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Opened 5 weeks ago
Closed 5 weeks ago
#19059 closed defect (duplicate)
pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
just opened a model and clicked tools, binding analysis and find cavities
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_pentamer_20250930.cxs
Log from Tue Sep 30 15:26:10 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/VLP-structures_20250922.cxs
Error opening map "/Users/jl209164/Library/CloudStorage/OneDrive-
GSK/OneDrive_Documents/Norovirus/structures/VLP-structures_20250922.cxs": File
VLP-structures_20250922.cxs, format ccp4
MRC header value nsymbt (1953788019) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P279_J36_005_volume_map.mrc as #6, grid size 360,360,360,
pixel 2.32, shown at level 0.145, step 1, values float32
Opened emd_10756.map as #8, grid size 400,400,400, pixel 1.38, shown at level
0.238, step 1, values float32
Log from Mon Sep 22 14:32:25 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jl209164/Downloads/cryosparc_P325_J153_004_volume_map_sharp
> (1).mrc"
Opened cryosparc_P325_J153_004_volume_map_sharp (1).mrc as #1, grid size
300,300,300, pixel 3.58, shown at level 0.714, step 2, values float32
> volume #1 level 0.3238
> volume #1 step 1
> volume #1 level 0.2822
> open
> "/Users/jl209164/Documents/hPV/68-Fab/HPV68_68H6_P311_J394_005_volume_map_sharp
> (1).mrc"
Opened HPV68_68H6_P311_J394_005_volume_map_sharp (1).mrc as #2, grid size
320,320,320, pixel 0.894, shown at level 0.025, step 2, values float32
> volume #2 step 1
> close #1
> volume #2 level 0.05467
> open /Users/jl209164/Documents/hPV/68-Fab/HPV_68_Full_Isolde1.pdb
Chain information for HPV_68_Full_Isolde1.pdb #1
---
Chain | Description
A C E G I | No description available
B D F H J | No description available
M N O P Q | No description available
> volume #2 level 0.03547
> volume #2 level 0.04943
> select add #1
49890 atoms, 50565 bonds, 20 pseudobonds, 3225 residues, 2 models selected
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> volume #2 color #ffffb27c
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes true
> select ::name="ASN"
1790 atoms, 1670 bonds, 130 residues, 1 model selected
> color sel red
> open 7kzf
7kzf title:
High resolution cryo EM analysis of HPV16 identifies minor structural protein
L2 and describes capsid flexibility [more info...]
Chain information for 7kzf #3
---
Chain | Description | UniProt
A B C D E F | Major capsid protein L1 | VL1_HPV16 1-503
7kzf mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> mmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 HPV_68_Full_Isolde1.pdb, chain M (#1) with 7kzf, chain E (#3),
sequence alignment score = 1549.3
RMSD between 380 pruned atom pairs is 0.510 angstroms; (across all 413 pairs:
3.973)
> select add #3
24281 atoms, 24782 bonds, 2994 residues, 2 models selected
> hide sel target a
> cartoon sel
> ui tool show "Show Sequence Viewer"
> sequence chain #1/M
Alignment identifier is 1/M
> select #1/M:39
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/M
6461 atoms, 6548 bonds, 4 pseudobonds, 414 residues, 2 models selected
> open "/Users/jl209164/Downloads/7k6v GII4 crystal structure.cif"
Summary of feedback from opening /Users/jl209164/Downloads/7k6v GII4 crystal
structure.cif
---
note | Fetching CCD CD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CD/CD.cif
7k6v GII4 crystal structure.cif title:
Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus
(HOV) [more info...]
Chain information for 7k6v GII4 crystal structure.cif #4
---
Chain | Description | UniProt
AA AB AC BA BB BC CA CB CC DA DB DC EA EB EC FA FB FC GA GB GC HA HB HC IA IB IC JA JB JC KA KB KC LA LB LC MA MB MC NA NB NC OA OB OC | Capsid protein VP1 | A9YYE4_9CALI 1-540
Non-standard residues in 7k6v GII4 crystal structure.cif #4
---
CD — cadmium ion
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
7k6v GII4 crystal structure.cif mmCIF Assemblies
---
1| author_defined_assembly
> open "/Users/jl209164/Downloads/7k6v GII4 crystal structure.cif"
7k6v GII4 crystal structure.cif title:
Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus
(HOV) [more info...]
Chain information for 7k6v GII4 crystal structure.cif #5
---
Chain | Description | UniProt
AA AB AC BA BB BC CA CB CC DA DB DC EA EB EC FA FB FC GA GB GC HA HB HC IA IB IC JA JB JC KA KB KC LA LB LC MA MB MC NA NB NC OA OB OC | Capsid protein VP1 | A9YYE4_9CALI 1-540
Non-standard residues in 7k6v GII4 crystal structure.cif #5
---
CD — cadmium ion
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
7k6v GII4 crystal structure.cif mmCIF Assemblies
---
1| author_defined_assembly
> open "/Users/jl209164/Downloads/7k6v GII4 crystal structure.cif"
7k6v GII4 crystal structure.cif title:
Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus
(HOV) [more info...]
Chain information for 7k6v GII4 crystal structure.cif #6
---
Chain | Description | UniProt
AA AB AC BA BB BC CA CB CC DA DB DC EA EB EC FA FB FC GA GB GC HA HB HC IA IB IC JA JB JC KA KB KC LA LB LC MA MB MC NA NB NC OA OB OC | Capsid protein VP1 | A9YYE4_9CALI 1-540
Non-standard residues in 7k6v GII4 crystal structure.cif #6
---
CD — cadmium ion
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
7k6v GII4 crystal structure.cif mmCIF Assemblies
---
1| author_defined_assembly
> volume #2 level 0.03809
> hide #3 models
> show #3 models
> close #5-6
> close #4
> select #1/M:40
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/M:40-191
2260 atoms, 2289 bonds, 2 pseudobonds, 146 residues, 2 models selected
> select #1/M:39
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/M:39-43
82 atoms, 81 bonds, 5 residues, 1 model selected
> select
> #1/M:47-49,53-56,62-66,90-95,115-128,137-139,166-168,172-179,184-190,207-213,267-273,279-281,310-312,329-331,348-356,363-367,380-402,501-504
1945 atoms, 1958 bonds, 117 residues, 1 model selected
> select clear
> select #1/M:44
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/M:44-55
202 atoms, 205 bonds, 12 residues, 1 model selected
> hide #3 models
> select #1/M:39
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/M:39-48
157 atoms, 157 bonds, 10 residues, 1 model selected
> volume #2 level 0.03111
> select #1/M:525
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/M:455-525
621 atoms, 631 bonds, 1 pseudobond, 37 residues, 2 models selected
> select clear
> select #1/M:525
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/M:521-525
97 atoms, 97 bonds, 5 residues, 1 model selected
> volume #2 level 0.04856
> volume #2 level 0.04071
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/D
Alignment identifier is 3/D
> hide #3 models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.03198
> volume #2 level 0.03983
> open
> /Users/jl209164/Documents/hPV/68-Fab/HPV-68_68H6_P311_J394_005_volume_map_half_A.mrc
Opened HPV-68_68H6_P311_J394_005_volume_map_half_A.mrc as #4, grid size
320,320,320, pixel 0.894, shown at level 0.0359, step 2, values float32
> volume #4 step 1
> volume #4 level 0.01885
> volume #4 level 0.0359
> close #4
> open
> /Users/jl209164/Documents/hPV/68-Fab/HPV-68_68H6_P311_J394_005_volume_map_half_B.mrc
Opened HPV-68_68H6_P311_J394_005_volume_map_half_B.mrc as #4, grid size
320,320,320, pixel 0.894, shown at level 0.0359, step 2, values float32
> close #4
> open /Users/jl209164/Downloads/6OUU.pdb1
6OUU.pdb1 title:
Symmetric reconstruction of human norovirus gii.4 minerva strain VLP In T=4
symmetry [more info...]
