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#14631 closed defect (fixed)

ISOLDE: ResidueStepper references dead Structure

Reported by:	tmckeith@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Tried to save as .cxs; failed, but could save as .pdb

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.cxs"

Restoring stepper: working  
Log from Mon Feb 5 19:13:04 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb"

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAV1 working 2a.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 2
ILE A 4 1 3  
Start residue of secondary structure not found: HELIX 2 2 GLY A 54 SER A 59 1
6  
Start residue of secondary structure not found: HELIX 3 3 TRP A 78 ASN A 91 1
14  
Start residue of secondary structure not found: HELIX 4 4 LYS A 112 GLU A 124
1 13  
Start residue of secondary structure not found: HELIX 5 5 GLN A 136 SER A 144
1 9  
235 messages similar to the above omitted  
  
Chain information for VAV1 working 2a.pdb  
---  
Chain | Description  
1.1/A 1.2/B 1.3/C 1.4/D 1.6/F 1.7/G | No description available  
1.5/E | No description available  
1.8/H | No description available  
1.9/Q | No description available  
  

> combine #1 close true name working

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select /E:1

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /E:0-1

23 atoms, 22 bonds, 2 residues, 1 model selected  

> isolde sim start /D,E

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
Loading residue template for ADP from internal database  
ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb" format pdb

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAV1 working 2a.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 2
ILE A 4 1 3  
Start residue of secondary structure not found: HELIX 2 2 GLY A 54 SER A 59 1
6  
Start residue of secondary structure not found: HELIX 3 3 TRP A 78 ASN A 91 1
14  
Start residue of secondary structure not found: HELIX 4 4 LYS A 112 GLU A 124
1 13  
Start residue of secondary structure not found: HELIX 5 5 GLN A 136 SER A 144
1 9  
235 messages similar to the above omitted  
  
Chain information for VAV1 working 2a.pdb  
---  
Chain | Description  
1.1/A 1.2/B 1.3/C 1.4/D 1.6/F 1.7/G | No description available  
1.5/E | No description available  
1.8/H | No description available  
1.9/Q | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.5/E

Alignment identifier is 1.5/E  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb" format pdb

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAV1 working 2a.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 2
ILE A 4 1 3  
Start residue of secondary structure not found: HELIX 2 2 GLY A 54 SER A 59 1
6  
Start residue of secondary structure not found: HELIX 3 3 TRP A 78 ASN A 91 1
14  
Start residue of secondary structure not found: HELIX 4 4 LYS A 112 GLU A 124
1 13  
Start residue of secondary structure not found: HELIX 5 5 GLN A 136 SER A 144
1 9  
235 messages similar to the above omitted  
  
Chain information for VAV1 working 2a.pdb  
---  
Chain | Description  
1.1/A 1.2/B 1.3/C 1.4/D 1.6/F 1.7/G | No description available  
1.5/E | No description available  
1.8/H | No description available  
1.9/Q | No description available  
  

> show atoms

> style sphere

Changed 54240 atom styles  

> ui tool show "Color Actions"

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> select #1.8/H

13824 atoms, 13977 bonds, 841 residues, 1 model selected  

> select C

17244 atoms, 13699 bonds, 3431 residues, 9 models selected  

> color sel spring green target apf

> color sel forest green target c

> select #1.5/E

2676 atoms, 2705 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select intersect C

855 atoms, 685 bonds, 167 residues, 1 model selected  

> color sel orange target c

[Repeated 1 time(s)]

> color sel orange target aspf

> select clear

> select #1.8/H

13824 atoms, 13977 bonds, 841 residues, 1 model selected  

> select intersect C

4407 atoms, 3552 bonds, 841 residues, 1 model selected  

> color sel plum target aspf

[Repeated 1 time(s)]

> color sel plum target c

> select clear

> select H

26910 atoms, 3431 residues, 9 models selected  

> hide sel target a

> select clear

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.cxs"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 4n.pdb"

Chain information for SPTBN2 working 4n.pdb #1  
---  
Chain | Description  
A B C D F G | No description available  
H | No description available  
J | No description available  
K | No description available  
Q | No description available  
b | No description available  
  

> select /K

5313 atoms, 5361 bonds, 379 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain /J

Alignment identifier is 1/J  

> select /J:178-179

32 atoms, 31 bonds, 2 residues, 1 model selected  

> select /J:178-534

5845 atoms, 5897 bonds, 357 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /J:173-177

92 atoms, 91 bonds, 5 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb"

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAV1 working 2a.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 2
ILE A 4 1 3  
Start residue of secondary structure not found: HELIX 2 2 GLY A 54 SER A 59 1
6  
Start residue of secondary structure not found: HELIX 3 3 TRP A 78 ASN A 91 1
14  
Start residue of secondary structure not found: HELIX 4 4 LYS A 112 GLU A 124
1 13  
Start residue of secondary structure not found: HELIX 5 5 GLN A 136 SER A 144
1 9  
235 messages similar to the above omitted  
  
