id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18703	Crash in garbage collection	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs""

Log from Thu Sep 4 14:59:35 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs""

Log from Thu Sep 4 14:44:21 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs""

Log from Thu Sep 4 13:33:38 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs""

Log from Thu Sep 4 12:58:57 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs""
> format session

Log from Wed Sep 3 18:54:37 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo107-coot-0.pdb""

Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo107-coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
714 messages similar to the above omitted  
  
Chain information for Fit_6596_redo107-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo104-coot-0.pdb""

Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo104-coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
714 messages similar to the above omitted  
  
Chain information for Fit_6596_redo104-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo106-coot-0.pdb""

Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo106-coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
655 messages similar to the above omitted  
  
Chain information for Fit_6596_redo106-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo108-coot-0.pdb""

Summary of feedback from opening /Users/julia/Desktop/cryo-EM data
processing/ChimeraX/structures/ternary0529_DEG6596/Fit_6596_redo108-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 GLN C
33 SER C 41 1 9  
Start residue of secondary structure not found: HELIX 13 13 ALA C 71 LEU C 81
1 11  
Start residue of secondary structure not found: SHEET 15 1515 ASN C 21 ASN C
25 0  
Start residue of secondary structure not found: SHEET 16 1616 VAL C 46 LEU C
51 0  
Start residue of secondary structure not found: SHEET 17 1717 TYR C 63 TYR C
68 0  
1 messages similar to the above omitted  
  
Chain information for Fit_6596_redo108-coot-0.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> matchmaker #2-4 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
Alignment identifier is 2  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo106-coot-0.pdb #3/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
Alignment identifier is 3  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo108-coot-0.pdb #4/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> matchmaker #2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> ui tool show Matchmaker

> matchmaker #!2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> ui tool show ""Render by Attribute""

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 5,#fffb00:5,blue:5,red noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844  

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow
> noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844  

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow

46518 atoms, 6313 residues, atom seq_rmsd range 0 to 0.000844  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!4 models

> hide #!1 models

> show #!1 models

> matchmaker #2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> show #!2 models

> show #!3 models

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  

> sequence header 3 rmsd show

Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  

> sequence header 1 rmsd show

Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  

> ui tool show ""Render by Attribute""

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 1.66667,#0433ff:3,#fffb00:5,#fffb00:5,blue:5,red:5,#ff2600:5,yellow
> noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> ui tool show ""Render by Attribute""

[Repeated 1 time(s)]

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:0.760137,white:1.69034,red

46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:0.760137,#fffb00:1.69034,red

46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4  

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> show #!2 models

> show #!3 models

> show #!4 models

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4  

> hide #!4 models

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:1,#fffb00:3,red noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4  

> show #!4 models

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #1/A#2/A#3/A#4/A

32112 atoms, 32688 bonds, 4 pseudobonds, 4528 residues, 8 models selected  

> show #!1 models

> show #!2 models

> show #!3 models

> cartoon hide (#!1-4 & sel)

> select add #1

35908 atoms, 36569 bonds, 8 pseudobonds, 4996 residues, 9 models selected  

> select add #2

39704 atoms, 40450 bonds, 12 pseudobonds, 5464 residues, 10 models selected  

> select add #3

43441 atoms, 44267 bonds, 16 pseudobonds, 5931 residues, 11 models selected  

> select add #4

46518 atoms, 47416 bonds, 20 pseudobonds, 6313 residues, 12 models selected  

> select subtract #3

34753 atoms, 35427 bonds, 15 pseudobonds, 4714 residues, 9 models selected  

> select subtract #2

22929 atoms, 23374 bonds, 10 pseudobonds, 3114 residues, 6 models selected  

> select subtract #1

11105 atoms, 11321 bonds, 5 pseudobonds, 1514 residues, 3 models selected  

> select subtract #4

Nothing selected  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> ui tool show ""Render by Attribute""

> key blue:0 #fffb00:1 red:3 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> ui tool show ""Render by Attribute""

> color byattribute r:seq_rmsd #!1-4 target sabc palette
> 0.000165002,blue:1.5,#fffb00:3,red noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0.000165 to 12.5  

> close #5

> key blue:0.0 #fffb00:1.5 red:3.0 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.000165 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000165 to 3.4  

> hide #6 models

> show #6 models

> ui tool show ""Render by Attribute""