Chain information for 6OUU.pdb1
---
Chain | Description
4.1/A 4.1/B 4.1/C 4.1/D | No description available
4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A 4.21/A 4.22/A 4.23/A 4.24/A 4.25/A 4.26/A 4.27/A 4.28/A 4.29/A 4.30/A 4.31/A 4.32/A 4.33/A 4.34/A 4.35/A 4.36/A 4.37/A 4.38/A 4.39/A 4.40/A 4.41/A 4.42/A 4.43/A 4.44/A 4.45/A 4.46/A 4.47/A 4.48/A 4.49/A 4.50/A 4.51/A 4.52/A 4.53/A 4.54/A 4.55/A 4.56/A 4.57/A 4.58/A 4.59/A 4.60/A 4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.7/C 4.8/C 4.9/C 4.10/C 4.11/C 4.12/C 4.13/C 4.14/C 4.15/C 4.16/C 4.17/C 4.18/C 4.19/C 4.20/C 4.21/C 4.22/C 4.23/C 4.24/C 4.25/C 4.26/C 4.27/C 4.28/C 4.29/C 4.30/C 4.31/C 4.32/C 4.33/C 4.34/C 4.35/C 4.36/C 4.37/C 4.38/C 4.39/C 4.40/C 4.41/C 4.42/C 4.43/C 4.44/C 4.45/C 4.46/C 4.47/C 4.48/C 4.49/C 4.50/C 4.51/C 4.52/C 4.53/C 4.54/C 4.55/C 4.56/C 4.57/C 4.58/C 4.59/C 4.60/C 4.2/D 4.3/D 4.4/D 4.5/D 4.6/D 4.7/D 4.8/D 4.9/D 4.10/D 4.11/D 4.12/D 4.13/D 4.14/D 4.15/D 4.16/D 4.17/D 4.18/D 4.19/D 4.20/D 4.21/D 4.22/D 4.23/D 4.24/D 4.25/D 4.26/D 4.27/D 4.28/D 4.29/D 4.30/D 4.31/D 4.32/D 4.33/D 4.34/D 4.35/D 4.36/D 4.37/D 4.38/D 4.39/D 4.40/D 4.41/D 4.42/D 4.43/D 4.44/D 4.45/D 4.46/D 4.47/D 4.48/D 4.49/D 4.50/D 4.51/D 4.52/D 4.53/D 4.54/D 4.55/D 4.56/D 4.57/D 4.58/D 4.59/D 4.60/D | No description available
4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B 4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B 4.17/B 4.18/B 4.19/B 4.20/B 4.21/B 4.22/B 4.23/B 4.24/B 4.25/B 4.26/B 4.27/B 4.28/B 4.29/B 4.30/B 4.31/B 4.32/B 4.33/B 4.34/B 4.35/B 4.36/B 4.37/B 4.38/B 4.39/B 4.40/B 4.41/B 4.42/B 4.43/B 4.44/B 4.45/B 4.46/B 4.47/B 4.48/B 4.49/B 4.50/B 4.51/B 4.52/B 4.53/B 4.54/B 4.55/B 4.56/B 4.57/B 4.58/B 4.59/B 4.60/B | No description available
> view #4
> select #4.1/A
3754 atoms, 3871 bonds, 485 residues, 1 model selected
> color sel red
> select #4.1/B
3720 atoms, 3836 bonds, 1 pseudobond, 480 residues, 2 models selected
> color (#!4.1 & sel) orange
> select #4.1/C
3754 atoms, 3871 bonds, 485 residues, 1 model selected
> color sel yellow
> select #4.1/D
3754 atoms, 3871 bonds, 485 residues, 1 model selected
> color sel lime
> close #1-2
> close #3
> open 7K6V
Summary of feedback from opening 7K6V fetched from pdb
---
note | Fetching compressed mmCIF 7k6v from http://files.rcsb.org/download/7k6v.cif
7k6v title:
Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus
(HOV) [more info...]