Chain information for VAV1 working 2a.pdb  
---  
Chain | Description  
2.1/A 2.2/B 2.3/C 2.4/D 2.6/F 2.7/G | No description available  
2.5/E | No description available  
2.8/H | No description available  
2.9/Q | No description available  
  

> select add #1

56514 atoms, 57109 bonds, 10 pseudobonds, 3575 residues, 2 models selected  

> select #2.5/E

2676 atoms, 2705 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select ~sel & ##selected

Nothing selected  

> close #2.8#2.6-7,9

> close #2.1-4

> combine #1,2 close true name working

> select /E

2676 atoms, 2705 bonds, 1 pseudobond, 168 residues, 2 models selected  

> color (#!1 & sel) orange

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> show sel atoms

> style sel sphere

Changed 2676 atom styles  

> select clear

> select H

29395 atoms, 3735 residues, 1 model selected  

> hide sel target a

> select clear

> select /E

2676 atoms, 2705 bonds, 1 pseudobond, 168 residues, 2 models selected  

> isolde sim start #E,J,H

Expected an atoms specifier or a keyword  

> isolde sim start /E,J,H

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: started sim  

> isolde sim pause

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /J

Alignment identifier is 1.2/J  

> select /J:2

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /J:2-13

170 atoms, 171 bonds, 12 residues, 1 model selected  

> select /J:2

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /J:2-8

96 atoms, 96 bonds, 7 residues, 1 model selected  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /J:8

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /J:2-8

96 atoms, 96 bonds, 7 residues, 1 model selected  

> select

59190 atoms, 59814 bonds, 11 pseudobonds, 3743 residues, 18 models selected  

> show sel cartoons

> select /J:7

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

> select /J:2-7

82 atoms, 82 bonds, 6 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right zoom

> isolde sim start /E,J,H

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde sim start /E,J,H

ISOLDE: started sim  

> select up

39 atoms, 41 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde sim start /E,J,H

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.cxs"

Taking snapshot of stepper: working  

——— End of log from Mon Feb 5 19:13:04 2024 ———

opened ChimeraX session  

> close #1.3

> set bgColor white

> hide sel atoms

> show sel atoms

> style sel sphere

Changed 19217 atom styles  

> interfaces #1 areaCutoff 20

25 buried areas: D J 2274, H Q 2082, B b 1698, J E 1684, H J 1404, B F 1348, A
D 1303, B C 1294, D G 1279, H E 1031, H A 935, D F 721, F G 697, A C 659, H D
646, A B 621, B D 594, G J 498, D E 410, F b 409, A E 328, B E 302, B J 268, A
J 239, C E 38  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1.2/E  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1.2/H  

> select
> /E:3-13,22-24,30-39,41-50,64-66,68-84,96-98,105-116,119-123,140-150,159-161

1430 atoms, 1433 bonds, 88 residues, 1 model selected  

> select /E:142

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:142

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select add sel @< 4

118 atoms, 104 bonds, 17 residues, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select add sel @< 4

89 atoms, 78 bonds, 13 residues, 1 model selected  

> select

59150 atoms, 59773 bonds, 10 pseudobonds, 3741 residues, 19 models selected  

> show sel atoms

> style sel sphere

Changed 59150 atom styles  

> hide sel cartoons

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> select add H

59150 atoms, 59773 bonds, 10 pseudobonds, 3741 residues, 18 models selected  

> select clear

> select add H

29383 atoms, 3734 residues, 1 model selected  

> hide (#!1.2 & sel) target a

> select clear

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb"

Chain information for VAV1 working 2a.pdb #1  
---  
Chain | Description  
A B C D F G | No description available  
E | No description available  
H | No description available  
J | No description available  
Q | No description available  
b | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/3BJI.pdb format pdb

3BJI.pdb title:  
Structural basis of promiscuous guanine nucleotide exchange by the T- cell
essential VAV1 [more info...]  
  
Chain information for 3BJI.pdb #1  
---  
Chain | Description | UniProt  
A B | proto-oncogene vav | VAV_HUMAN 189-565  
C D | ras-related C3 botulinum toxin substrate 1 precursor | RAC1_HUMAN 1-177  
  
Non-standard residues in 3BJI.pdb #1  
---  
ZN — zinc ion  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> open "/Users/tmckeithan/Desktop/Cell biology and also early evolution/DCTN1
> AF-Q14203.pdb"

DCTN1 AF-Q14203.pdb title:  
Alphafold monomer V2.0 prediction for dynactin subunit 1 (Q14203) [more
info...]  
  
