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Opened 97 minutes ago
#19479 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.11rc202512020129 (2025-12-02 01:29:55 UTC)
Description
selected residues in MatchMaker Alignment
Log:
UCSF ChimeraX version: 1.11rc202512020129 (2025-12-02)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:/Users/evc1/Downloads/12_3_2025_GII.17_workspace_epitopeColored.cxs
Log from Thu Dec 4 10:11:43 2025UCSF ChimeraX version: 1.11rc202512020129
(2025-12-02)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:\Users\evc1\Downloads\12_3_2025_GII.17_workspace.cxs format session
Log from Wed Dec 3 15:50:48 2025UCSF ChimeraX version: 1.11rc202512020129
(2025-12-02)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> \\\groups.biotech.cdc.gov\groups\OID\NCIRD\DVD\VGB\Norovirus\Helen\phylogenetics\protein_modeling\GII.17_2025\work_session_superimposition.cxs
> format session
Log from Tue Dec 2 14:05:21 2025UCSF ChimeraX version: 1.11rc202512020129
(2025-12-02)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/reference_backbone/8V97.cif
Summary of feedback from opening
//groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/reference_backbone/8V97.cif
---
notes | Fetching CCD EDO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
8V97.cif title:
GII.17 CS-E1 norovirus protruding domain [more info...]
Chain information for 8V97.cif #1
---
Chain | Description | UniProt
A B | Capsid protein VP1 | Q6EAX3_9CALI 1-540
Non-standard residues in 8V97.cif #1
---
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
47 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/AlphaFold_output/fold_2025_12_01_gii17_new_orf2/fold_2025_12_01_gii17_new_orf2_model_0.cif
Chain information for fold_2025_12_01_gii17_new_orf2_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> open
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/AlphaFold_output/gii17_santaclara_vehq_orf2/fold_2025_12_02_gii17_santaclara_vehq_orf2_model_0.cif
Chain information for fold_2025_12_02_gii17_santaclara_vehq_orf2_model_0.cif
#3
---
Chain | Description
A | .
Computing secondary structure
> open
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/AlphaFold_output/gii17_santaclara_venq_orf2/fold_2025_12_02_gii17_santaclara_venq_orf2_model_0.cif
Chain information for fold_2025_12_02_gii17_santaclara_venq_orf2_model_0.cif
#4
---
Chain | Description
A | .
Computing secondary structure
> hide #3 models
> hide #4 models
> select :270-415
5568 atoms, 5713 bonds, 730 residues, 4 models selected
> select ~sel
12603 atoms, 12060 bonds, 2369 residues, 4 models selected
> color (#1-2 & sel) gray
> show #3 models
> show #4 models
> color sel gray
> select ~sel
5568 atoms, 5713 bonds, 730 residues, 4 models selected
> hide #3 models
> hide #4 models
> ui tool show Matchmaker
> rename #2 NEW
> rename #3 SantaClara_VEHQ
> rename #4 SantaClara_VENQ
> rename #1 prototype_8V97
> rename #2 new
> ui tool show Matchmaker
> matchmaker #2 & sel to #1 & sel 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 prototype_8V97, chain A (#1) with new, chain A (#2), sequence
alignment score = 667
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: prototype_8V97 #1/A, new #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 139 pruned atom pairs is 0.494 angstroms; (across all 143 pairs:
0.790)
> select clear
> show #3 models
> show #4 models
> ui tool show Matchmaker
> matchmaker #2-4 & sel to #1 & sel showAlignment true
No 'to' model specified
> matchmaker #2-4 & sel to #1 & sel showAlignment true
No 'to' model specified
> matchmaker #3 & sel to #1 & sel showAlignment true
No 'to' model specified
> select :270-415
5568 atoms, 5713 bonds, 730 residues, 4 models selected
> matchmaker #2-4 & sel to #1 & sel 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 prototype_8V97, chain A (#1) with new, chain A (#2), sequence
alignment score = 667
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: prototype_8V97 #1/A, new #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 139 pruned atom pairs is 0.494 angstroms; (across all 143 pairs:
0.790)
Matchmaker prototype_8V97, chain A (#1) with SantaClara_VEHQ, chain A (#3),
sequence alignment score = 664.4
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: prototype_8V97 #1/A,
SantaClara_VEHQ #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 136 pruned atom pairs is 0.487 angstroms; (across all 145 pairs:
1.061)
Matchmaker prototype_8V97, chain A (#1) with SantaClara_VENQ, chain A (#4),
sequence alignment score = 665.1
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: prototype_8V97 #1/A,
SantaClara_VENQ #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 141 pruned atom pairs is 0.510 angstroms; (across all 145 pairs:
0.704)
> matchmaker #2-4 & sel to #1 & sel 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 prototype_8V97, chain A (#1) with new, chain A (#2), sequence
alignment score = 667
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: prototype_8V97 #1/A, new #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 139 pruned atom pairs is 0.494 angstroms; (across all 143 pairs:
0.790)
Matchmaker prototype_8V97, chain A (#1) with SantaClara_VEHQ, chain A (#3),
sequence alignment score = 664.4
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: prototype_8V97 #1/A,
SantaClara_VEHQ #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 136 pruned atom pairs is 0.487 angstroms; (across all 145 pairs:
1.061)
Matchmaker prototype_8V97, chain A (#1) with SantaClara_VENQ, chain A (#4),
sequence alignment score = 665.1
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: prototype_8V97 #1/A,
SantaClara_VENQ #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 141 pruned atom pairs is 0.510 angstroms; (across all 145 pairs:
0.704)
> ui tool show "Selection Inspector"
> select ~sel
12603 atoms, 12060 bonds, 2369 residues, 4 models selected
> select clear
> hide #3 models
> hide #4 models
> morph #1,2 warp true frames 60
Expected a keyword
> morph #1,2 wrap true frames 60
models have different number of chains, 2 (Morph - prototype_8V97 #/A,Morph -
prototype_8V97 #/B) and 1 (new #2/A)
> split #1
Split prototype_8V97 (#1) into 2 models
Chain information for prototype_8V97 A #1.1
---
Chain | Description
A | No description available
Associated prototype_8V97 A (1.1) chain A to prototype_8V97, chain A with 0
mismatches
Associated prototype_8V97 B (1.2) chain B to prototype_8V97, chain A with 0
mismatches
Associated prototype_8V97 A (1.1) chain A to prototype_8V97, chain A with 0
mismatches
Associated prototype_8V97 B (1.2) chain B to prototype_8V97, chain A with 0
mismatches
Associated prototype_8V97 A (1.1) chain A to prototype_8V97, chain A with 0
mismatches
Associated prototype_8V97 B (1.2) chain B to prototype_8V97, chain A with 0
mismatches
Chain information for prototype_8V97 B #1.2
---
Chain | Description
B | No description available
Chains used in RMSD evaluation for alignment 2: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, new #2/A
Chains used in RMSD evaluation for alignment 3: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, SantaClara_VEHQ #3/A
Chains used in RMSD evaluation for alignment 4: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, SantaClara_VENQ #4/A
> morph #1,2 wrap true frames 60
Associated Morph - prototype_8V97 A chain A to prototype_8V97, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 2: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, new #2/A, Morph - prototype_8V97 A #5/A
Associated Morph - prototype_8V97 A chain A to prototype_8V97, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 3: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, SantaClara_VEHQ #3/A, Morph - prototype_8V97 A #5/A
Associated Morph - prototype_8V97 A chain A to prototype_8V97, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 4: prototype_8V97 A #1.1/A,
prototype_8V97 B #1.2/B, SantaClara_VENQ #4/A, Morph - prototype_8V97 A #5/A
Computed 181 frame morph #5
> coordset #5 1,181
> hide #5.1 models
> show #2 models
> show #5.1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!5 models
> show target m
> hide target m
> show target m
> hide target m
> show #1.1 models
> show #2 models
> save
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/work_session_superimposition.cxs
> hide #2 models
> show #3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #1.1 models
> coulombic #3-4
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for SantaClara_VEHQ_A SES surface #3.1:
minimum, -19.64, mean -2.45, maximum 11.97
Coulombic values for SantaClara_VENQ_A SES surface #4.1: minimum, -17.14, mean