Chain information for 7k6v #1
---
Chain | Description | UniProt
AA AB AC BA BB BC CA CB CC DA DB DC EA EB EC FA FB FC GA GB GC HA HB HC IA IB IC JA JB JC KA KB KC LA LB LC MA MB MC NA NB NC OA OB OC | Capsid protein VP1 | A9YYE4_9CALI 1-540
Non-standard residues in 7k6v #1
---
CD — cadmium ion
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
7k6v mmCIF Assemblies
---
1| author_defined_assembly
> mmaker #1 to #6
No 'to' model specified
> hide #!4 models
> mmaker #1 to #4
Specify a single 'to' model only
> show #!4 models
> hide #!4 models
> show #!4 models
> mmaker #1 to #4
Specify a single 'to' model only
> mmaker #1 to #4.1
Computing secondary structure
[Repeated 1 time(s)] 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 6OUU.pdb1, chain C (#4.1) with 7k6v, chain OB (#1), sequence
alignment score = 2461.5
RMSD between 270 pruned atom pairs is 0.954 angstroms; (across all 485 pairs:
16.156)
> hide #!4 models
> select add #4
898920 atoms, 926940 bonds, 60 pseudobonds, 116100 residues, 122 models
selected
> select subtract #4
Nothing selected
> show #!4 models
> hide #!4 models
> show #!4 models
> select add #1
176522 atoms, 181805 bonds, 19 pseudobonds, 22978 residues, 2 models selected
> hide (#!1 & sel) target a
> cartoon (#!1 & sel)
> select subtract #1
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/AA
Alignment identifier is 1/AA
> select clear
> select #1/AA:26-531
3860 atoms, 3978 bonds, 1 pseudobond, 500 residues, 2 models selected
> select clear
> select #1/AA:26-531
3860 atoms, 3978 bonds, 1 pseudobond, 500 residues, 2 models selected
> select clear
> select #1/AA:26-531
3860 atoms, 3978 bonds, 1 pseudobond, 500 residues, 2 models selected
> color #1 darkgrey
> select #1/AA
3863 atoms, 3978 bonds, 1 pseudobond, 503 residues, 2 models selected
> color (#!1 & sel) orange red
> select clear
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/7MRY.pdb1
7MRY.pdb1 title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7MRY.pdb1
---
Chain | Description
2.1/A 2.1/B 2.1/C | No description available
2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.21/A 2.22/A 2.23/A 2.24/A 2.25/A 2.26/A 2.27/A 2.28/A 2.29/A 2.30/A 2.31/A 2.32/A 2.33/A 2.34/A 2.35/A 2.36/A 2.37/A 2.38/A 2.39/A 2.40/A 2.41/A 2.42/A 2.43/A 2.44/A 2.45/A 2.46/A 2.47/A 2.48/A 2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A 2.57/A 2.58/A 2.59/A 2.60/A | No description available
2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B 2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B 2.21/B 2.22/B 2.23/B 2.24/B 2.25/B 2.26/B 2.27/B 2.28/B 2.29/B 2.30/B 2.31/B 2.32/B 2.33/B 2.34/B 2.35/B 2.36/B 2.37/B 2.38/B 2.39/B 2.40/B 2.41/B 2.42/B 2.43/B 2.44/B 2.45/B 2.46/B 2.47/B 2.48/B 2.49/B 2.50/B 2.51/B 2.52/B 2.53/B 2.54/B 2.55/B 2.56/B 2.57/B 2.58/B 2.59/B 2.60/B 2.2/C 2.3/C 2.4/C 2.5/C 2.6/C 2.7/C 2.8/C 2.9/C 2.10/C 2.11/C 2.12/C 2.13/C 2.14/C 2.15/C 2.16/C 2.17/C 2.18/C 2.19/C 2.20/C 2.21/C 2.22/C 2.23/C 2.24/C 2.25/C 2.26/C 2.27/C 2.28/C 2.29/C 2.30/C 2.31/C 2.32/C 2.33/C 2.34/C 2.35/C 2.36/C 2.37/C 2.38/C 2.39/C 2.40/C 2.41/C 2.42/C 2.43/C 2.44/C 2.45/C 2.46/C 2.47/C 2.48/C 2.49/C 2.50/C 2.51/C 2.52/C 2.53/C 2.54/C 2.55/C 2.56/C 2.57/C 2.58/C 2.59/C 2.60/C | No description available
> mmaker #2 to #1
Computing secondary structure
[Repeated 60 time(s)] 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 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.1), sequence
alignment score = 2671.1
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.2), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.3), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.4), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.5), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.6), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.7), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.8), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.9), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.10), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.11), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.12), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.13), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.14), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.15), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.16), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.17), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.18), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.19), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.20), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.21), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.22), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.23), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.24), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.25), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.26), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.27), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.28), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.29), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.30), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.31), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.32), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.33), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.34), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.35), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.36), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.37), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.38), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.39), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.40), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.41), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.42), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.43), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.44), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.45), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.46), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.47), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.48), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.49), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.50), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.51), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.52), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.53), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.54), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.55), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.56), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.57), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.58), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.59), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
Matchmaker 7k6v, chain AB (#1) with 7MRY.pdb1, chain B (#2.60), sequence
alignment score = 2486.3
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #2
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/7MRY.pdb1
7MRY.pdb1 title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7MRY.pdb1
---
Chain | Description
2.1/A 2.1/B 2.1/C | No description available
2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.21/A 2.22/A 2.23/A 2.24/A 2.25/A 2.26/A 2.27/A 2.28/A 2.29/A 2.30/A 2.31/A 2.32/A 2.33/A 2.34/A 2.35/A 2.36/A 2.37/A 2.38/A 2.39/A 2.40/A 2.41/A 2.42/A 2.43/A 2.44/A 2.45/A 2.46/A 2.47/A 2.48/A 2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A 2.57/A 2.58/A 2.59/A 2.60/A | No description available
2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B 2.11/B 2.12/B 2.13/B 2.14/B 2.15/B 2.16/B 2.17/B 2.18/B 2.19/B 2.20/B 2.21/B 2.22/B 2.23/B 2.24/B 2.25/B 2.26/B 2.27/B 2.28/B 2.29/B 2.30/B 2.31/B 2.32/B 2.33/B 2.34/B 2.35/B 2.36/B 2.37/B 2.38/B 2.39/B 2.40/B 2.41/B 2.42/B 2.43/B 2.44/B 2.45/B 2.46/B 2.47/B 2.48/B 2.49/B 2.50/B 2.51/B 2.52/B 2.53/B 2.54/B 2.55/B 2.56/B 2.57/B 2.58/B 2.59/B 2.60/B 2.2/C 2.3/C 2.4/C 2.5/C 2.6/C 2.7/C 2.8/C 2.9/C 2.10/C 2.11/C 2.12/C 2.13/C 2.14/C 2.15/C 2.16/C 2.17/C 2.18/C 2.19/C 2.20/C 2.21/C 2.22/C 2.23/C 2.24/C 2.25/C 2.26/C 2.27/C 2.28/C 2.29/C 2.30/C 2.31/C 2.32/C 2.33/C 2.34/C 2.35/C 2.36/C 2.37/C 2.38/C 2.39/C 2.40/C 2.41/C 2.42/C 2.43/C 2.44/C 2.45/C 2.46/C 2.47/C 2.48/C 2.49/C 2.50/C 2.51/C 2.52/C 2.53/C 2.54/C 2.55/C 2.56/C 2.57/C 2.58/C 2.59/C 2.60/C | No description available
> mmaker #1 to #2
Specify a single 'to' model only
> mmaker #1/AA to #2.1
Computing secondary structure
[Repeated 1 time(s)] 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 7MRY.pdb1, chain B (#2.1) with 7k6v, chain AA (#1), sequence
alignment score = 2655.5
RMSD between 417 pruned atom pairs is 1.101 angstroms; (across all 480 pairs:
1.471)
> select #2.57/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> mmaker #1/AA to #2
Specify a single 'to' model only
> mmaker #1/AB to #2.1
Computing secondary structure
[Repeated 1 time(s)] 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 7MRY.pdb1, chain B (#2.1) with 7k6v, chain AB (#1), sequence
alignment score = 2671.1
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
> open 7mry
Summary of feedback from opening 7mry fetched from pdb
---
note | Fetching compressed mmCIF 7mry from http://files.rcsb.org/download/7mry.cif
7mry title:
Norovirus T=3 GII.4 HOV VLP [more info...]