Chain information for DCTN1 AF-Q14203.pdb #2  
---  
Chain | Description | UniProt  
A | dynactin subunit 1 | DCTN1_HUMAN 1-1278  
  

> close #1

> select add #2

9930 atoms, 10063 bonds, 1278 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 9930 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> select C

6142 atoms, 4773 bonds, 1278 residues, 1 model selected  

> color sel light sea green

> color sel orange

> select H

Nothing selected  

> hide cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  
Drag select of 2603 atoms  

> select /A:594

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:594-910

2453 atoms, 2494 bonds, 317 residues, 1 model selected  

> select ~sel & ##selected

7477 atoms, 7569 bonds, 961 residues, 1 model selected  

> hide sel target a

> select clear

> graphics silhouettes true

> lighting shadows true

Drag select of 2453 atoms  

> combine #1 name DCTN1

No structures specified  

> combine #2 name DCTN1

> select #2/A:858@ND2

1 atom, 1 residue, 1 model selected  

> select add #2

9930 atoms, 10063 bonds, 1278 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.56192,0.6399,-0.52418,-1.0899,-0.26224,-0.4632,-0.84657,30.079,-0.78452,0.61316,-0.092472,6.9165

> view matrix models
> #2,0.64716,0.07283,-0.75887,12.634,0.36005,-0.90661,0.22004,18.358,-0.67197,-0.41563,-0.61295,33.516

> ui mousemode right "translate selected models"

> undo

[Repeated 1 time(s)]

> help help:user

> roll y 180 1 models #1

> view matrix models #2,1,0,0,-0.12128,0,1,0,41.927,0,0,1,-21.525

> view matrix models #2,1,0,0,18.333,0,1,0,-10.003,0,0,1,40.409

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9859,0.12216,0.11433,13.61,-0.043199,0.846,-0.53143,5.7694,-0.16165,0.519,0.83935,36.735

> select subtract #2

Nothing selected  

> select add #1

9930 atoms, 10063 bonds, 1278 residues, 1 model selected  

> view matrix models
> #1,0.79179,-0.59398,-0.14233,8.2956,0.14305,0.40688,-0.90221,37.436,0.59381,0.694,0.40713,24.027

> view matrix models
> #1,0.56798,-0.29481,-0.76843,18.503,0.51887,0.853,0.056261,15.29,0.63888,-0.43067,0.63746,27.59

> view matrix models
> #1,0.66371,-0.36399,-0.65346,18.152,0.54788,0.83132,0.09341,15.122,0.50923,-0.42001,0.75118,20.818

> view matrix models
> #1,0.41928,-0.85,0.3189,-12.777,0.3922,0.48638,0.78078,-6.2905,-0.81877,-0.20229,0.5373,-8.88

> view matrix models
> #1,0.18611,-0.16152,-0.96916,13.481,0.20598,0.97089,-0.12225,11.518,0.9607,-0.17687,0.21396,46.265

> view matrix models
> #1,0.25576,-0.17739,-0.95033,14.851,0.14766,0.97865,-0.14294,10.56,0.9554,-0.10377,0.2765,43.693

> view matrix models
> #1,0.26754,-0.31977,-0.90894,15.099,0.1307,0.94665,-0.29457,14.844,0.95464,-0.039984,0.29506,42.607

> view matrix models
> #1,-0.75966,-0.51107,-0.40215,-24.708,-0.58436,0.80781,0.077244,-13.38,0.28539,0.29368,-0.91231,58.152

> view matrix models
> #1,-0.74939,-0.50177,-0.43202,-23.641,-0.5776,0.81439,0.056061,-12.637,0.3237,0.29155,-0.90012,58.798

> select add #2

19860 atoms, 20126 bonds, 2556 residues, 2 models selected  

> view matrix models
> #2,0.98597,0.12121,0.11474,13.611,-0.042224,0.84623,-0.53114,5.8016,-0.16148,0.51884,0.83948,36.74,#1,-0.74885,-0.50265,-0.43193,-23.625,-0.5783,0.81394,0.05543,-12.638,0.3237,0.2913,-0.9002,58.801

> view matrix models
> #2,0.99889,0.010269,-0.045924,11.359,-0.032813,0.85152,-0.5233,7.1665,0.033731,0.52423,0.85091,43.078,#1,-0.79223,-0.55709,-0.24906,-29.288,-0.58383,0.8107,0.043728,-11.502,0.17755,0.18005,-0.9675,57.656

> select subtract #1

9930 atoms, 10063 bonds, 1278 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select clear

Drag select of 4906 atoms  

> select #2/A:922

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:541-922

2980 atoms, 3036 bonds, 382 residues, 1 model selected  

> show sel atoms

> close #1

> combine #2 name DCTN1

> close #1

> select ~sel & ##selected

6950 atoms, 7027 bonds, 896 residues, 1 model selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select ~sel & ##selected

Nothing selected  

> select add #2

2980 atoms, 3036 bonds, 382 residues, 2 models selected  

> combine #2 name DCTN1

> select #2/A:591@CE1

1 atom, 1 residue, 1 model selected  

> cofr sel

> roll y 180 1 models #1

> hide #1 models

> show #1 models

> hide #!2 models

> open "/Users/tmckeithan/Desktop/Cell biology and also early evolution/DCTN2
> AF-Q13561.pdb"

DCTN2 AF-Q13561.pdb title:  
Alphafold monomer V2.0 prediction for dynactin subunit 2 (Q13561) [more
info...]  
  