-2.47, maximum 13.55
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #3.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #3.1 models
> mlp #!3-4
Map values for surface "SantaClara_VENQ_A SES surface": minimum -29.38, mean
-5.265, maximum 22.48
Map values for surface "SantaClara_VEHQ_A SES surface": minimum -28.05, mean
-5.403, maximum 22.27
To also show corresponding color key, enter the above mlp command and add key
true
> hide #4.1 models
> show #4.1 models
> hide #3.1 models
> show #3.1 models
> hide #4.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
> show #4.1 models
> show #3.1 models
> show #1.1 models
> show #1.2 models
> hide #1.2 models
> mlp #1.1#!3-4
Map values for surface "SantaClara_VENQ_A SES surface": minimum -29.38, mean
-5.265, maximum 22.48
Map values for surface "SantaClara_VEHQ_A SES surface": minimum -28.05, mean
-5.403, maximum 22.27
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> hide #1.1.1 models
> show #1.1.1 models
> hide #4.1 models
> hide #!4 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #1.1.1 models
> hide #3.1 models
> show #1.1.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> coulombic #!3#!1.1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for SantaClara_VEHQ_A SES surface #3.1: minimum, -19.64, mean
-2.45, maximum 11.97
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #3.1 models
> show #3.1 models
> show #4.1 models
> hide #4.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> color #!3-4#!1.1 bynucleotide
> hide #1.1.1 models
> hide #3.1 models
> label #!1,3-4#!1.1 text "{0.name} {0.number}{0.insertion_code}"
> label clear
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label clear residues
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label residues \clear
Expected a keyword
> label residues clear
Expected a keyword
> ~label #3.2#4.2#1.1.2#!1,3-4#!1.1 residues
> select
20470 atoms, 20146 bonds, 1 pseudobond, 3401 residues, 8 models selected
> select :341-346
211 atoms, 207 bonds, 1 pseudobond, 33 residues, 7 models selected
> style sel & #!3-4#!1.1 ball
Changed 107 atom styles
> style sel & #!3-4#!1.1 stick
Changed 107 atom styles
> mlp sel & #!3-4#!1.1
Map values for surface "SantaClara_VENQ_A SES surface": minimum -29.38, mean
-5.265, maximum 22.48
Map values for surface "SantaClara_VEHQ_A SES surface": minimum -28.05, mean
-5.403, maximum 22.27
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> select subtract #3.1
177 atoms, 174 bonds, 1 pseudobond, 27 residues, 9 models selected
> select add #3.1
4344 atoms, 174 bonds, 1 pseudobond, 568 residues, 9 models selected
> select subtract #4.1
4311 atoms, 142 bonds, 1 pseudobond, 562 residues, 9 models selected
> select subtract #3.1
144 atoms, 142 bonds, 1 pseudobond, 21 residues, 7 models selected
> select subtract #5.1
144 atoms, 142 bonds, 21 residues, 5 models selected
> hide #1.1.1 models
> hide #3.1 models
> hide #4.1 models
> show #4.1 models
> show #3.1 models
> hide #3.1 models
> show #1.1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #1.1.1 models
> show #1.1.1 models
> show #3.1 models
> hide #1.1.1 models
> show #1.1.1 models
> color sel & #!1.1 bynucleotide
> hide #1.1.1 models
> show #1.1.1 models
> hide #3.1 models
> hide #1.1.1 models
> show #1.1.1 models
> show #3.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> select :330-350
884 atoms, 887 bonds, 1 pseudobond, 123 residues, 7 models selected
> mlp sel & #!3-4#!1.1
Map values for surface "SantaClara_VENQ_A SES surface": minimum -29.38, mean
-5.265, maximum 22.48
Map values for surface "SantaClara_VEHQ_A SES surface": minimum -28.05, mean
-5.403, maximum 22.27
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> select subtract #4.1
741 atoms, 744 bonds, 1 pseudobond, 102 residues, 9 models selected
> select subtract #3.1
597 atoms, 600 bonds, 1 pseudobond, 81 residues, 7 models selected
> select subtract #5.1
597 atoms, 600 bonds, 81 residues, 5 models selected
> hide #4.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> save
> //groups.biotech.cdc.gov/groups/OID/NCIRD/DVD/VGB/Norovirus/Helen/phylogenetics/protein_modeling/GII.17_2025/work_session_superimposition.cxs
——— End of log from Tue Dec 2 14:05:21 2025 ———
> view name session-start
opened ChimeraX session
> select :270-415
6626 atoms, 6797 bonds, 1 pseudobond, 873 residues, 7 models selected
> select add #1.2
8357 atoms, 8122 bonds, 1 pseudobond, 1477 residues, 10 models selected
> select subtract #1.2
5514 atoms, 5656 bonds, 1 pseudobond, 727 residues, 9 models selected
> hide #!4 models
> hide #!3 models
> show #2 models
> color sel & #2#!1.1 bychain
> color (#2#!1.1 & sel) light gray
> mlp sel & #2#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!2#!1.1 bychain
> color (#!2#!1.1 & sel) light gray
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show sel & #!1.1 cartoons
> hide sel & #!1.1 surfaces
> show #!2 models
> hide sel & #!2#!1.1 surfaces
> show sel & #!2#!1.1 cartoons
> show sel & #!2#!1.1 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide sel & #!2#!1.1 surfaces
> select :405-415
516 atoms, 525 bonds, 66 residues, 6 models selected
> show sel & #!2#!1.1 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1.1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!2 models
> show #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> select ~sel
19954 atoms, 19609 bonds, 1 pseudobond, 3335 residues, 8 models selected
> hide sel & #!2 cartoons
> select ~sel
516 atoms, 525 bonds, 66 residues, 6 models selected
> show #!1.1 models
> select :270-415
6626 atoms, 6797 bonds, 1 pseudobond, 873 residues, 7 models selected
> select ~sel
13844 atoms, 13337 bonds, 2528 residues, 7 models selected
> hide sel & #!2#!1.1 cartoons
> select :270-415
6626 atoms, 6797 bonds, 1 pseudobond, 873 residues, 7 models selected
> select :405-415
516 atoms, 525 bonds, 66 residues, 6 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide sel & #!2#!1.1 cartoons
[Repeated 1 time(s)]
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> select :400-415
802 atoms, 831 bonds, 96 residues, 6 models selected
> mlp sel & #!2#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!2#!1.1 bychain
> select :390-415
1247 atoms, 1285 bonds, 156 residues, 6 models selected
> mlp sel & #!2#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> select ~sel
19223 atoms, 18849 bonds, 1 pseudobond, 3245 residues, 8 models selected
> hide sel & #!2#!1.1 cartoons
> select ~sel
1247 atoms, 1285 bonds, 156 residues, 6 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> coulombic sel & #!2#!1.1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> mlp sel & #!2#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide sel & #!2#!1.1 surfaces
[Repeated 1 time(s)]
> show sel & #!2#!1.1 cartoons
> style sel & #!2#!1.1 ball
Changed 426 atom styles
> show sel & #!2#!1.1 atoms
> color sel & #!2#!1.1 bynucleotide
> select :285-305
1039 atoms, 1064 bonds, 126 residues, 6 models selected
> show sel & #!2#!1.1 surfaces
> show sel & #!2#!1.1 cartoons
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> show sel & #!2#!1.1 cartoons
> select :294-299
277 atoms, 279 bonds, 36 residues, 6 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> show sel & #!2#!1.1 surfaces
> show sel & #!2#!1.1 cartoons
> select ~sel
19154 atoms, 18809 bonds, 3218 residues, 7 models selected
> hide sel & #!2#!1.1 surfaces
> hide sel & #!2#!1.1 cartoons
> hide sel & #!2#!1.1 atoms
> select ~sel
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> select :344-347
154 atoms, 150 bonds, 23 residues, 6 models selected
> select :342-345
128 atoms, 123 bonds, 21 residues, 6 models selected
> select :341-345
176 atoms, 170 bonds, 1 pseudobond, 27 residues, 7 models selected
> hide sel & #!2#!1.1 surfaces
> show sel & #!2#!1.1 atoms
> style sel & #!2#!1.1 ball
Changed 70 atom styles
> select ~sel
20294 atoms, 19964 bonds, 3374 residues, 7 models selected
> transparency 80
> transparency 70
> select :341-345
176 atoms, 170 bonds, 1 pseudobond, 27 residues, 7 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> color sel & #!2#!1.1 bychain
> coulombic sel & #!2#!1.1
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!2#!1.1 bychain
> transparency 75
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> color sel & #!1.1 bychain
> coulombic sel & #!1.1
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!1.1 bychain
> show #!2 models
> mlp sel & #!2#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!2#!1.1 bychain
> select :330-375
1971 atoms, 1997 bonds, 1 pseudobond, 273 residues, 7 models selected