> hide #6 models

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs""
> includeMaps true

——— End of log from Wed Sep 3 18:54:37 2025 ———

opened ChimeraX session  

> show #!4 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/B:338

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

> select #4/B:338-339

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

> select #4/B:341

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #4/B:341-361

157 atoms, 162 bonds, 21 residues, 1 model selected  

> select clear

> show #!1 models

> hide #!4 models

> hide #!1 models

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class1-model-
> coot-11.pdb""

Chain information for Fit_class1-model-coot-11.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class2-model-
> coot-10.pdb""

Chain information for Fit_class2-model-coot-10.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class4-model-
> coot-3.pdb""

Chain information for Fit_class4-model-coot-3.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class3-model-
> coot-2.pdb""

Chain information for Fit_class3-model-coot-2.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!5 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!5 models

> hide #!5 models

> show #!7 models

> show #!5 models

> hide #!5 models

> hide #!7 models

> show #!1 models

> show #!2 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!7 models

> hide #!7 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!5 models

> show #!7 models

> show #!8 models

> hide #!5 models

> hide #!7 models

> hide #!1 models

> hide #!8 models

> show #!8 models

> show #!7 models

> hide #!8 models

> show #!5 models

> show #!9 models

> hide #!5 models

> hide #!7 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #6 models

> hide #6 models

> show #!7 models

> show #!8 models

> show #!9 models

> close #6

> close #5

> close #7

> close #8

> close #9

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class1-model-
> coot-11.pdb""

Chain information for Fit_class1-model-coot-11.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class2-model-
> coot-10.pdb""

Chain information for Fit_class2-model-coot-10.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class4-model-
> coot-3.pdb""

Chain information for Fit_class4-model-coot-3.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0616_DEG3515/Fit_class3-model-
> coot-2.pdb""

Chain information for Fit_class3-model-coot-2.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show ""Show Sequence Viewer""

[Repeated 2 time(s)]

> sequence chain #5/A

Alignment identifier is 5/A  

> sequence chain #5/B

Alignment identifier is 5/B  

> sequence chain #5/C

Alignment identifier is 5/C  

> sequence chain #6/A

Alignment identifier is 6/A  

> sequence chain #6/B

Alignment identifier is 6/B  

> sequence chain #6/C

Alignment identifier is 6/C  

> sequence chain #7/A

Alignment identifier is 7/A  

> sequence chain #7/B

Alignment identifier is 7/B  

> sequence chain #7/C

Alignment identifier is 7/C  

> sequence chain #8/A

Alignment identifier is 8/A  

> sequence chain #8/B

Alignment identifier is 8/B  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A

Alignment identifier is 1  

> sequence header rmsd show

Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A, Fit_class1-model-coot-11.pdb #5/A,
Fit_class2-model-coot-10.pdb #6/A, Fit_class4-model-coot-3.pdb #7/A,
Fit_class3-model-coot-2.pdb #8/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B

Alignment identifier is 2  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/C #2/C #3/C #5/C #6/C #7/C

Alignment identifier is 3  

> sequence header 3 rmsd show

Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C,
Fit_class1-model-coot-11.pdb #5/C, Fit_class2-model-coot-10.pdb #6/C,
Fit_class4-model-coot-3.pdb #7/C  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  

> ui tool show ""Render by Attribute""

> key blue:0.18 #fffb00:1.00 red:3.00 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1,#fffb00:3,red noValueColor grey

45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2  

> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1,#fffb00:3,red noValueColor grey

45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2  

> ui tool show ""Render by Attribute""

> key blue:0.18 #fffb00:1.50 red:3.00 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute r:seq_rmsd #!5-8 target csab palette
> 0.180098,blue:1.5,#fffb00:3,red noValueColor grey

45869 atoms, 6220 residues, atom seq_rmsd range 0.18 to 10.2  

> color byattribute seq_rmsd #5 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.18 to 10.2  

> color byattribute seq_rmsd #6 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.18 to 10.2  

> color byattribute seq_rmsd #7 palette blue:yellow:red

11078 atoms, 1505 residues, atom seq_rmsd range 0.18 to 4.34  

> color byattribute seq_rmsd #8 palette blue:yellow:red

11157 atoms, 1515 residues, atom seq_rmsd range 0.18 to 4.43  

> hide #9 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!5 models

> show #!8 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!8 models

> show #!8 models

> hide #!5 models

> hide #!8 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> hide #!6 models

> show #!8 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!8 models

> show #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!1 models

> show #!5 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> show #!8 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!8 models

> show #!8 models

> hide #!5 models

> show #!5 models

> hide #!8 models

> show #!8 models

> hide #!5 models

> hide #!8 models

> show #!1 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!1 models

> show #!8 models

> ui tool show ""Render by Attribute""