Chain information for DCTN2 AF-Q13561.pdb #3  
---  
Chain | Description | UniProt  
A | dynactin subunit 2 | DCTN2_HUMAN 1-401  
  

> close #1#2

> rainbow

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 3/A  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8h.pdb"

SPTBN2 working 8h.pdb title:  
Cryo-em structure of F-actin complexed with the β-III-spectrin actin-binding
domain [more info...]  
  
Chain information for SPTBN2 working 8h.pdb #1  
---  
Chain | Description | UniProt  
A | β-actin | ACTB_HUMAN 1-375  
B C D E F | β-actin | ACTB_HUMAN 1-375  
G | No description available |  
H I L | No description available |  
J | No description available |  
K | No description available |  
Q | No description available |  
b | spectrin β chain, non-erythrocytic 2 | SPTN2_HUMAN 1001-1284  
  
Non-standard residues in SPTBN2 working 8h.pdb #1  
---  
ACE — acetyl group  
ADP — adenosine-5&#x27;-diphosphate  
GTP — (GTP)  
MG — magnesium ion  
  

> close #3

> select

82383 atoms, 83238 bonds, 12 pseudobonds, 5256 residues, 2 models selected  

> cofr sel

> view sel

> hide sel atoms

> show sel cartoons

> select clear

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb" format pdb

Chain information for VAV1 working 2a.pdb #1  
---  
Chain | Description  
A B C D F G | No description available  
E | No description available  
H | No description available  
J | No description available  
Q | No description available  
b | No description available  
  

> close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #1  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #1  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod.pdb

1NVV-REDmod.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod.pdb #1  
---  
Chain | Description | UniProt  
Q | C-H-RAS | RASH_HUMAN 1-166  
R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod.pdb #1  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> dssp

> close session

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb format pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #1  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #1  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> dssp

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2a.pdb" format pdb

Chain information for VAV1 working 2a.pdb #1  
---  
Chain | Description  
A B C D F G | No description available  
E | No description available  
H | No description available  
J | No description available  
Q | No description available  
b | No description available  
  

> hide atoms

> show cartoons

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #2  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #2  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> ui tool show Matchmaker

> matchmaker #2/S to #1/H pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2a.pdb, chain H (#1) with 1NVV-REDmod2i.pdb, chain S
(#2), sequence alignment score = 2339.6  
RMSD between 167 pruned atom pairs is 1.283 angstroms; (across all 469 pairs:
4.835)  
  

> select

72252 atoms, 73008 bonds, 14 pseudobonds, 4544 residues, 4 models selected  

> select subtract #1/H

58431 atoms, 59034 bonds, 14 pseudobonds, 3703 residues, 4 models selected  

> select subtract #2/S

50613 atoms, 51122 bonds, 14 pseudobonds, 3234 residues, 4 models selected  

> select subtract #1/Q

47949 atoms, 48438 bonds, 10 pseudobonds, 3066 residues, 4 models selected  

> select subtract #2/Q#2/R

42665 atoms, 43115 bonds, 6 pseudobonds, 2732 residues, 2 models selected  

> select subtract sel :< 4

Nothing selected  

> select add #1

59150 atoms, 59773 bonds, 10 pseudobonds, 3741 residues, 2 models selected  

> select subtract #1/H

45329 atoms, 45799 bonds, 10 pseudobonds, 2900 residues, 2 models selected  

> select subtract #1/Q

42665 atoms, 43115 bonds, 6 pseudobonds, 2732 residues, 2 models selected  

> select sel :< 4 & ~sel

2441 atoms, 2446 bonds, 146 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2/S to #1/H & sel pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2a.pdb, chain H (#1) with 1NVV-REDmod2i.pdb, chain S
(#2), sequence alignment score = 343.1  
RMSD between 23 pruned atom pairs is 1.066 angstroms; (across all 67 pairs:
8.514)  
  

> select #1/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> select #1/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain #1/H

Alignment identifier is 1/H  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/S

Alignment identifier is 2/S  

> ui tool show "Color Actions"