Chain information for 7mry #3
---
Chain | Description | UniProt
A B C | VP1 | A9YYE4_9CALI 1-540 1001-1540 2001-2540
7mry mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> mmaker #1 to #3
Computing secondary structure
[Repeated 1 time(s)] 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 7mry, chain B (#3) with 7k6v, chain AB (#1), sequence alignment
score = 2671.1
RMSD between 472 pruned atom pairs is 0.921 angstroms; (across all 486 pairs:
1.040)
> hide #3 models
> show #3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> mmaker #1/AA to #3/A
Computing secondary structure
[Repeated 1 time(s)] 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 7mry, chain A (#3) with 7k6v, chain AA (#1), sequence alignment
score = 2605.1
RMSD between 446 pruned atom pairs is 1.047 angstroms; (across all 481 pairs:
1.240)
> hide #!1 models
> show #!1 models
> hide #3 models
> select #1/AA
3863 atoms, 3978 bonds, 1 pseudobond, 503 residues, 2 models selected
> select #1/BA
3856 atoms, 3971 bonds, 1 pseudobond, 502 residues, 2 models selected
> color (#!1 & sel) orange
> select #1/CA
3856 atoms, 3971 bonds, 1 pseudobond, 502 residues, 2 models selected
> open 6ouu
6ouu title:
Symmetric reconstruction of human norovirus GII.4 Minerva strain VLP in T=4
symmetry [more info...]
Chain information for 6ouu #5
---
Chain | Description | UniProt
A B C D | Major capsid protein | R4I3T2_9CALI 1-540
6ouu mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> mmaker #5 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain OB (#1) with 6ouu, chain C (#5), sequence alignment
score = 2461.5
RMSD between 270 pruned atom pairs is 0.954 angstroms; (across all 485 pairs:
16.156)
> show #!2 models
> hide #!1 models
> select #2:41-213
78600 atoms, 81120 bonds, 10140 residues, 60 models selected
> color sel yellow
> select #2:1-40
Nothing selected
> select #2:221-418
90660 atoms, 92880 bonds, 11880 residues, 60 models selected
> color sel magenta
> show #3 models
> hide #!2 models
> select #3:221-418
1511 atoms, 1548 bonds, 198 residues, 1 model selected
> select #3/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3:1221-1418
1511 atoms, 1548 bonds, 198 residues, 1 model selected
> color sel magenta
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> select #3:2221-2418
1511 atoms, 1548 bonds, 198 residues, 1 model selected
> color sel magenta
> select #3:221-418
1511 atoms, 1548 bonds, 198 residues, 1 model selected
> color sel magenta
> select #2:221-418
90660 atoms, 92880 bonds, 11880 residues, 60 models selected
> color #3,5 magenta
> undo
> show #!2 models
> select #2:1221-1418
90660 atoms, 92880 bonds, 11880 residues, 60 models selected
> color sel magenta
> select #2:2221-2418
90660 atoms, 92880 bonds, 11880 residues, 60 models selected
> color sel hot pink
> color sel magenta
> select #2:1041-1220
82560 atoms, 85260 bonds, 10560 residues, 60 models selected
> select #2:1041-1213
79320 atoms, 81840 bonds, 10140 residues, 60 models selected
> color sel yellow
> select #2:2041-2213
79320 atoms, 81840 bonds, 10140 residues, 60 models selected
> color sel yellow
> hide #!5 models
> hide #3 models
> select #2:2041-2213
79320 atoms, 81840 bonds, 10140 residues, 60 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel sandy brown
> select #2:1041-1213
79320 atoms, 81840 bonds, 10140 residues, 60 models selected
> ui tool show "Color Actions"
> color sel coral
> hide #!2 models
> show #3 models
> show #!1 models
> hide #3 models
> select #1/C
Nothing selected
> select #1/CA
3856 atoms, 3971 bonds, 1 pseudobond, 502 residues, 2 models selected
> color (#!1 & sel) yellow
> select #1/DA
3847 atoms, 3963 bonds, 1 pseudobond, 500 residues, 2 models selected
> color (#!1 & sel) lime
> select #1/EA
3857 atoms, 3971 bonds, 1 pseudobond, 503 residues, 2 models selected
> color (#!1 & sel) purple
> select clear
[Repeated 1 time(s)]
> select #1/AB
4014 atoms, 4134 bonds, 524 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> color sel crimson
> select #1/AB,BA
7870 atoms, 8105 bonds, 1 pseudobond, 1026 residues, 2 models selected
> select #1
176522 atoms, 181805 bonds, 19 pseudobonds, 22978 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/AB,BA
7870 atoms, 8105 bonds, 1 pseudobond, 1026 residues, 2 models selected
> cartoon (#!1 & sel)
> select #1
176522 atoms, 181805 bonds, 19 pseudobonds, 22978 residues, 2 models selected
> cartoon (#!1 & sel)
> select #1/BC,KC
7830 atoms, 8064 bonds, 1018 residues, 1 model selected
> color sel medium blue
> color sel cornflower blue
> select clear
> select #1/BC,KC
7830 atoms, 8064 bonds, 1018 residues, 1 model selected
> surface sel
> select #1/AB, BA
7870 atoms, 8105 bonds, 1 pseudobond, 1026 residues, 2 models selected
> surface (#!1 & sel)
> select #1/AB:434
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1
176522 atoms, 181805 bonds, 19 pseudobonds, 22978 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select #1/AB:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts intraRes true ignoreHiddenModels true
125985 contacts
> close #6
> ui tool show Contacts
> help help:user/tools/clashes.html
Restriction atom specifier must not be blank
> contacts sel restrict #1/AB:484 ignoreHiddenModels true
No contacts
> select #1/BC:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
> style (#!1 & sel) sphere
Changed 11 atom styles