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B

Alignment identifier is 1  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B

Alignment identifier is 1  

> sequence header rmsd show

Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> hide #!8 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> matchmaker #2-8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class1-model-
coot-11.pdb, chain A (#5), sequence alignment score = 5752  
RMSD between 1128 pruned atom pairs is 0.191 angstroms; (across all 1132
pairs: 0.280)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class2-model-
coot-10.pdb, chain A (#6), sequence alignment score = 5741.2  
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class4-model-
coot-3.pdb, chain A (#7), sequence alignment score = 5741.2  
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with Fit_class3-model-
coot-2.pdb, chain A (#8), sequence alignment score = 5741.2  
RMSD between 1128 pruned atom pairs is 0.185 angstroms; (across all 1132
pairs: 0.277)  
  

> show #9 models

> hide #9 models

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08  

> color byattribute seq_rmsd #5 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #6 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #7 palette blue:yellow:red

11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34  

> color byattribute seq_rmsd #8 palette blue:yellow:red

11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08  

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!7 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!8 models

> show #!4 models

> hide #!8 models

> hide #!4 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #9 models

> show #!6 models

> show #!7 models

> show #!8 models

> ui tool show ""Render by Attribute""

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 0.00785371,blue:1.96353,#fffb00:5,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> key blue:0.01 #fffb00:1.96 red:5.00 showTool true

> ui mousemode right ""color key""

> key blue:0.01 #fffb00:2 red:5.00

> ui mousemode right translate

> key blue:0.01 #fffb00:1.96 red:4.00 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> key blue:0.01 #fffb00:1.96 red:4.00 showTool true

> ui mousemode right ""color key""

> key blue:0.01 #fffb00:2 red:4.00

> ui mousemode right translate

> hide #9 models

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08  

> color byattribute seq_rmsd #5 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #6 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #7 palette blue:yellow:red

11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34  

> color byattribute seq_rmsd #8 palette blue:yellow:red

11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08  

> show #9 models

> hide #9 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!8 models

> hide #!4 models

> show #9 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> ui tool show ""Render by Attribute""

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1,blue:2,#fffb00:4,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 0,blue:1.99367,#fffb00:3.99521,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1.2,blue:1.99367,#fffb00:3.99521,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1.2,blue:1.99367,#fffb00:3.99521,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> ui tool show ""Render by Attribute""

> key blue:1 #fffb00:2 red:3 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute r:seq_rmsd #!1-8 target csab palette
> 1,blue:2,#fffb00:3,red noValueColor grey

92387 atoms, 12533 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.00785 to 5.08  

> color byattribute seq_rmsd #5 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #6 palette blue:yellow:red

11817 atoms, 1600 residues, atom seq_rmsd range 0.00785 to 10.2  

> color byattribute seq_rmsd #7 palette blue:yellow:red

11078 atoms, 1505 residues, atom seq_rmsd range 0.00785 to 4.34  

> color byattribute seq_rmsd #8 palette blue:yellow:red

11157 atoms, 1515 residues, atom seq_rmsd range 0.00785 to 5.08  

> hide #9 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!1 models

> show #!4 models

> hide #!1 models

> show #!8 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!8 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> matchmaker #2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> matchmaker #6-8 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class2-model-
coot-10.pdb, chain A (#6), sequence alignment score = 5767.6  
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)  
  
Matchmaker Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class4-model-
coot-3.pdb, chain A (#7), sequence alignment score = 5767.6  
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)  
  
Matchmaker Fit_class1-model-coot-11.pdb, chain A (#5) with Fit_class3-model-
coot-2.pdb, chain A (#8), sequence alignment score = 5767.6  
RMSD between 1132 pruned atom pairs is 0.041 angstroms; (across all 1132
pairs: 0.041)  
  

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!5 models

> hide #!6 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A

Alignment identifier is 2  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A, Fit_class1-model-coot-11.pdb #5/A,
Fit_class2-model-coot-10.pdb #6/A, Fit_class4-model-coot-3.pdb #7/A,
Fit_class3-model-coot-2.pdb #8/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/B #2/B #3/B #4/B #5/B #6/B #7/B #8/B

Alignment identifier is 3  

> sequence header 3 rmsd show

Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B, Fit_class1-model-coot-11.pdb #5/B,
Fit_class2-model-coot-10.pdb #6/B, Fit_class4-model-coot-3.pdb #7/B,
Fit_class3-model-coot-2.pdb #8/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd.cxs""
> includeMaps true