> coulombic sel & #!2#!1.1
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> select :320-360
1739 atoms, 1772 bonds, 1 pseudobond, 243 residues, 7 models selected
> coulombic sel & #!2#!1.1
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> coulombic sel & #!2#!1.1
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> undo
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> mlp sel & #!2
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
To also show corresponding color key, enter the above mlp command and add key
true
> show #!1.1 models
> color sel & #!2#!1.1 bychain
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide sel & #!2#!1.1 atoms
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> style sel & #!2#!1.1 ball
Changed 457 atom styles
> show sel & #!2#!1.1 atoms
> transparency 75
> hide #2.1 models
> show #2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> select ~sel
19154 atoms, 18809 bonds, 3218 residues, 7 models selected
> coulombic sel & #!2
Coulombic values for new_A SES surface #2.1: minimum, -18.37, mean -2.63,
maximum 11.52
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!2 bychain
> color (#!2 & sel) gray
> select ~sel
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> show sel & #!2 surfaces
> color sel & #!2 bychain
> transparency 75
> set bgColor white
> show #!1.1 models
> hide #!1.1 models
> hide #2.1 models
> show #!1.1 models
> hide #!1.1 models
> show #2.1 models
> hide #!2 models
> show #!1.1 models
> show #!2 models
> hide #!2 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> hide sel & #!1.1 surfaces
> select :330-340
481 atoms, 481 bonds, 66 residues, 6 models selected
> hide sel & #!1.1 atoms
> select :349-360
533 atoms, 534 bonds, 72 residues, 6 models selected
> hide sel & #!1.1 atoms
> select :346-360
659 atoms, 662 bonds, 90 residues, 6 models selected
> select :349-360
533 atoms, 534 bonds, 72 residues, 6 models selected
> hide sel & #!1.1 atoms
> show #!2 models
> hide #!1.1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1.1 models
> hide #!1.1 models
> hide sel & #!2 atoms
> select :330-341
529 atoms, 529 bonds, 72 residues, 6 models selected
> hide sel & #!2 atoms
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show sel & #!2#!1.1 surfaces
> hide #!1.1 models
> show #!1.1 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> show sel & #!2#!1.1 surfaces
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> show #!2 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> select ~sel
19154 atoms, 18809 bonds, 3218 residues, 7 models selected
> coulombic sel & #!1.1
Coulombic values for prototype_8V97 A_A SES surface #1.1.1: minimum, -14.58,
mean -1.76, maximum 14.31
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel & #!1.1 bychain
> color (#!1.1 & sel) gray
> transparency 75
> select ~sel
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> mlp sel & #!1.1
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> select :270-415
6626 atoms, 6797 bonds, 1 pseudobond, 873 residues, 7 models selected
> mlp sel & #!1.1
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color sel & #!1.1 bychain
> show #!2 models
> hide #!2 models
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> select ~sel
19154 atoms, 18809 bonds, 3218 residues, 7 models selected
> color (#!1.1 & sel) gray
> transparency 75
> select ~sel
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save C:/Users/evc1/Downloads/12_3_2025_GII.17_workspace.cxs
> select :342-344
88 atoms, 84 bonds, 15 residues, 5 models selected
> hide #1.1.1 models
> select :342-345
128 atoms, 123 bonds, 21 residues, 6 models selected
> color (#!1.1 & sel) magenta
> show #1.1.1 models
> hide sel & #!1.1 surfaces
> show sel & #!1.1 surfaces
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> show #!2 models
> hide #!1 models
> select clear
> select :330-360
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> color (#!2 & sel) gray
> color (#!2 & sel) dim gray
> select ~sel
19154 atoms, 18809 bonds, 3218 residues, 7 models selected
> color (#!2 & sel) dim gray
> show #!1 models
> hide #!2 models
> color (#!1.1 & sel) dim gray
> select ~sel
1316 atoms, 1325 bonds, 1 pseudobond, 183 residues, 7 models selected
> color (#!1.1 & sel) dim gray
> select :342-345
128 atoms, 123 bonds, 21 residues, 6 models selected
> color (#!1.1 & sel) light sea green
> color (#!1.1 & sel) cornflower blue
> color (#!1.1 & sel) medium blue
> color (#!1.1 & sel) blue
> color (#!1.1 & sel) light sea green
> hide #!1 models
> show #!2 models
> select clear
> show #1.2 models
> hide #!1 models
> hide #1.2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> hide #!1 models
> show #!2 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> save C:/Users/evc1/Downloads/12_3_2025_GII.17_workspace.cxs
——— End of log from Wed Dec 3 15:50:48 2025 ———
> view name session-start
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> show #!2 models
> hide #!1 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> ui mousemode right "mark point"
> select :342
36 atoms, 32 bonds, 5 residues, 5 models selected
> ui mousemode right "mark point"
[Repeated 1 time(s)]
> select clear
> show #!1 models
> hide #!2 models
> select #1.1/A:224-225,342-344 #1.2/B:342-344
50 atoms, 47 bonds, 8 residues, 2 models selected
> select #1.1/A:270-341,346-410,414-415 #1.2/B:270-341,346-410,414-415
> #5/A:270-341,346-410,414-415 #2/A:270-341,343-407,411-412
4222 atoms, 4324 bonds, 556 residues, 4 models selected
> select #1.1/A:224-225,342-344 #1.2/B:342-344
50 atoms, 47 bonds, 8 residues, 2 models selected
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> select #3/A:294
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:294-298
45 atoms, 46 bonds, 5 residues, 1 model selected
> select #3/A:294-298 #1.1/A:294-298 #1.2/B:294-298 #5/A:294-298
147 atoms, 148 bonds, 20 residues, 4 models selected
MatchMaker Alignment [ID: 3] region SantaClara_VEHQ, chain A [294-298] + 1
other block RMSD: 33.112
> select #1.1/A:224-225,342-344 #1.2/B:342-344 #2/A:294-298
90 atoms, 88 bonds, 13 residues, 3 models selected
MatchMaker Alignment [ID: 2] region partial missing structure of
prototype_8V97, chain A RMSD: 49.603
> select #1.1/A:224-225,294-298,342-344 #1.2/B:294-298,342-344 #2/A:294-298
> #5/A:294-298
192 atoms, 190 bonds, 28 residues, 4 models selected
MatchMaker Alignment [ID: 2] region partial missing structure of
prototype_8V97, chain A RMSD: 36.383
> select :294-299,368,372-373
411 atoms, 406 bonds, 54 residues, 6 models selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select all
20470 atoms, 20146 bonds, 1 pseudobond, 3401 residues, 8 models selected
> mlp sel & #!2-4#!1.1
Map values for surface "new_A SES surface": minimum -28.04, mean -5.29,
maximum 22.61
Map values for surface "SantaClara_VEHQ_A SES surface": minimum -28.05, mean
-5.403, maximum 22.27
Map values for surface "SantaClara_VENQ_A SES surface": minimum -29.38, mean
-5.265, maximum 22.48
Map values for surface "prototype_8V97 A_A SES surface": minimum -28.72, mean
-5.694, maximum 22.19
To also show corresponding color key, enter the above mlp command and add key
true
> color (#!2-4#!1.1 & sel) dim gray
> color (#!2-4#!1.1 & sel) light gray
> color (#!2-4#!1.1 & sel) gray
> select :294-299,368,372-373
411 atoms, 406 bonds, 54 residues, 6 models selected
> color (#!2-4#!1.1 & sel) red
> select :333,382,389
136 atoms, 121 bonds, 18 residues, 6 models selected
> color (#!2-4#!1.1 & sel) orange red
> select :339-341,375-378
343 atoms, 332 bonds, 42 residues, 6 models selected
> select :333,382,389
136 atoms, 121 bonds, 18 residues, 6 models selected
> select :333,382,389
136 atoms, 121 bonds, 18 residues, 6 models selected
> select #1.1/A:382 #1.2/B:382 #5/A:382
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:382 #1.2/B:382 #5/A:382 #2/A:379
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[382] RMSD: 30.792
> select #1.1/A:381 #1.2/B:381 #5/A:381
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:381 #1.2/B:381 #5/A:381 #2/A:378
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[381] RMSD: 27.911
> select :333,382,389
136 atoms, 121 bonds, 18 residues, 6 models selected
> color (#!2-4#!1.1 & sel) gray
> select #1.1/A:381 #1.2/B:381 #5/A:381 #2/A:378
28 atoms, 24 bonds, 4 residues, 4 models selected
> color (#!2#!1.1 & sel) orange red
> select #1.1/A:270-342,345-411,414 #1.2/B:270-342,345-411,414
> #5/A:270-411,414 #4/A:270-342,346-412,415
4271 atoms, 4376 bonds, 1 pseudobond, 563 residues, 5 models selected
> select #3/A:382