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #1/AB:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/BA:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (#!1 & sel) target ab
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> contacts sel restrict #1/BA:484 ignoreHiddenModels true
No contacts
> select #1/KB
4010 atoms, 4130 bonds, 524 residues, 1 model selected
> color sel cyan
> select #1/LC
3867 atoms, 3981 bonds, 1 pseudobond, 504 residues, 2 models selected
> color (#!1 & sel) light sea green
> select #1/FB
4019 atoms, 4140 bonds, 523 residues, 1 model selected
> color sel forest green
> select #1/GC
3915 atoms, 4032 bonds, 509 residues, 1 model selected
> color sel dark gray
> color sel dim gray
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/KC
3915 atoms, 4032 bonds, 509 residues, 1 model selected
> color (#!1 & sel) dark gray
> select #1/AC,GC
7838 atoms, 8072 bonds, 1019 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select clear
> select #1:1-41
6578 atoms, 6653 bonds, 980 residues, 1 model selected
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #3 models
> show #!1 models
> hide #!1 models
> select #3/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> color sel red
> select #3/B
3778 atoms, 3892 bonds, 489 residues, 1 model selected
> color sel orange red
> select #3/C
3776 atoms, 3892 bonds, 487 residues, 1 model selected
> color sel blue
> show #!2 models
> color #2 #919191ff models
> color #2 silver models
> select add #3
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> transparency #2 C 50%
Missing or invalid "percent" argument: Expected a number
> transparency #2 C 50
Missing or invalid "percent" argument: Expected a number
> transparency #2 50
> transparency #2 50 cartoons
> show #!1 models
> hide #!2 models
> hide #3 models
> select add #1
187852 atoms, 193481 bonds, 19 pseudobonds, 24443 residues, 3 models selected
> select subtract #1
11330 atoms, 11676 bonds, 1465 residues, 5 models selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #3 models
> save "/Users/jl209164/OneDrive -
> GSK/OneDrive_Documents/Norovirus/structures/VLP-structures_20250919.cxs"
> select :221-496
740245 atoms, 761022 bonds, 4 pseudobonds, 96567 residues, 124 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/AA
Destroying pre-existing alignment with identifier 1/AA
Alignment identifier is 1/AA
> select :221-540
837279 atoms, 862362 bonds, 4 pseudobonds, 108629 residues, 124 models
selected
> cartoon hide (#3#!1 & sel)
> hide #3 models
> show #3 models
> hide #3 models
> hide #!1 models
> show #!1 models
> show #3 models
> hide #!1 models
> show #!1 models
> hide #3 models
> select :190
2009 atoms, 1735 bonds, 274 residues, 123 models selected
> select :113
1750 atoms, 1400 bonds, 350 residues, 123 models selected
> select :189-192
6972 atoms, 6637 bonds, 1157 residues, 123 models selected
> select :42-80
97314 atoms, 100814 bonds, 12491 residues, 123 models selected
> select :42-60
45864 atoms, 47264 bonds, 5491 residues, 123 models selected
> select :60-80
53900 atoms, 56000 bonds, 7350 residues, 123 models selected
> select :100-120
51100 atoms, 51450 bonds, 7350 residues, 123 models selected
> select :150-180
89356 atoms, 91562 bonds, 10850 residues, 123 models selected
> delete #3:221-540
No model chosen to save relative to
> show #3 models
> delete #1:221-540
No model chosen to save relative to
> save "/Users/jl209164/OneDrive -
> GSK/OneDrive_Documents/Norovirus/structures/7k6v_S.pdb" models #1 relModel
> #3
> hide #!1 models
> select #3:1221-1540
2399 atoms, 2470 bonds, 310 residues, 1 model selected
> delete #3:1221-1540
> delete #3:2221-2540
> save "/Users/jl209164/OneDrive -
> GSK/OneDrive_Documents/Norovirus/structures/7mry_S.pdb" models #3 relModel
> #2
> show #!1 models
> mmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain OC (#1) with 7mry, chain B (#3), sequence alignment
score = 2271.5
RMSD between 154 pruned atom pairs is 0.910 angstroms; (across all 176 pairs:
1.586)
> show #!5 models
> hide #3 models
> hide #!1 models
> show #!4 models
> select #6:221-540
Nothing selected
> select #4:221-540
572880 atoms, 590160 bonds, 74400 residues, 60 models selected
> cartoon hide sel
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> select #5:221-540
9548 atoms, 9836 bonds, 1240 residues, 1 model selected
> cartoon hide sel
> open /Users/jl209164/Downloads/cryosparc_P279_J184_004_volume_map.mrc
Opened cryosparc_P279_J184_004_volume_map.mrc as #6, grid size 160,160,160,
pixel 2.32, shown at level 0.296, step 1, values float32
> open /Users/jl209164/Downloads/cryosparc_P279_J184_004_volume_map.mrc
Opened cryosparc_P279_J184_004_volume_map.mrc as #7, grid size 160,160,160,
pixel 2.32, shown at level 0.296, step 1, values float32
> close #7
> volume #6 level 0.1974
> close #6
> open /Users/jl209164/Downloads/cryosparc_P279_J36_005_volume_map.mrc
Opened cryosparc_P279_J36_005_volume_map.mrc as #6, grid size 360,360,360,
pixel 2.32, shown at level 0.194, step 2, values float32
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!2 models
> hide #!4 models
> select add #2
689348 atoms, 710396 bonds, 89140 residues, 62 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0,0,106.83,0,1,0,109.41,0,0,1,110.34,#5,0.66427,0.41882,-0.61914,232.37,0.60968,0.17566,0.77294,-275.81,0.43248,-0.89092,-0.13866,701.53