——— End of log from Thu Sep 4 12:58:57 2025 ———

opened ChimeraX session  

> close #5

> close #6

> close #7

> close #8

> close #9

> matchmaker #2-4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo104-coot-0.pdb, chain A (#2), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo106-coot-0.pdb, chain A (#3), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #2/A #3/A #4/A

Alignment identifier is 1  

> sequence header rmsd show

Chains used in RMSD evaluation for alignment 1: Fit_6596_redo107-coot-0.pdb
#1/A, Fit_6596_redo104-coot-0.pdb #2/A, Fit_6596_redo106-coot-0.pdb #3/A,
Fit_6596_redo108-coot-0.pdb #4/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/B #2/B #3/B #4/B

Alignment identifier is 2  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2: Fit_6596_redo107-coot-0.pdb
#1/B, Fit_6596_redo104-coot-0.pdb #2/B, Fit_6596_redo106-coot-0.pdb #3/B,
Fit_6596_redo108-coot-0.pdb #4/B  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/C #2/C #3/C

Alignment identifier is 3  

> sequence header 3 rmsd show

Chains used in RMSD evaluation for alignment 3: Fit_6596_redo107-coot-0.pdb
#1/C, Fit_6596_redo104-coot-0.pdb #2/C, Fit_6596_redo106-coot-0.pdb #3/C  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  

> ui tool show ""Render by Attribute""

> key blue:0 #fffb00:2 red:4 showTool true

> ui mousemode right ""color key""

> ui mousemode right translate

> color byattribute r:seq_rmsd #!1-4 target cabs palette
> 0,blue:1.99986,#fffb00:3.99989,red noValueColor grey

46518 atoms, 6313 residues, atom seq_rmsd range 0.000164 to 12.5  

> color byattribute seq_rmsd #1 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000164 to 12.5  

> color byattribute seq_rmsd #2 palette blue:yellow:red

11824 atoms, 1600 residues, atom seq_rmsd range 0.000164 to 12.5  

> color byattribute seq_rmsd #3 palette blue:yellow:red

11765 atoms, 1599 residues, atom seq_rmsd range 0.000164 to 12.5  

> color byattribute seq_rmsd #4 palette blue:yellow:red

11105 atoms, 1514 residues, atom seq_rmsd range 0.000164 to 3.4  

> hide #5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"" includeMaps true

> show #!4 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> hide #!4 models

> show #5 models

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"" includeMaps true

——— End of log from Thu Sep 4 13:33:38 2025 ———

opened ChimeraX session  

> hide #5 models

> show #!4 models

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit_6596_redo107-coot-0.pdb, chain A (#1) with
Fit_6596_redo108-coot-0.pdb, chain A (#4), sequence alignment score = 5778.4  
RMSD between 1132 pruned atom pairs is 0.000 angstroms; (across all 1132
pairs: 0.000)  
  

> rmsd #4/B #1/B

Missing required ""to"" argument  

> rmsd #4/B to #1/B

RMSD between 3077 atom pairs is 1.011  

> ui tool show Log

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"" includeMaps true

——— End of log from Thu Sep 4 14:44:21 2025 ———

opened ChimeraX session  

> rmsd #8/B:145-155 to #5/B:145-155

Given atom specs don't contain any atoms  

> rmsd #4/B:145-155 to #1/B:145-155

RMSD between 93 atom pairs is 2.964  

> rmsd #4/B:42-74 to #1/B:42-74

RMSD between 241 atom pairs is 1.463  

> rmsd #4/B:125-130 to #1/B:125-130

RMSD between 51 atom pairs is 2.027  

> rmsd #4/B:173-177 to #1/B:173-177

RMSD between 35 atom pairs is 0.290  

> rmsd #4/B:375-383 to #1/B:375-383

RMSD between 74 atom pairs is 3.151  

> rmsd #4/B:368-375 to #1/B:368-375

RMSD between 60 atom pairs is 0.985  

> save ""/Users/julia/Desktop/cryo-EM data
> processing/ChimeraX/structures/ternary0529_DEG6596/surface-charge/Rmsd
> 6596.cxs"" includeMaps true

——— End of log from Thu Sep 4 14:59:35 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-23.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: en_US.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: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
      OS Loader Version: 583~2210

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 13 days, 20 hours, 44 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL SE2723DS:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 1JF2WP3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: 15.75


Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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-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: 1.7.1
    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-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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    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: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    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: 10.2.0
    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: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
}}}
"	defect	closed	normal		Core		duplicate						all	ChimeraX