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:381 #1.2/B:381 #5/A:381 #3/A:382
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [382] RMSD: 27.910
> color (#!3#!1.1 & sel) orange red
> select #4/A:382
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:381 #1.2/B:381 #5/A:381 #4/A:382
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [382] RMSD: 27.907
> color (#!4#!1.1 & sel) orange red
> select :368,372-373
134 atoms, 127 bonds, 18 residues, 6 models selected
> select #1.1/A:367 #1.2/B:367 #5/A:367
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:367 #1.2/B:367 #5/A:367 #2/A:364
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[367] RMSD: 35.674
> select :368,372-373
134 atoms, 127 bonds, 18 residues, 6 models selected
> color (#!2-4#!1.1 & sel) gray
> select #1.1/A:367 #1.2/B:367 #5/A:367
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:367 #1.2/B:367 #5/A:367 #2/A:364
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[367] RMSD: 35.674
> color (#!2#!1.1 & sel) orange
> color (#!2#!1.1 & sel) red
> select #1.1/A:367 #1.2/B:367 #5/A:367
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:367 #1.2/B:367 #5/A:367 #4/A:368
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [368] RMSD: 35.693
> color (#!4#!1.1 & sel) red
> select #1.1/A:367 #1.2/B:367 #5/A:367
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:367 #1.2/B:367 #5/A:367 #3/A:368
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [368] RMSD: 35.688
> color (#!3#!1.1 & sel) red
> select :368,372-373
134 atoms, 127 bonds, 18 residues, 6 models selected
> select #1.1/A:371 #1.2/B:371 #5/A:371
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:371-372 #1.2/B:371-372 #5/A:371-372 #2/A:368-369
76 atoms, 76 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[371-372] RMSD: 21.371
> color (#!2#!1.1 & sel) red
> select #1.1/A:371 #1.2/B:371 #5/A:371
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:371-372 #1.2/B:371-372 #5/A:371-372 #4/A:372-373
76 atoms, 76 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [372-373] RMSD: 21.328
> color (#!4#!1.1 & sel) red
> select #1.1/A:371 #1.2/B:371 #5/A:371
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:371-372 #1.2/B:371-372 #5/A:371-372 #3/A:372-373
76 atoms, 76 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [372-373] RMSD: 21.320
> color (#!3#!1.1 & sel) red
> select :339-341
168 atoms, 162 bonds, 18 residues, 6 models selected
> color (#!2-4#!1.1 & sel) orange
> select #1.1/A:373-374 #1.2/B:373-374 #5/A:373-374
30 atoms, 27 bonds, 6 residues, 3 models selected
> select #1.1/A:373-375 #1.2/B:373-375 #5/A:373-375 #2/A:370-372
68 atoms, 64 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[373-375] RMSD: 13.055
> select #1.1/A:374 #1.2/B:374 #5/A:374
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:374-376 #1.2/B:374-376 #5/A:374-376 #2/A:371-373
76 atoms, 72 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[374-376] RMSD: 10.465
> color (#!2#!1.1 & sel) orange
> select #1.1/A:374-375 #1.2/B:374-375 #5/A:374-375
37 atoms, 34 bonds, 6 residues, 3 models selected
> select #1.1/A:374-377 #1.2/B:374-377 #5/A:374-377 #2/A:371-374
104 atoms, 100 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[374-377] RMSD: 11.727
> color (#!2#!1.1 & sel) orange
> select #1.1/A:374 #1.2/B:374 #5/A:374
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:374-377 #1.2/B:374-377 #5/A:374-377 #4/A:375-378
105 atoms, 101 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [375-378] RMSD: 11.701
> color (#!4#!1.1 & sel) orange
> select #1.1/A:374 #1.2/B:374 #5/A:374
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:374-377 #1.2/B:374-377 #5/A:374-377 #3/A:375-378
105 atoms, 101 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [375-378] RMSD: 11.696
> color (#!3#!1.1 & sel) orange
> select #1.1/A:390 #1.2/B:390 #5/A:390
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:390-396 #1.2/B:390-396 #5/A:390-396 #2/A:387-393
202 atoms, 198 bonds, 28 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[390-396] RMSD: 19.332
> color (#!2#!1.1 & sel) yellow
> select #1.1/A:390 #1.2/B:390 #5/A:390
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:390-396 #1.2/B:390-396 #5/A:390-396 #4/A:391-397
201 atoms, 197 bonds, 28 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [391-397] RMSD: 19.314
> color (#!4#!1.1 & sel) yellow
> select #1.1/A:390 #1.2/B:390 #5/A:390
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:390-396 #1.2/B:390-396 #5/A:390-396 #3/A:391-397
201 atoms, 197 bonds, 28 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [391-397] RMSD: 19.319
> color (#!3#!1.1 & sel) yellow
> select #1.1/A:405 #1.2/B:405 #5/A:405
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:405 #1.2/B:405 #5/A:405 #2/A:402
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[405] RMSD: 31.236
> color (#!2#!1.1 & sel) lime
> select #1.1/A:405 #1.2/B:405 #5/A:405
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:405 #1.2/B:405 #5/A:405 #4/A:406
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [406] RMSD: 31.241
> color (#!4#!1.1 & sel) lime
> select #1.1/A:405 #1.2/B:405 #5/A:405
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:405 #1.2/B:405 #5/A:405 #3/A:406
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [406] RMSD: 31.234
> color (#!3#!1.1 & sel) lime
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #2/A:406-409
112 atoms, 112 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-412] RMSD: 39.656
> color (#!2#!1.1 & sel) lime
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #4/A:410-413
106 atoms, 105 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [410-413] RMSD: 39.646
> color (#!4#!1.1 & sel) lime
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #3/A:410-413
106 atoms, 105 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [410-413] RMSD: 39.673
> color (#!3#!1.1 & sel) lime
> select :327
42 atoms, 42 bonds, 6 residues, 6 models selected
> color (#!2-4#!1.1 & sel) forest green
> select #1.1/A:402 #1.2/B:402 #5/A:402
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1.1/A:402 #1.2/B:402 #5/A:402 #2/A:399
36 atoms, 32 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[402] RMSD: 26.934
> color (#!2#!1.1 & sel) forest green
> select #1.1/A:402 #1.2/B:402 #5/A:402
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1.1/A:402 #1.2/B:402 #5/A:402 #4/A:403
36 atoms, 32 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [403] RMSD: 26.943
> color (#!4#!1.1 & sel) forest green
> select #1.1/A:402 #1.2/B:402 #5/A:402
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1.1/A:402 #1.2/B:402 #5/A:402 #3/A:403
36 atoms, 32 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [403] RMSD: 26.926
> color (#!3#!1.1 & sel) forest green
> select #1.1/A:351 #1.2/B:351 #5/A:351
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:351 #1.2/B:351 #5/A:351 #4/A:352
20 atoms, 16 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [352] RMSD: 11.055
> color (#!4#!1.1 & sel) cyan
> select #1.1/A:351 #1.2/B:351 #5/A:351
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:351 #1.2/B:351 #5/A:351 #2/A:348
20 atoms, 16 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[351] RMSD: 11.080
> color (#!2#!1.1 & sel) cyan
> select #1.1/A:351 #1.2/B:351 #5/A:351
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:351 #1.2/B:351 #5/A:351 #3/A:352
20 atoms, 16 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [352] RMSD: 11.045
> color (#!3#!1.1 & sel) cyan
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #2/A:351-353
79 atoms, 75 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354-356] RMSD: 14.291
> color (#!2#!1.1 & sel) light sea green
> color (#!2#!1.1 & sel) blue
> color (#!2#!1.1 & sel) cornflower blue
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #4/A:355-357
77 atoms, 73 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [355-357] RMSD: 14.282
> color (#!4#!1.1 & sel) cornflower blue
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #3/A:355-357
77 atoms, 73 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [355-357] RMSD: 14.287
> color (#!3#!1.1 & sel) cornflower blue
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #4/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [359] RMSD: 25.070
> select #1.1/A:359 #1.2/B:359 #5/A:359
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:359 #1.2/B:359 #5/A:359 #4/A:360
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [360] RMSD: 29.537
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #4/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [359] RMSD: 25.070
> color (#!4#!1.1 & sel) medium blue