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99898,-0.034048,-0.029696,126.91,0.035582,0.99797,0.052779,82.642,0.027839,-0.053782,0.99816,118.95,#5,0.62999,0.43887,-0.64071,247.89,0.65491,0.14319,0.74202,-266.13,0.41739,-0.88707,-0.19721,733.26
> color #6 #b2b2b266 models
> view matrix models
> #2,0.3849,-0.91529,0.11876,543.9,0.90272,0.40013,0.1581,-33.042,-0.19223,0.046356,0.98026,161.41,#5,-0.25099,-0.10538,-0.96224,1015,0.91197,0.30751,-0.27156,19.618,0.32451,-0.94569,0.018924,698.93
> color #6 #b2b2b273 models
> view matrix models
> #2,-0.35711,-0.8914,0.27908,716.03,0.86061,-0.19786,0.46925,68.706,-0.36307,0.40775,0.83781,146.61,#5,-0.65999,-0.55478,-0.50659,1179.6,0.65399,-0.092381,-0.75085,530.39,0.36976,-0.82685,0.42379,439.26
> view matrix models
> #2,-0.40478,-0.86483,0.29701,716.99,0.83748,-0.22022,0.50014,73.257,-0.36713,0.45119,0.81342,141.92,#5,-0.6677,-0.58606,-0.45903,1174.9,0.63835,-0.13351,-0.75808,558.9,0.383,-0.79919,0.46326,402.91
> hide #!6 models
> view matrix models
> #2,0.19303,-0.91629,-0.35092,748.56,0.95055,0.085952,0.29843,5.9263,-0.24329,-0.39118,0.88758,342.31,#5,-0.58219,0.23253,-0.77909,918.3,0.81289,0.14733,-0.56347,268.58,-0.016243,-0.96137,-0.2748,987.18
> select clear
[Repeated 1 time(s)]
> show #!6 models
> select add #2
679800 atoms, 700560 bonds, 87900 residues, 61 models selected
> view matrix models
> #2,0.33453,-0.72566,-0.60125,722.89,0.94236,0.25318,0.21875,-19.01,-0.0065119,-0.63977,0.76854,383.49
> ui tool show "Fit in Map"
> color #2 #73fdffff models
> color #2 #7a81ffff models
> view matrix models
> #2,0.38295,-0.7773,-0.49914,692.35,0.92361,0.31225,0.22235,-32.688,-0.016978,-0.54617,0.8375,336.28
> view matrix models
> #2,0.41095,-0.7504,-0.51771,681.13,0.9114,0.35163,0.21377,-38.492,0.021633,-0.55969,0.82842,331.39
> view matrix models
> #2,0.42501,-0.7177,-0.55161,677.14,0.90331,0.37547,0.20747,-41.408,0.058218,-0.58646,0.80789,334.79
> view matrix models
> #2,0.48398,-0.63834,-0.59857,648.77,0.81834,0.087865,0.56797,-37.356,-0.30997,-0.76472,0.56491,578.94
> view matrix models
> #2,0.61674,-0.64524,-0.45089,564.2,0.75436,0.32082,0.57273,-91.469,-0.2249,-0.69335,0.6846,493.44
> hide #!2 models
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/emd_20206_GII4-T4.map
Opened emd_20206_GII4-T4.map as #7, grid size 800,800,800, pixel 1.07, shown
at step 1, values float32
> volume #7 level -0.04627,0 level 0.1974,0.8 level 0.6958,1
> volume #7 level -0.04627,0 level -0.09035,0.8923 level 0.6958,1
> volume #6 step 1
> volume #7 level 0.003942,0.6923 level -0.09035,0.8923 level 0.6958,1
> volume #7 level 0.003942,0.6923 level -0.05559,0.06154 level 0.6958,1
> volume #7 level 7.959e-05,0.5538 level -0.05559,0.06154 level 0.6958,1
> close #7
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/emd_10755.map
Opened emd_10755.map as #7, grid size 500,500,500, pixel 1.38, shown at level
0.393, step 2, values float32
> volume #7 step 1
> volume #7 level 0.5524
> volume #6 level 0.1791
> select add #6
679800 atoms, 700560 bonds, 87900 residues, 63 models selected
> view matrix models
> #2,0.1111,0.1086,-0.98786,652.67,0.61754,0.77127,0.15424,-60.193,0.77865,-0.62718,0.018619,364.35,#6,0.44385,-0.44713,-0.77658,744.55,-0.18634,0.80162,-0.56805,398.56,0.87651,0.39684,0.27249,-228.33
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.1111,0.1086,-0.98786,559.01,0.61754,0.77127,0.15424,-143.25,0.77865,-0.62718,0.018619,308.41,#6,0.44385,-0.44713,-0.77658,650.89,-0.18634,0.80162,-0.56805,315.5,0.87651,0.39684,0.27249,-284.27
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.24386,0.0044501,-0.9698,544.39,0.074714,0.99693,0.023362,-3.9754,0.96693,-0.078155,0.24278,11.036,#6,0.58479,-0.37005,-0.72186,536.8,-0.60771,0.38958,-0.69204,716.01,0.53731,0.84338,0.0029362,-216.42
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.24386,0.0044501,-0.9698,549.23,0.074714,0.99693,0.023362,-2.0526,0.96693,-0.078155,0.24278,0.011155,#6,0.58479,-0.37005,-0.72186,541.63,-0.60771,0.38958,-0.69204,717.93,0.53731,0.84338,0.0029362,-227.44
> volume #7 level 0.3519
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/emd_10756.map
Opened emd_10756.map as #8, grid size 400,400,400, pixel 1.38, shown at level
0.34, step 2, values float32
> volume #8 step 1
> volume #8 level 0.238
> select add #8
679800 atoms, 700560 bonds, 87900 residues, 65 models selected
> view matrix models
> #2,0.24386,0.0044501,-0.9698,553.24,0.074714,0.99693,0.023362,-29.388,0.96693,-0.078155,0.24278,-25.702,#6,0.58479,-0.37005,-0.72186,545.64,-0.60771,0.38958,-0.69204,690.6,0.53731,0.84338,0.0029362,-253.15,#8,1,0,0,4.0095,0,1,0,-27.335,0,0,1,-25.713
> view matrix models
> #2,0.24386,0.0044501,-0.9698,555.59,0.074714,0.99693,0.023362,-28.263,0.96693,-0.078155,0.24278,-35.136,#6,0.58479,-0.37005,-0.72186,548,-0.60771,0.38958,-0.69204,691.72,0.53731,0.84338,0.0029362,-262.59,#8,1,0,0,6.3648,0,1,0,-26.211,0,0,1,-35.147
> select subtract #6
679800 atoms, 700560 bonds, 87900 residues, 63 models selected
> view matrix models
> #2,0.24386,0.0044501,-0.9698,545.78,0.074714,0.99693,0.023362,38.079,0.96693,-0.078155,0.24278,27.625,#8,1,0,0,-3.4515,0,1,0,40.131,0,0,1,27.614
> view matrix models
> #2,0.24386,0.0044501,-0.9698,583.43,0.074714,0.99693,0.023362,17.48,0.96693,-0.078155,0.24278,68.062,#8,1,0,0,34.201,0,1,0,19.533,0,0,1,68.051
> view matrix models
> #2,0.24386,0.0044501,-0.9698,622.07,0.074714,0.99693,0.023362,26.002,0.96693,-0.078155,0.24278,39.889,#8,1,0,0,72.84,0,1,0,28.054,0,0,1,39.878
> view matrix models
