_a2b3_Mb25_Nb146_Map_J483_2.67A.mrc as #3, grid size
520,520,520, pixel 0.652, shown at level 0.0268, step 4, values float32  

> hide #!3 models

> show #!3 models

> volume #3 step 1

> volume #3 level 0.05572

> transparency 50

> volume #3 level 0.07018

> split map

Expected a structures specifier or a keyword  

> split #3

> ui tool show "Surface Color"

> ui tool show "Color Zone"

> color zone #3 near #1 distance 3.91

> volume splitbyzone #3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.8\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 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 536. MiB for an
array with shape (520, 520, 520) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 536. MiB for an
array with shape (520, 520, 520) and data type float32  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.70
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Vivobook_ASUSLaptop K6604JI_K6604JI
OS: Microsoft Windows 11 Enterprise (Build 22621)
Memory: 16,791,195,648
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13650HX
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

[Tom Goddard]

Ran out of memory making copies of a 520 by 520 by 520 map splitting it by color zone. Computer at 16 Gbytes. Windows 10. Always seems to be Windows that runs out of memory.