> select #1/H

13821 atoms, 13974 bonds, 841 residues, 1 model selected  

> select #2/S

7818 atoms, 7912 bonds, 469 residues, 1 model selected  

> color sel orange target cs

> select #1/H:740

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/H:201-740

8763 atoms, 8852 bonds, 534 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/H:976

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/H:784-976

3194 atoms, 3223 bonds, 193 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/H:1047

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

> select #1/H:1047

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

> select #2/S:1046

25 atoms, 24 bonds, 1 residue, 1 model selected  

> select #2/S:985-1046

1038 atoms, 1055 bonds, 62 residues, 1 model selected  

> cartoon hide sel

> select #1/H:781

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

> select #1/H:781-984

185 atoms, 186 bonds, 1 pseudobond, 11 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> select #2/S:780

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/S:742-780

526 atoms, 535 bonds, 33 residues, 1 model selected  

> cartoon hide sel

> dssp

> select clear

[Repeated 1 time(s)]

> select #1/H:781

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

> select #1/H:781-984

185 atoms, 186 bonds, 1 pseudobond, 11 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select #2/S:985

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/S:985-1046

1038 atoms, 1055 bonds, 62 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/H:741

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/H:741

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select #1/H:985-1003

307 atoms, 309 bonds, 19 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain #1/H

Alignment identifier is 1/H  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/S

Alignment identifier is 2/S  

> select #1/H:741

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/H:741

22 atoms, 21 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/S:742

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

> select #2/S:742-780

526 atoms, 535 bonds, 33 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> combine #1,2 close true name 2b

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> select /S:741@C/H:742@N

2 atoms, 2 residues, 1 model selected  

> view sel

> ui mousemode right zoom

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select /S:780@C/S:781@N

2 atoms, 2 residues, 1 model selected  

> view sel

> bond sel reasonable false

Created 1 bond  

> select /S:984@C/S:985@N

2 atoms, 2 residues, 1 model selected  

> view sel

> bond sel reasonable false

Created 1 bond  

> ui tool show "Show Sequence Viewer"

> sequence chain /S

Alignment identifier is 1/S  

> addh

Summary of feedback from adding hydrogens to 2b #1  
---  
notes | Termini for 2b (#1) chain A determined from SEQRES records  
Termini for 2b (#1) chain B determined from SEQRES records  
Termini for 2b (#1) chain C determined from SEQRES records  
Termini for 2b (#1) chain D determined from SEQRES records  
Termini for 2b (#1) chain E determined from SEQRES records  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ACE 0, /B ACE 0, /C ACE
0, /D ACE 0, /E ACE 0, /F ACE 0, /G ACE 0, /J SER 2, /b ASN 1035, /Q MET 1, /R
MET 1, /S GLN 566  
Chain-initial residues that are not actual N termini: /S GLY 597, /S PRO 781,
/S ILE 742  
Chain-final residues that are actual C termini: /A PHE 374, /B PHE 374, /C PHE
374, /D PHE 374, /E ASN 165, /F PHE 374, /G PHE 374, /b VAL 1167, /Q HIS 166,
/R HIS 166, /S PRO 1047  
Chain-final residues that are not actual C termini: /J ASN 172, /S GLU 590, /S
LYS 741, /S GLU 984  
Missing OXT added to C-terminal residue /E ASN 165  
3613 hydrogen bonds  
/J ASN 172 is not terminus, removing H atom from 'C'  
/S GLU 590 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> isolde sim start /S

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: started sim  

> isolde sim pause

> close #1.3

> show sel cartoons

> hide sel atoms

> isolde sim resume

> show sel atoms

> select

55861 atoms, 56447 bonds, 10 pseudobonds, 3542 residues, 17 models selected  

> show sel atoms

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb"

> close #1.3

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb" format pdb

VAV1 working 2b.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2b.pdb #1  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
b | No description available |  
  
Non-standard residues in VAV1 working 2b.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> interfaces #1 areaCutoff 10

26 buried areas: D J 2191, S R 1705, S Q 1651, B b 1580, J E 1579, B F 1311, S
J 1275, A D 1251, B C 1251, D G 1245, S A 937, S E 934, D F 667, F G 640, A C
600, A B 572, B D 558, S D 508, G J 460, F b 383, D E 377, A E 313, B E 277, B
J 249, A J 214, C E 32  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

Drag select of 3679 atoms, 1020 bonds  

> cofr sel

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> sequence chain /F

Alignment identifier is 1/F  

> sequence chain /G

Alignment identifier is 1/G  

> sequence chain /J

Alignment identifier is 1/J  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /R