> #2,0.24386,0.0044501,-0.9698,617.47,0.074714,0.99693,0.023362,32.923,0.96693,-0.078155,0.24278,34.217,#8,1,0,0,68.237,0,1,0,34.975,0,0,1,34.206
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.16011,0.14491,-0.9764,602.5,-0.091765,0.98707,0.13145,35.342,0.98282,0.068554,0.17133,17.767,#8,0.98661,0.13362,-0.093563,60.905,-0.14546,0.98025,-0.13396,117.25,0.073816,0.14578,0.98656,-22.486
> view matrix models
> #2,0.24905,0.25513,-0.93428,540.73,0.014129,0.96362,0.26691,-27.927,0.96839,-0.079674,0.23639,36.449,#8,0.96794,0.25113,-0.0059463,9.6292,-0.25111,0.96795,0.0031497,111.98,0.0065467,-0.0015556,0.99998,32.839
> view matrix models
> #2,-0.21676,0.089787,-0.97209,697.82,-0.33823,0.92718,0.16106,94.632,0.91576,0.3637,-0.17061,73.667,#8,0.89027,0.050607,-0.45261,208.96,-0.23455,0.90283,-0.3604,225.31,0.39039,0.42702,0.81563,-139.88
> hide #!8 models
> hide #!6 models
> show #!8 models
> view matrix models
> #2,-0.49216,0.15919,-0.85583,701.3,-0.68068,0.54248,0.49234,155.03,0.54264,0.82485,-0.15863,34.688,#8,0.71067,0.10194,-0.6961,311.2,-0.64104,0.50146,-0.58103,508.14,0.28984,0.85915,0.42172,-122.74
> show #!6 models
> hide #!8 models
> show #!8 models
> view matrix models
> #2,-0.46009,0.15274,-0.87464,702.27,-0.66256,0.5967,0.45273,150.74,0.59105,0.78779,-0.17334,38.436,#8,0.7367,0.09746,-0.66915,297.86,-0.59797,0.55594,-0.57737,480.31,0.31574,0.82549,0.46785,-133.29
> fitmap #8 inMap #6
Fit map emd_10756.map in map cryosparc_P279_J36_005_volume_map.mrc using
2728673 points
correlation = 0.8093, correlation about mean = -0.01111, overlap = 1.213e+05
steps = 180, shift = 10.2, angle = 20.7 degrees
Position of emd_10756.map (#8) relative to
cryosparc_P279_J36_005_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.80905132 0.30899918 0.49995547 -26.63321852
-0.49996093 0.80903487 0.30903339 248.32544689
-0.30899035 -0.49998207 0.80903825 418.32178180
Axis -0.57738001 0.57733030 -0.57734050
Axis point 0.00000000 895.67094753 -404.71235794
Rotation angle (degrees) 44.47450836
Shift along axis -82.77081426
> fitmap #8 inMap #6
Fit map emd_10756.map in map cryosparc_P279_J36_005_volume_map.mrc using
2728673 points
correlation = 0.8093, correlation about mean = -0.01111, overlap = 1.213e+05
steps = 24, shift = 0.000192, angle = 0.000111 degrees
Position of emd_10756.map (#8) relative to
cryosparc_P279_J36_005_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.80905139 0.30899754 0.49995636 -26.63288575
-0.49995990 0.80903545 0.30903354 248.32505559
-0.30899182 -0.49998215 0.80903764 418.32245553
Axis -0.57738019 0.57733200 -0.57733861
Axis point 0.00000000 895.67292801 -404.71103044
Rotation angle (degrees) 44.47450670
Shift along axis -82.77040328
> volume #7 level 0.4855
> volume #7 level 0.3107
> volume #6 level 0.1105
> volume #6 level 0.1453
> ui tool show "Show Sequence Viewer"
> sequence chain #4.11/A
Alignment identifier is 4.11/A
> select #4.11/A:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.11/A:46-526
3726 atoms, 3842 bonds, 481 residues, 1 model selected
> select #4.11/A:530
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.11/A
3754 atoms, 3871 bonds, 485 residues, 1 model selected
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/emd_10756.map
Opened emd_10756.map as #9, grid size 400,400,400, pixel 1.38, shown at level
0.34, step 2, values float32
> volume #9 level 0.225
> volume #9 step 1
> close #9
> open /Users/jl209164/Documents/hPV/7KZF.pdb1
7KZF.pdb1 title:
High resolution cryo em analysis of HPV16 identifies minor structural protein
L2 and describes capsid flexibility [more info...]
Chain information for 7KZF.pdb1
---
Chain | Description
9.1/A 9.1/B 9.1/C 9.1/D 9.1/E 9.1/F | No description available
9.2/A 9.3/A 9.4/A 9.5/A 9.6/A 9.7/A 9.8/A 9.9/A 9.10/A 9.11/A 9.12/A 9.13/A 9.14/A 9.15/A 9.16/A 9.17/A 9.18/A 9.19/A 9.20/A 9.21/A 9.22/A 9.23/A 9.24/A 9.25/A 9.26/A 9.27/A 9.28/A 9.29/A 9.30/A 9.31/A 9.32/A 9.33/A 9.34/A 9.35/A 9.36/A 9.37/A 9.38/A 9.39/A 9.40/A 9.41/A 9.42/A 9.43/A 9.44/A 9.45/A 9.46/A 9.47/A 9.48/A 9.49/A 9.50/A 9.51/A 9.52/A 9.53/A 9.54/A 9.55/A 9.56/A 9.57/A 9.58/A 9.59/A 9.60/A | No description available
9.2/B 9.3/B 9.4/B 9.5/B 9.6/B 9.7/B 9.8/B 9.9/B 9.10/B 9.11/B 9.12/B 9.13/B 9.14/B 9.15/B 9.16/B 9.17/B 9.18/B 9.19/B 9.20/B 9.21/B 9.22/B 9.23/B 9.24/B 9.25/B 9.26/B 9.27/B 9.28/B 9.29/B 9.30/B 9.31/B 9.32/B 9.33/B 9.34/B 9.35/B 9.36/B 9.37/B 9.38/B 9.39/B 9.40/B 9.41/B 9.42/B 9.43/B 9.44/B 9.45/B 9.46/B 9.47/B 9.48/B 9.49/B 9.50/B 9.51/B 9.52/B 9.53/B 9.54/B 9.55/B 9.56/B 9.57/B 9.58/B 9.59/B 9.60/B | No description available
9.2/C 9.3/C 9.4/C 9.5/C 9.6/C 9.7/C 9.8/C 9.9/C 9.10/C 9.11/C 9.12/C 9.13/C 9.14/C 9.15/C 9.16/C 9.17/C 9.18/C 9.19/C 9.20/C 9.21/C 9.22/C 9.23/C 9.24/C 9.25/C 9.26/C 9.27/C 9.28/C 9.29/C 9.30/C 9.31/C 9.32/C 9.33/C 9.34/C 9.35/C 9.36/C 9.37/C 9.38/C 9.39/C 9.40/C 9.41/C 9.42/C 9.43/C 9.44/C 9.45/C 9.46/C 9.47/C 9.48/C 9.49/C 9.50/C 9.51/C 9.52/C 9.53/C 9.54/C 9.55/C 9.56/C 9.57/C 9.58/C 9.59/C 9.60/C 9.2/D 9.3/D 9.4/D 9.5/D 9.6/D 9.7/D 9.8/D 9.9/D 9.10/D 9.11/D 9.12/D 9.13/D 9.14/D 9.15/D 9.16/D 9.17/D 9.18/D 9.19/D 9.20/D 9.21/D 9.22/D 9.23/D 9.24/D 9.25/D 9.26/D 9.27/D 9.28/D 9.29/D 9.30/D 9.31/D 9.32/D 9.33/D 9.34/D 9.35/D 9.36/D 9.37/D 9.38/D 9.39/D 9.40/D 9.41/D 9.42/D 9.43/D 9.44/D 9.45/D 9.46/D 9.47/D 9.48/D 9.49/D 9.50/D 9.51/D 9.52/D 9.53/D 9.54/D 9.55/D 9.56/D 9.57/D 9.58/D 9.59/D 9.60/D | No description available