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #2/A:355
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[358] RMSD: 25.069
> color (#!2#!1.1 & sel) medium blue
> select #1.1/A:358 #1.2/B:358 #5/A:358 #3/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #3/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [359] RMSD: 25.070
> color (#!3#!1.1 & sel) medium blue
> color (#!3#!1.1 & sel) cornflower blue
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #4/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [359] RMSD: 25.070
> color (#!4#!1.1 & sel) cornflower blue
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #2/A:355
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[358] RMSD: 25.069
> color (#!2#!1.1 & sel) cornflower blue
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #4/A:364
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [364] RMSD: 28.431
> color (#!4#!1.1 & sel) cornflower blue
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #2/A:360
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[363] RMSD: 28.432
> color (#!2#!1.1 & sel) cornflower blue
[Repeated 1 time(s)]
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #3/A:364
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [364] RMSD: 28.439
> color (#!3#!1.1 & sel) cornflower blue
> select :309-310
96 atoms, 90 bonds, 12 residues, 6 models selected
> color (#!2-4#!1.1 & sel) medium blue
> select :333
48 atoms, 42 bonds, 6 residues, 6 models selected
> select #1.1/A:381 #1.2/B:381 #5/A:381
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:381 #1.2/B:381 #5/A:381 #2/A:378
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[381] RMSD: 27.911
> select #1.1/A:376 #1.2/B:376 #5/A:376
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:376 #1.2/B:376 #5/A:376 #2/A:373
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[376] RMSD: 9.862
> select #4/A:390-391
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1.1/A:389-394 #1.2/B:389-394 #5/A:389-394 #4/A:390-395
169 atoms, 169 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [390-395] RMSD: 14.508
> select #4/A:410
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #4/A:410-413
106 atoms, 105 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [410-413] RMSD: 39.646
> select #1.1/A:327 #1.2/B:327 #5/A:327
21 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:327 #1.2/B:327 #5/A:327 #4/A:327
28 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [327] RMSD: 19.935
> select #1.1/A:402 #1.2/B:402 #5/A:402
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1.1/A:402 #1.2/B:402 #5/A:402 #4/A:403
36 atoms, 32 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [403] RMSD: 26.943
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-357 #1.2/B:354-357 #5/A:354-357
75 atoms, 72 bonds, 12 residues, 3 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A [354-357] RMSD:
19.201
> select #4/A:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:355-357
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #4/A:355
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #4/A:355-357
77 atoms, 73 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [355-357] RMSD: 14.282
> color (#!4#!1.1 & sel) cyan
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #2/A:351-353
79 atoms, 75 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354-356] RMSD: 14.291
> select :354-356
119 atoms, 113 bonds, 18 residues, 6 models selected
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #2/A:351-353
79 atoms, 75 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354-356] RMSD: 14.291
> color (#!2#!1.1 & sel) cyan
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #3/A:355-357
77 atoms, 73 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [355-357] RMSD: 14.287
> color (#!3#!1.1 & sel) cyan
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #4/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [359] RMSD: 25.070
> color (#!4#!1.1 & sel) cyan
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #2/A:355
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[358] RMSD: 25.069
> color (#!2#!1.1 & sel) cyan
> select #3/A:359
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #3/A:359
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [359] RMSD: 25.070
> color (#!3#!1.1 & sel) cyan
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #4/A:364
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [364] RMSD: 28.431
> color (#!4#!1.1 & sel) cyan
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #2/A:360
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[363] RMSD: 28.432
> color (#!2#!1.1 & sel) cyan
> select #1.1/A:363 #1.2/B:363 #5/A:363
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:363 #1.2/B:363 #5/A:363 #3/A:364
44 atoms, 44 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [364] RMSD: 28.439
> color (#!3#!1.1 & sel) cyan
> select :309-310
96 atoms, 90 bonds, 12 residues, 6 models selected
> color (#!2-4#!1.1 & sel) cornflower blue
> select #1.1/A:400 #1.2/B:400 #5/A:400
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:400-401 #1.2/B:400-401 #5/A:400-401 #4/A:401-402
77 atoms, 77 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [401-402] RMSD: 28.336
> color (#!4#!1.1 & sel) medium blue
> select #1.1/A:400 #1.2/B:400 #5/A:400
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:400-401 #1.2/B:400-401 #5/A:400-401 #2/A:397-398
76 atoms, 76 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[400-401] RMSD: 28.360
> color (#!2#!1.1 & sel) medium blue
> select #1.1/A:400 #1.2/B:400 #5/A:400
33 atoms, 33 bonds, 3 residues, 3 models selected
> select #1.1/A:400-401 #1.2/B:400-401 #5/A:400-401 #3/A:401-402
77 atoms, 77 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [401-402] RMSD: 28.339
> color (#!3#!1.1 & sel) medium blue
> select #1.1/A:502 #1.2/B:502 #5/A:502
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:502 #1.2/B:502 #5/A:502 #3/A:503
25 atoms, 21 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [503] RMSD: 46.375
> color (#!3#!1.1 & sel) purple
> select #1.1/A:502 #1.2/B:502 #5/A:502
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:502 #1.2/B:502 #5/A:502 #4/A:503
25 atoms, 21 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [503] RMSD: 46.405
> color (#!4#!1.1 & sel) purple
> select #1.1/A:502 #1.2/B:502 #5/A:502
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:502 #1.2/B:502 #5/A:502 #2/A:499
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[502] RMSD: 46.423
> color (#!2#!1.1 & sel) purple
> select #1.1/A:504 #1.2/B:504 #5/A:504
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:504 #1.2/B:504 #5/A:504 #2/A:501
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[504] RMSD: 40.802
> color (#!2#!1.1 & sel) purple
> select #4/A:505
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:504 #1.2/B:504 #5/A:504 #4/A:505
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [505] RMSD: 40.805
> color (#!4#!1.1 & sel) purple
> select #3/A:505
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:503-504 #1.2/B:503-504 #5/A:503-504 #3/A:504-505
48 atoms, 44 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [504-505] RMSD: 42.960
> select #1.1/A:504 #1.2/B:504 #5/A:504
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:504 #1.2/B:504 #5/A:504 #3/A:505
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 3] region prototype_8V97, chain A..SantaClara_VEHQ,
chain A [505] RMSD: 40.765
> color (#!3#!1.1 & sel) purple
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1.2 models
> hide #1.2 models
> hide #1.1.1 models
> show #1.1.1 models
> show #!2 models
> show #1.2 models
> hide #1.2 models
> save C:/Users/evc1/Downloads/12_3_2025_GII.17_workspace_epitopeColored.cxs
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select all
20470 atoms, 20146 bonds, 1 pseudobond, 3401 residues, 8 models selected
> transparency 75
> select #4/A:410
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #4/A:410-413
106 atoms, 105 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [410-413] RMSD: 39.646
> select all
20470 atoms, 20146 bonds, 1 pseudobond, 3401 residues, 8 models selected
> hide sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 cartoons
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> select #2/A:406
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #2/A:406-409
112 atoms, 112 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-412] RMSD: 39.656
> select #1.1/A:401-402 #1.2/B:401-402 #5/A:401-402
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #1.1/A:401-420 #1.2/B:401-420 #5/A:401-420 #2/A:398-417