Alignment identifier is 1/R  

> sequence chain /S

Alignment identifier is 1/S  

> select clear

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select P

17 atoms, 9 residues, 1 model selected  

> color sel purple

> select sel :< 1 & ~sel

309 atoms, 272 bonds, 9 residues, 1 model selected  

> select intersect O

84 atoms, 9 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel red target a

> select /E:160@O

1 atom, 1 residue, 1 model selected  

> color sel hot pink target a

> select /E:142

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:142

24 atoms, 24 bonds, 1 residue, 1 model selected  

> dssp

> isolde sim start /S,E,R,Q

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
VAV1 working 2b.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2b.pdb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/F 1.2/G | No description available |  
1.2/E | No description available |  
1.2/J | No description available |  
1.2/Q 1.2/R | C-H-RAS | RASH_HUMAN 1-166  
1.2/S | SOS-1 | SOS1_HUMAN 566-1046  
1.2/b | No description available |  
  
Non-standard residues in VAV1 working 2b.pdb #1.2  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: started sim  

> isolde sim pause

> close #1.3

> hide sel atoms

> show sel cartoons

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /S,E,R,Q,J

Loading residue template for ADP from internal database  
ISOLDE: started sim  

> isolde sim pause

> close #1.3

> show sel cartoons

> hide sel atoms

> isolde sim resume

> show sel atoms

> select

55861 atoms, 56447 bonds, 10 pseudobonds, 3542 residues, 17 models selected  

> show sel atoms

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb" format pdb

VAV1 working 2b.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2b.pdb #1  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
b | No description available |  
  
Non-standard residues in VAV1 working 2b.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> interfaces #1 areaCutoff 10

26 buried areas: D J 2193, S R 1697, S Q 1657, J E 1594, B b 1580, B F 1311, S
J 1263, B C 1250, A D 1250, D G 1246, S A 947, S E 913, D F 667, F G 640, A C
600, A B 572, B D 558, S D 490, G J 463, D E 384, F b 383, A E 305, B E 268, B
J 249, A J 213, C E 34  

> select /S

7911 atoms, 8008 bonds, 476 residues, 1 model selected  

> color sel orange

> select clear

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SOS1-GRB2 mono3.pdb"

Chain information for SOS1-GRB2 mono3.pdb #2  
---  
Chain | Description  
A | No description available  
Q R | No description available  
T U | No description available  
  

> hide atoms

> show cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain #1/S

Alignment identifier is 1/S  

> select #1/S:740-741

44 atoms, 43 bonds, 2 residues, 1 model selected  

> select #1/S:586-741

2562 atoms, 2591 bonds, 150 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/S & sel pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2b.pdb, chain S (#1) with SOS1-GRB2 mono3.pdb, chain A
(#2), sequence alignment score = 712.6  
RMSD between 117 pruned atom pairs is 0.635 angstroms; (across all 150 pairs:
2.962)  
  

> matchmaker #2/Q to #1/Q & sel pairing ss

No 'to' chains specified  

> matchmaker #2/Q to #1/Q pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2b.pdb, chain Q (#1) with SOS1-GRB2 mono3.pdb, chain Q
(#2), sequence alignment score = 832.3  
RMSD between 157 pruned atom pairs is 0.862 angstroms; (across all 166 pairs:
1.024)  
  

> ui mousemode right zoom

> ui tool show "Side View"

> select

89564 atoms, 90564 bonds, 14 pseudobonds, 5643 residues, 4 models selected  

> view sel

> select clear

[Repeated 1 time(s)]

> select add #1

55861 atoms, 56447 bonds, 10 pseudobonds, 3542 residues, 2 models selected  

> select subtract #1/S

47950 atoms, 48439 bonds, 10 pseudobonds, 3066 residues, 2 models selected  

> select subtract #1/E

45313 atoms, 45774 bonds, 10 pseudobonds, 2900 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:614-615

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select #2/A:614-1047

7223 atoms, 7315 bonds, 434 residues, 1 model selected  

> cartoon hide sel

> select #1/S:742

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

> select #1/S:741-742

41 atoms, 40 bonds, 2 residues, 1 model selected  

> select #1/S:604

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/S:566-604

518 atoms, 522 bonds, 33 residues, 1 model selected  

> cartoon hide sel

> select
> #1/S:606-613,621-633,637-648,658-664,673-699,701-704,708-720,725-741,771-773,776-778,783-798,801-803,808-810,814-817,819-840,845-864,868-879,881-884,887-892,895-907,910-919,931-940,958-976,985-994,1004-1016

4693 atoms, 4715 bonds, 272 residues, 1 model selected  

> select #2/A:606

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

> select #2/A:606-618

243 atoms, 245 bonds, 13 residues, 1 model selected  

> cartoon hide sel

> select #2/A:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/A:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:606-607

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select #2/A:606-1038

7238 atoms, 7327 bonds, 433 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/S:603-604

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/S:566-604

518 atoms, 522 bonds, 33 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/S:605-606

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select #1/S:605-606

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select #1/S:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/S:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/A:1