640 atoms, 660 bonds, 80 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[401-420] RMSD: 35.732
> show sel & #!2#!1.1 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> select #1.1/A:406 #1.2/B:406 #5/A:406
21 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:406-408 #1.2/B:406-408 #5/A:406-408 #2/A:403-405
114 atoms, 118 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[406-408] RMSD: 32.500
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:401-402 #1.2/B:401-402 #5/A:401-402
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #1.1/A:401-420 #1.2/B:401-420 #5/A:401-420 #2/A:398-417
640 atoms, 660 bonds, 80 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[401-420] RMSD: 35.732
> hide sel & #!2#!1.1 cartoons
[Repeated 1 time(s)]
> show sel & #!2#!1.1 cartoons
> hide sel & #!2#!1.1 cartoons
> show sel & #!2#!1.1 atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #2.1 models
> hide #1.1.1 models
> style sel & #!2#!1.1 ball
Changed 322 atom styles
> select #1.1/A:406 #1.2/B:406 #5/A:406
21 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:406 #1.2/B:406 #5/A:406 #2/A:403
28 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[406] RMSD: 30.672
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:270-341,346-410,414-415 #1.2/B:270-341,346-410,414-415
> #5/A:270-341,346-410,414-415 #2/A:270-341,343-407,411-412
4222 atoms, 4324 bonds, 556 residues, 4 models selected
> select #2/A:404
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:404
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A [407] RMSD: 39.708
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/A:401-402 #1.2/B:401-402 #5/A:401-402
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #1.1/A:401-420 #1.2/B:401-420 #5/A:401-420 #2/A:398-417
640 atoms, 660 bonds, 80 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[401-420] RMSD: 35.732
> select #1.1/A:404 #1.2/B:404 #5/A:404
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:404 #1.2/B:404 #5/A:404 #2/A:401
22 atoms, 18 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[404] RMSD: 32.904
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> show #!1 models
> show #1.1.1 models
> show #2.1 models
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407-412 #1.2/B:407-412 #5/A:407-412 #4/A:408-413
191 atoms, 194 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [408-413] RMSD: 37.674
> select #1.1/A:401 #1.2/B:401 #5/A:401
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:401-420 #1.2/B:401-420 #5/A:401-420 #2/A:398-417
640 atoms, 660 bonds, 80 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[401-420] RMSD: 35.732
> hide sel & #!2#!1.1 atoms
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407-412 #1.2/B:407-412 #5/A:407-412 #2/A:404-409
198 atoms, 202 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407-412] RMSD: 37.679
> select #1.1/A:405 #1.2/B:405 #5/A:405
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:405-412 #1.2/B:405-412 #5/A:405-412 #2/A:402-409
258 atoms, 266 bonds, 32 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[405-412] RMSD: 36.116
> show sel & #!2#!1.1 atoms
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> select #1.1/A:405 #1.2/B:405 #5/A:405
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:405-406 #1.2/B:405-406 #5/A:405-406 #2/A:402-403
60 atoms, 60 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[405-406] RMSD: 30.955
> hide sel & #!2#!1.1 atoms
> select #1.1/A:270-341,346-410,414-415 #1.2/B:270-341,346-410,414-415
> #5/A:270-341,346-410,414-415 #2/A:270-341,343-407,411-412
4222 atoms, 4324 bonds, 556 residues, 4 models selected
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #2/A:406-409
112 atoms, 112 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-412] RMSD: 39.656
> hide sel & #!2#!1.1 atoms
> show sel & #!2#!1.1 atoms
> select #1.1/A:413 #1.2/B:413 #5/A:413
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:413-415 #1.2/B:413-415 #5/A:413-415 #2/A:410-412
92 atoms, 88 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[413-415] RMSD: 41.554
> hide sel & #!2#!1.1 atoms
> select #1.1/A:408 #1.2/B:408 #5/A:408
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1.1/A:408 #1.2/B:408 #5/A:408 #2/A:405
48 atoms, 48 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[408] RMSD: 32.308
> hide sel & #!2#!1.1 atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #2.1 models
> select #1.1/A:407 #1.2/B:407 #5/A:407
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> show #!1.1 models
> show #2.1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #1.2 models
> hide #1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> hide #!1 models
> show #!2 models
> save C:\Users\evc1/Desktop\image3.png supersample 3
> show #!1 models
> select #1.1/A:412 #1.2/B:412 #5/A:412
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:412 #1.2/B:412 #5/A:412 #4/A:413
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 4] region prototype_8V97, chain A..SantaClara_VENQ,
chain A [413] RMSD: 44.814
> hide #!2 models
> select #1.1/A:411 #1.2/B:411 #5/A:411
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:411 #1.2/B:411 #5/A:411 #2/A:408
40 atoms, 40 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[411] RMSD: 39.991
> select #1.1/A:408 #1.2/B:408 #5/A:408
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1.1/A:408-409 #1.2/B:408-409 #5/A:408-409 #2/A:405-406
72 atoms, 72 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[408-409] RMSD: 34.499
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-410 #1.2/B:409-410 #5/A:409-410 #2/A:406-407
40 atoms, 36 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-410] RMSD: 36.619
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409 #1.2/B:409 #5/A:409 #2/A:406
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409] RMSD: 36.560
> select #1.1/A:410 #1.2/B:410 #5/A:410
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1.1/A:410 #1.2/B:410 #5/A:410 #2/A:407
16 atoms, 12 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[410] RMSD: 36.679
> select #1.1/A:411 #1.2/B:411 #5/A:411
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:411 #1.2/B:411 #5/A:411 #2/A:408
40 atoms, 40 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[411] RMSD: 39.991
> select #1.1/A:410 #1.2/B:410 #5/A:410
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1.1/A:410 #1.2/B:410 #5/A:410 #2/A:407
16 atoms, 12 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[410] RMSD: 36.679
> select #1.1/A:412 #1.2/B:412 #5/A:412
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:412 #1.2/B:412 #5/A:412 #2/A:409
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[412] RMSD: 44.824
> select #1.1/A:410 #1.2/B:410 #5/A:410
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1.1/A:410 #1.2/B:410 #5/A:410 #2/A:407
16 atoms, 12 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[410] RMSD: 36.679
> select #1.1/A:410 #1.2/B:410 #5/A:410
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1.1/A:410 #1.2/B:410 #5/A:410 #2/A:407
16 atoms, 12 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[410] RMSD: 36.679
> select #1.1/A:411 #1.2/B:411 #5/A:411
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:411 #1.2/B:411 #5/A:411 #2/A:408
40 atoms, 40 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[411] RMSD: 39.991
> select #1.1/A:410 #1.2/B:410 #5/A:410
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #1.1/A:409-410 #1.2/B:409-410 #5/A:409-410 #2/A:406-407
40 atoms, 36 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-410] RMSD: 36.619
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409 #1.2/B:409 #5/A:409 #2/A:406
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409] RMSD: 36.560
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:409 #1.2/B:409 #5/A:409
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:409-412 #1.2/B:409-412 #5/A:409-412 #2/A:406-409
112 atoms, 112 bonds, 16 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[409-412] RMSD: 39.656
> hide sel & #!2#!1.1 atoms
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
> select #1.1/A:407 #1.2/B:407 #5/A:407 #2/A:404
38 atoms, 34 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[407] RMSD: 34.411
> hide sel & #!2#!1.1 atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:299 #1.2/B:299 #5/A:299
23 atoms, 20 bonds, 3 residues, 3 models selected
> select #1.1/A:299 #1.2/B:299 #5/A:299 #2/A:299
31 atoms, 27 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[299] RMSD: 23.714
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:297 #1.2/B:297 #5/A:297
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:297 #1.2/B:297 #5/A:297 #2/A:297
26 atoms, 22 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[297] RMSD: 31.596
> select #1.1/A:295 #1.2/B:295 #5/A:295
22 atoms, 19 bonds, 3 residues, 3 models selected
> select #1.1/A:295-299 #1.2/B:295-299 #5/A:295-299 #2/A:295-299
145 atoms, 146 bonds, 20 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[295-299] RMSD: 27.583
> show sel & #!2#!1.1 atoms
> style sel & #!2#!1.1 ball
Changed 77 atom styles
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #1.1.1 models
> show #1.1.1 models
> show #2.1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save C:/Users/evc1/Downloads/12_3_2025_GII.17_workspace_epitopeColored.cxs
——— End of log from Thu Dec 4 10:11:43 2025 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1.1/A:361-362 #1.2/B:361-362 #5/A:361-362
44 atoms, 41 bonds, 6 residues, 3 models selected
> select #1.1/A:361-368 #1.2/B:361-368 #5/A:361-368 #2/A:358-365
244 atoms, 248 bonds, 32 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361-368] RMSD: 31.765
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361-366 #1.2/B:361-366 #5/A:361-366 #2/A:358-363
196 atoms, 200 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361-366] RMSD: 31.029
> select #1.1/A:367 #1.2/B:367 #5/A:367
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:367-368 #1.2/B:367-368 #5/A:367-368 #2/A:364-365
48 atoms, 44 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[367-368] RMSD: 33.877
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358-362 #1.2/B:358-362 #5/A:358-362 #2/A:355-359
140 atoms, 136 bonds, 20 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[358-362] RMSD: 29.738
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361 #1.2/B:361 #5/A:361 #2/A:358
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361] RMSD: 33.632
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356 #1.2/B:356 #5/A:356 #2/A:353
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356] RMSD: 17.947
> select #1.1/A:370 #1.2/B:370 #5/A:370
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:370 #1.2/B:370 #5/A:370 #2/A:367
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[370] RMSD: 25.553
> select #1.1/A:361-380 #1.2/B:361-380 #5/A:361-380 #2/A:358-377
605 atoms, 617 bonds, 80 residues, 4 models selected
> select #1.1/A:361-380 #1.2/B:361-380 #5/A:361-380 #2/A:358-377
605 atoms, 617 bonds, 80 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361-380] RMSD: 25.016
> select #1.1/A:382 #1.2/B:382 #5/A:382
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:382-383 #1.2/B:382-383 #5/A:382-383 #2/A:379-380
68 atoms, 64 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[382-383] RMSD: 29.073
> show #!2 models
> select #1.1/A:382 #1.2/B:382 #5/A:382
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:382 #1.2/B:382 #5/A:382 #2/A:379
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[382] RMSD: 30.792
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361 #1.2/B:361 #5/A:361 #2/A:358
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361] RMSD: 33.632
> select #1.1/A:375 #1.2/B:375 #5/A:375
19 atoms, 16 bonds, 3 residues, 3 models selected
> select #1.1/A:375 #1.2/B:375 #5/A:375 #2/A:372
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[375] RMSD: 9.264
> select #1.1/A:370 #1.2/B:370 #5/A:370
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:370 #1.2/B:370 #5/A:370 #2/A:367
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[370] RMSD: 25.553
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356 #1.2/B:356 #5/A:356 #2/A:353
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356] RMSD: 17.947
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361 #1.2/B:361 #5/A:361 #2/A:358
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361] RMSD: 33.632
> style sel & #!2#!1.1 ball
Changed 13 atom styles
> show sel & #!2#!1.1 atoms
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354 #1.2/B:354 #5/A:354 #2/A:351
22 atoms, 18 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354] RMSD: 10.010
> select #1.1/A:360 #1.2/B:360 #5/A:360
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:360 #1.2/B:360 #5/A:360 #2/A:357
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[360] RMSD: 29.238
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361 #1.2/B:361 #5/A:361 #2/A:358
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361] RMSD: 33.632
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:362 #1.2/B:362 #5/A:362
27 atoms, 24 bonds, 3 residues, 3 models selected
> select #1.1/A:362 #1.2/B:362 #5/A:362 #2/A:359
36 atoms, 32 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[362] RMSD: 30.565
> select #1.1/A:357 #1.2/B:357 #5/A:357
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:357-364 #1.2/B:357-364 #5/A:357-364 #2/A:354-361
236 atoms, 236 bonds, 32 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[357-364] RMSD: 29.009
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:354-356 #1.2/B:354-356 #5/A:354-356 #2/A:351-353
79 atoms, 75 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354-356] RMSD: 14.291
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> select #1.1/A:297 #1.2/B:297 #5/A:297
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:297 #1.2/B:297 #5/A:297 #2/A:297
26 atoms, 22 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[297] RMSD: 31.596
> select #1.1/A:295 #1.2/B:295 #5/A:295
22 atoms, 19 bonds, 3 residues, 3 models selected
> select #1.1/A:295 #1.2/B:295 #5/A:295 #2/A:295
32 atoms, 29 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[295] RMSD: 25.607
> select #1.1/A:299 #1.2/B:299 #5/A:299
23 atoms, 20 bonds, 3 residues, 3 models selected
> select #1.1/A:299 #1.2/B:299 #5/A:299 #2/A:299
31 atoms, 27 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[299] RMSD: 23.714
> select #1.1/A:294 #1.2/B:294 #5/A:294
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:294 #1.2/B:294 #5/A:294 #2/A:294
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[294] RMSD: 28.988
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356 #1.2/B:356 #5/A:356 #2/A:353
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356] RMSD: 17.947
> select #1.1/A:359 #1.2/B:359 #5/A:359
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:359 #1.2/B:359 #5/A:359 #2/A:356
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[359] RMSD: 29.549
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356 #1.2/B:356 #5/A:356 #2/A:353
29 atoms, 25 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356] RMSD: 17.947
> select #1.1/A:357 #1.2/B:357 #5/A:357
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1.1/A:357 #1.2/B:357 #5/A:357 #2/A:354
24 atoms, 20 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[357] RMSD: 22.258
> select #1.1/A:358 #1.2/B:358 #5/A:358
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:358 #1.2/B:358 #5/A:358 #2/A:355
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[358] RMSD: 25.069
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354 #1.2/B:354 #5/A:354 #2/A:351
22 atoms, 18 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354] RMSD: 10.010
> select #1.1/A:355 #1.2/B:355 #5/A:355
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:355 #1.2/B:355 #5/A:355 #2/A:352
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[355] RMSD: 13.799
> select #1.1/A:355 #1.2/B:355 #5/A:355
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:355-360 #1.2/B:355-360 #5/A:355-360 #2/A:352-357
161 atoms, 157 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[355-360] RMSD: 23.680
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> show sel & #!2#!1.1 atoms
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361-365 #1.2/B:361-365 #5/A:361-365
119 atoms, 122 bonds, 15 residues, 3 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A [361-365] RMSD:
35.349
> undo
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356-360 #1.2/B:356-360 #5/A:356-360 #2/A:353-357
133 atoms, 129 bonds, 20 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356-360] RMSD: 25.195
> hide sel & #!2#!1.1 atoms
> select #1.1/A:355 #1.2/B:355 #5/A:355
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:355 #1.2/B:355 #5/A:355 #2/A:352
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[355] RMSD: 13.799
> hide sel & #!2#!1.1 atoms
> select #1.1/A:354 #1.2/B:354 #5/A:354
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:354 #1.2/B:354 #5/A:354 #2/A:351
22 atoms, 18 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[354] RMSD: 10.010
> hide sel & #!2#!1.1 atoms
> select #1.1/A:361 #1.2/B:361 #5/A:361