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

> select #2/A:1

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

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.cxs"

Taking snapshot of stepper: working  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working':
Error while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'working':
Error while saving session data for 'isolde residue stepper 0' -> -> 'working'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working':
Error while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'working':
Error while saving session data for 'isolde residue stepper 0' -> -> 'working'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select #1/S:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/S:605-607

49 atoms, 48 bonds, 3 residues, 1 model selected  

> select #1/S:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/S:605

14 atoms, 13 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #1/S:606-607

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select #2/Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> cartoon hide (#!2 & sel)

> select #1/Q#1/R

5284 atoms, 5323 bonds, 4 pseudobonds, 334 residues, 2 models selected  

> cartoon (#!1 & sel)

> select #2/Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/R

2619 atoms, 2638 bonds, 166 residues, 1 model selected  

> cartoon hide sel

> delete atoms sel

> delete bonds sel

> combine #1,2 close true name 2c

Remapping chain ID 'A' in SOS1-GRB2 mono3.pdb #2 to 'H'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "add models":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "add models":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select /A

5846 atoms, 5910 bonds, 1 pseudobond, 377 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /D

Alignment identifier is 1/D  

> sequence chain /E

Alignment identifier is 1/E  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> sequence chain /J

Alignment identifier is 1/J  

> ui tool show "Show Sequence Viewer"

> sequence chain /S

Alignment identifier is 1/S  

> select clear

> select /S:606

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

> select /H:605@C/S:606@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> view sel

> bond sel reasonable false

Created 1 bond  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> ui mousemode right "translate selected models"

> select clear

> select /H:1039-1047

277 atoms, 281 bonds, 18 residues, 1 model selected  

> select /H:1047

29 atoms, 29 bonds, 2 residues, 1 model selected  

> select /H:1039-1047

277 atoms, 281 bonds, 18 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.pdb" relModel #1

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> ui tool show "Renumber Residues"

> help help:user/tools/renumber.html

> renumber /H seqStart 1 relative false

286 residues renumbered  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.pdb" format pdb

VAV1 working 2c.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2c.pdb #1  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
H | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
T U | No description available |  
b | No description available |  
  
Non-standard residues in VAV1 working 2c.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2b.pdb"

VAV1 working 2b.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2b.pdb #2  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
b | No description available |  
  
Non-standard residues in VAV1 working 2b.pdb #2  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> ui tool show Matchmaker

> matchmaker #2/Q to #1/Q pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2c.pdb, chain Q (#1) with VAV1 working 2b.pdb, chain Q
(#2), sequence alignment score = 859.9  
RMSD between 166 pruned atom pairs is 0.000 angstroms; (across all 166 pairs:
0.000)  
  

> split #2

Split VAV1 working 2b.pdb (#2) into 12 models  
Chain information for VAV1 working 2b.pdb A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for VAV1 working 2b.pdb B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for VAV1 working 2b.pdb C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for VAV1 working 2b.pdb D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for VAV1 working 2b.pdb E #2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for VAV1 working 2b.pdb F #2.6  
---  
Chain | Description  
F | No description available  
  
Chain information for VAV1 working 2b.pdb G #2.7  
---  
Chain | Description  
G | No description available  
  
Chain information for VAV1 working 2b.pdb J #2.8  
---  
Chain | Description  
J | No description available  
  
Chain information for VAV1 working 2b.pdb Q #2.9  
---  
Chain | Description  
Q | No description available  
  
Chain information for VAV1 working 2b.pdb R #2.10  
---  
Chain | Description  
R | No description available  
  
Chain information for VAV1 working 2b.pdb S #2.11  
---  
Chain | Description  
S | No description available  
  
Chain information for VAV1 working 2b.pdb b #2.12  
---  
Chain | Description  
b | No description available  
  

> close #2.5,8,10#2.1-4,6-7,9

> close #2.12

> select #1/H:1029

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/H:1029-1035

130 atoms, 132 bonds, 7 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2.11/S to #1/H & sel pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker VAV1 working 2c.pdb, chain H (#1) with VAV1 working 2b.pdb S, chain
S (#2.11), sequence alignment score = 35.7  
RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs:
0.000)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2.11/S

Alignment identifier is 2.11/S  

> select #2.11/S:1038

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

> select #2.11/S:1038

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

> select #2.11/S:1047

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

> select #2.11/S:1039-1047

139 atoms, 141 bonds, 9 residues, 1 model selected  

> select ~sel & ##selected

7772 atoms, 7867 bonds, 467 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> combine #2 close true name missing

> ui tool show "Show Sequence Viewer"

> sequence chain #2/S

Alignment identifier is 2/S  

> combine #1,2 close true name 2c

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "add models":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 391, in _items_change  
prev_value = self.get_value()  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
KeyError: 'missing #2/S'  
  