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:361-365 #1.2/B:361-365 #5/A:361-365 #2/A:358-362
160 atoms, 164 bonds, 20 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[361-365] RMSD: 30.668
> show sel & #!2#!1.1 atoms
> style sel & #!2#!1.1 ball
Changed 81 atom styles
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide sel & #!2#!1.1 atoms
> select #1.1/A:356 #1.2/B:356 #5/A:356
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:356-365 #1.2/B:356-365 #5/A:356-365 #2/A:353-362
293 atoms, 297 bonds, 40 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[356-365] RMSD: 28.065
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 cartoons
> hide sel & #!2#!1.1 atoms
> select #1.1/A:298 #1.2/B:298 #5/A:298
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:298-303 #1.2/B:298-303 #5/A:298-303 #2/A:298-303
243 atoms, 255 bonds, 24 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[298-303] RMSD: 24.477
> show sel & #!2#!1.1 atoms
> hide sel & #!2#!1.1 atoms
> show sel & #!2#!1.1 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:301 #1.2/B:301 #5/A:301
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:301-303 #1.2/B:301-303 #5/A:301-303 #2/A:301-303
140 atoms, 148 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[301-303] RMSD: 24.043
> hide sel & #!2#!1.1 atoms
> select #1.1/A:304 #1.2/B:304 #5/A:304
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:304 #1.2/B:304 #5/A:304 #2/A:304
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[304] RMSD: 25.015
> select #1.1/A:299 #1.2/B:299 #5/A:299
23 atoms, 20 bonds, 3 residues, 3 models selected
> select #1.1/A:299 #1.2/B:299 #5/A:299 #2/A:299
31 atoms, 27 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[299] RMSD: 23.714
> select #1.1/A:298 #1.2/B:298 #5/A:298
30 atoms, 30 bonds, 3 residues, 3 models selected
> select #1.1/A:298 #1.2/B:298 #5/A:298 #2/A:298
40 atoms, 40 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[298] RMSD: 28.354
> select #1.1/A:294 #1.2/B:294 #5/A:294
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:294 #1.2/B:294 #5/A:294 #2/A:294
28 atoms, 24 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[294] RMSD: 28.988
> select #1.1/A:293 #1.2/B:293 #5/A:293
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:293 #1.2/B:293 #5/A:293 #2/A:293
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[293] RMSD: 27.173
> select #1.1/A:292 #1.2/B:292 #5/A:292
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #1.1/A:292 #1.2/B:292 #5/A:292 #2/A:292
20 atoms, 16 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[292] RMSD: 30.452
> select #1.1/A:300 #1.2/B:300 #5/A:300
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:300 #1.2/B:300 #5/A:300 #2/A:300
32 atoms, 28 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[300] RMSD: 22.235
> hide sel & #!2#!1.1 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:304-305 #1.2/B:304-305 #5/A:304-305
51 atoms, 48 bonds, 6 residues, 3 models selected
> select #1.1/A:304-305 #1.2/B:304-305 #5/A:304-305 #2/A:304-305
68 atoms, 64 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[304-305] RMSD: 27.053
> select #1.1/A:313 #1.2/B:313 #5/A:313
21 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:313-315 #1.2/B:313-315 #5/A:313-315 #2/A:313-315
104 atoms, 108 bonds, 12 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[313-315] RMSD: 33.152
> select #1.1/A:304 #1.2/B:304 #5/A:304
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1.1/A:304-305 #1.2/B:304-305 #5/A:304-305 #2/A:304-305
68 atoms, 64 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[304-305] RMSD: 27.053
> select #1.1/A:307 #1.2/B:307 #5/A:307
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1.1/A:307-308 #1.2/B:307-308 #5/A:307-308 #2/A:307-308
60 atoms, 56 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[307-308] RMSD: 25.590
> select :307-400
4172 atoms, 4278 bonds, 1 pseudobond, 561 residues, 7 models selected
> hide sel & #!2#!1.1 surfaces
> show sel & #!2#!1.1 surfaces
> select :307-500
8882 atoms, 9136 bonds, 1 pseudobond, 1161 residues, 7 models selected
> hide sel & #!2#!1.1 surfaces
> select :240-290
2304 atoms, 2333 bonds, 306 residues, 6 models selected
> hide sel & #!2#!1.1 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save C:\Users\evc1/Desktop\image2.png supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select :295,299
97 atoms, 86 bonds, 12 residues, 6 models selected
> color (#!2 & sel) light sea green
> save C:\Users\evc1/Desktop\image3.png supersample 3
> show #!1 models
> hide #!2 models
> select :295,299
97 atoms, 86 bonds, 12 residues, 6 models selected
> show #!2 models
> hide #!1 models
> select :295
50 atoms, 45 bonds, 6 residues, 6 models selected
> color (#!2 & sel) forest green
> color (#!2 & sel) #aaff7fff
> color (#!2 & sel) #55ff00ff
> color (#!2 & sel) #aaff7fff
> transparency 75
> select clear
> save C:\Users\evc1/Desktop\image3.png supersample 3
> show #!1 models
> hide #!2 models
> select :299
47 atoms, 41 bonds, 6 residues, 6 models selected
> select clear
> save C:\Users\evc1/Desktop\image3.png supersample 3
> select #1.1/A:270-341,346-410,414-415 #1.2/B:270-341,346-410,414-415
> #5/A:270-341,346-410,414-415 #2/A:270-341,343-407,411-412
4222 atoms, 4324 bonds, 556 residues, 4 models selected
> select #1.1/A:299 #1.2/B:299 #5/A:299
23 atoms, 20 bonds, 3 residues, 3 models selected
> select #1.1/A:299 #1.2/B:299 #5/A:299 #2/A:299
31 atoms, 27 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[299] RMSD: 23.714
> select all
20470 atoms, 20146 bonds, 1 pseudobond, 3401 residues, 8 models selected
> show sel & #!1.1 surfaces
> hide sel & #!1.1 atoms
> show #!2 models
> show #!3 models
> show #!4 models
> hide sel & #!2-4#!1.1 cartoons
> hide sel & #!2-4#!1.1 atoms
> show sel & #!2-4#!1.1 surfaces
[Repeated 1 time(s)]
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1.1/A:511 #1.2/B:511 #5/A:511
17 atoms, 14 bonds, 3 residues, 3 models selected
> select #1.1/A:511 #1.2/B:511 #5/A:511 #2/A:508
22 atoms, 18 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[511] RMSD: 27.948
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1.1/A:494 #1.2/B:494 #5/A:494
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
19 atoms, 16 bonds, 3 residues, 3 models selected
> select #1.1/A:494 #1.2/B:494 #5/A:494 #2/A:491
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
25 atoms, 21 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[494] RMSD: 27.536
> select #1.1/A:494 #1.2/B:494 #5/A:494 #2/A:491
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
25 atoms, 21 bonds, 4 residues, 4 models selected
> select #1.1/A:494 #1.2/B:494 #5/A:494 #2/A:491
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
25 atoms, 21 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[494] RMSD: 27.536
> select #1.1/A:495-496 #1.2/B:495-496 #5/A:495-496
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
48 atoms, 48 bonds, 6 residues, 3 models selected
> select #1.1/A:495 #1.2/B:495 #5/A:495 #2/A:492
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 112, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 354, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 463, in add
self._history.enqueue((item, typed))
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 182, in enqueue
self.save()
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 212, in save
self._history.save(self._queue)
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\history.py", line 119, in save
with SaveTextFile(self._filename) as f:
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
Error processing trigger "command started":
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.17820.1764852553.6771607.tmp'
-> 'C:\\\Users\\\evc1\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'
File "C:\Users\evc1\OneDrive - CDC\Apps\ChimeraX_1.11\bin\Lib\site-
packages\chimerax\core\safesave.py", line 122, in __exit__
os.replace(self._tmp_filename, self.name)
See log for complete Python traceback.
16 atoms, 12 bonds, 4 residues, 4 models selected
MatchMaker Alignment [ID: 2] region prototype_8V97, chain A..new, chain A
[495] RMSD: 23.680
OpenGL version: 3.3.0 - Build 31.0.101.2114
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7060
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,966,090,752
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: en-US
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.11.1
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11rc202512020129
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.2
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
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