Error processing trigger "changes":  
KeyError: 'missing #2/S'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> select /H:1038@C/S1039@N

1 atom, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> select /H:1038@C/S:1039@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> ui mousemode right "rotate selected models"

> ui mousemode right zoom

> select /H:1047@C/H:1048@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select /H:1047@C/H:1048@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> isolde sim start /H:1042-1052

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: started sim  

> close #1.3

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.pdb"

> isolde sim start /H

ISOLDE: started sim  

> isolde sim pause

> close #1.3

> hide sel atoms

> show sel cartoons

> isolde sim resume

> show sel atoms

> hide sel cartoons

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close #1.3

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c.pdb" format pdb

VAV1 working 2c.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2c.pdb #1  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
H | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
T U | No description available |  
b | No description available |  
  
Non-standard residues in VAV1 working 2c.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> set bgColor black

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select /E:165

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

> select /E:162-165

57 atoms, 56 bonds, 4 residues, 1 model selected  

> select /E:165

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

> select /E:165

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

> interfaces #1 areaCutoff 10

29 buried areas: H U 3986, T U 3751, H T 3323, H Q 2368, D J 2193, H R 1700, J
E 1602, B b 1580, H E 1333, B F 1311, H J 1294, B C 1250, A D 1250, D G 1246,
H A 787, D F 667, F G 640, A C 600, A B 572, B D 558, H D 483, G J 463, D E
385, F b 383, A E 305, B E 268, B J 249, A J 212, C E 34  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> sequence chain /J

Alignment identifier is 1/J  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /R

Alignment identifier is 1/R  

> ui tool show "Show Sequence Viewer"

> select clear

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c1.pdb"

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAV1 working 2c1.pdb  
---  
warnings | Ignored bad PDB record found on line 70  
  
  
Duplicate atom serial number found: 1333  
Duplicate atom serial number found: 11333  
Duplicate atom serial number found: 21333  
Duplicate atom serial number found: 31333  
Duplicate atom serial number found: 41333  
13 messages similar to the above omitted  
  
VAV1 working 2c1.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for VAV1 working 2c1.pdb #1  
---  
Chain | Description | UniProt  
A B C D F G | No description available |  
E | No description available |  
H | No description available |  
J | No description available |  
Q R | C-H-RAS | RASH_HUMAN 1-166  
T U | No description available |  
b | No description available |  
  
Non-standard residues in VAV1 working 2c1.pdb #1  
---  
ACE — (ACE)  
ADP — (ADP)  
GTP — (GTP)  
MG — magnesium ion  
PTR — (PTR)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /H

Alignment identifier is 1/H  

> sequence chain /J

Alignment identifier is 1/J  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /R

Alignment identifier is 1/R  

> interfaces #1 areaCutoff 10

29 buried areas: H U 3986, T U 3751, H T 3323, H Q 2368, D J 2193, H R 1700, J
E 1602, B b 1580, H E 1333, B F 1311, H J 1294, B C 1250, A D 1250, D G 1246,
H A 787, D F 667, F G 640, A C 600, A B 572, B D 558, H D 483, G J 463, D E
385, F b 383, A E 305, B E 268, B J 249, A J 212, C E 34  

> select /Q/R

5284 atoms, 5323 bonds, 4 pseudobonds, 334 residues, 2 models selected  

> color (#!1 & sel) forest green

> select /T

3484 atoms, 3534 bonds, 217 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel plum target a

> select /U

3484 atoms, 3534 bonds, 217 residues, 1 model selected  

> color sel violet target a

> select clear

> select /H

21454 atoms, 21729 bonds, 1333 residues, 1 model selected  

> color sel orange target a

> select clear

> set bgColor white

> select /b

2193 atoms, 2208 bonds, 133 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J

2760 atoms, 2783 bonds, 171 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel khaki target a

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> select H

36767 atoms, 4693 residues, 1 model selected  

> hide sel target a

> select clear

> ui mousemode right zoom

> roll y 2 180

> roll x 2 180

> roll y 2 18

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAV1 working 2c1.cxs"

Taking snapshot of stepper: working  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working':
Error while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'working':
Error while saving session data for 'isolde residue stepper 0' -> -> 'working'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'isolde residue stepper 0'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working':
Error while saving session data for 'isolde residue stepper 0' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x17474ecd0> ->
<chimerax.atomic.structure.AtomicStructure object at 0x1aa279d50> 'working'  
  
ValueError: error processing: 'isolde residue stepper 0' -> -> 'working':
Error while saving session data for 'isolde residue stepper 0' -> -> 'working'  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 4 days, 10 hours

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 20 months ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: ResidueStepper references dead Structure

Reported by Tim McKeithan

comment:2 by Tristan Croll, 18 months ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed (finally!). See #14894.

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