9.2/E 9.3/E 9.4/E 9.5/E 9.6/E 9.7/E 9.8/E 9.9/E 9.10/E 9.11/E 9.12/E 9.13/E 9.14/E 9.15/E 9.16/E 9.17/E 9.18/E 9.19/E 9.20/E 9.21/E 9.22/E 9.23/E 9.24/E 9.25/E 9.26/E 9.27/E 9.28/E 9.29/E 9.30/E 9.31/E 9.32/E 9.33/E 9.34/E 9.35/E 9.36/E 9.37/E 9.38/E 9.39/E 9.40/E 9.41/E 9.42/E 9.43/E 9.44/E 9.45/E 9.46/E 9.47/E 9.48/E 9.49/E 9.50/E 9.51/E 9.52/E 9.53/E 9.54/E 9.55/E 9.56/E 9.57/E 9.58/E 9.59/E 9.60/E | No description available
9.2/F 9.3/F 9.4/F 9.5/F 9.6/F 9.7/F 9.8/F 9.9/F 9.10/F 9.11/F 9.12/F 9.13/F 9.14/F 9.15/F 9.16/F 9.17/F 9.18/F 9.19/F 9.20/F 9.21/F 9.22/F 9.23/F 9.24/F 9.25/F 9.26/F 9.27/F 9.28/F 9.29/F 9.30/F 9.31/F 9.32/F 9.33/F 9.34/F 9.35/F 9.36/F 9.37/F 9.38/F 9.39/F 9.40/F 9.41/F 9.42/F 9.43/F 9.44/F 9.45/F 9.46/F 9.47/F 9.48/F 9.49/F 9.50/F 9.51/F 9.52/F 9.53/F 9.54/F 9.55/F 9.56/F 9.57/F 9.58/F 9.59/F 9.60/F | No description available
> close #9
> open /Users/jl209164/Downloads/cryosparc_P279_J287_003_volume_map.mrc
Opened cryosparc_P279_J287_003_volume_map.mrc as #9, grid size 160,160,160,
pixel 2.32, shown at level 0.558, step 1, values float32
> close #9
> open 6N81
Summary of feedback from opening 6N81 fetched from pdb
---
note | Fetching compressed mmCIF 6n81 from http://files.rcsb.org/download/6n81.cif
6n81 title:
Crystal structure of GII.4 2002 norovirus P domain in complex with cross-
reactive human antibody A1227 [more info...]
Chain information for 6n81 #9
---
Chain | Description | UniProt
A B | Major capsid protein | R4I4P2_9CALI 225-530
C H | A1227 Fab heavy chain |
D L | A1227 Fab light chain |
> show #!1 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> mmaker #9 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain AB (#1) with 6n81, chain A (#9), sequence alignment
score = 73.6
RMSD between 8 pruned atom pairs is 1.240 angstroms; (across all 161 pairs:
24.538)
> select add #9
15293 atoms, 15390 bonds, 1 pseudobond, 2268 residues, 3 models selected
> hide (#!9 & sel) target a
> cartoon (#!9 & sel)
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #!5 models
> show #!1 models
> hide #!9 models
> mmaker #5 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain FB (#1) with 6ouu, chain A (#5), sequence alignment
score = 2123.1
RMSD between 120 pruned atom pairs is 1.300 angstroms; (across all 175 pairs:
2.250)
> hide #!1 models
> show #3 models
> show #!9 models
> mmaker #9 to #5
Computing secondary structure
[Repeated 1 time(s)] 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 6ouu, chain C (#5) with 6n81, chain A (#9), sequence alignment
score = 1454.5
RMSD between 284 pruned atom pairs is 0.965 angstroms; (across all 306 pairs:
1.204)
> show #!1 models
> hide #!1 models
> opn 7k6v
Unknown command: opn 7k6v
> open 7k6v
7k6v title:
Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus
(HOV) [more info...]
Chain information for 7k6v #10
---
Chain | Description | UniProt
AA AB AC BA BB BC CA CB CC DA DB DC EA EB EC FA FB FC GA GB GC HA HB HC IA IB IC JA JB JC KA KB KC LA LB LC MA MB MC NA NB NC OA OB OC | Capsid protein VP1 | A9YYE4_9CALI 1-540
Non-standard residues in 7k6v #10
---
CD — cadmium ion
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
7k6v mmCIF Assemblies
---
1| author_defined_assembly
> show #!1 models
> mmaker #10 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain EB (#1) with 7k6v, chain EB (#10), sequence alignment
score = 2321.9
RMSD between 211 pruned atom pairs is 0.000 angstroms; (across all 211 pairs:
0.000)
> select add #10
191815 atoms, 197195 bonds, 20 pseudobonds, 25246 residues, 5 models selected
> hide (#!9-10 & sel) target a
> cartoon (#!9-10 & sel)
> select subtract #10
15293 atoms, 15390 bonds, 1 pseudobond, 2268 residues, 3 models selected
> select subtract #9
3754 atoms, 3871 bonds, 485 residues, 1 model selected
> hide #!9 models
> show #!9 models
> mmaker #9 to #10
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain FB (#10) with 6n81, chain A (#9), sequence alignment
score = 1553.8
RMSD between 302 pruned atom pairs is 0.503 angstroms; (across all 306 pairs:
0.588)
> hide #!5 models
> hide #3 models
> hide #!1 models
> hide #!9 models
> show #!9 models
> color #9 #0433ffff
> hide #!10 models
> hide #!9 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> open 7kjp
7kjp title:
Disulfide Stabilized Norovirus GI.1 VLP Shell Region [more info...]
Chain information for 7kjp #11
---
Chain | Description | UniProt
A B C | Capsid protein VP1 | CAPSD_NVN68 1-530
7kjp mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> mmaker #11 to #1
Computing secondary structure
[Repeated 1 time(s)] 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 7k6v, chain FB (#1) with 7kjp, chain A (#11), sequence alignment
score = 987.9
RMSD between 136 pruned atom pairs is 1.138 angstroms; (across all 176 pairs:
2.198)
> hide #3 models
> hide #!5 models
> hide #!1 models
> select ::name="CYS"
17406 atoms, 14514 bonds, 2901 residues, 126 models selected
> show (#!11 & sel) target ab
> style (#!11 & sel) stick
Changed 90 atom styles
> color (#!11 & sel) byhetero
> show #!1 models
> select #11:37,41
Nothing selected
> hide #!1 models
> select #11:37,44
Nothing selected
> select #11:141,221
48 atoms, 45 bonds, 6 residues, 1 model selected
> show sel target ab
> select #11/B:145
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!1 models
> show #3 models
> hide #!1 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A
Alignment identifier is 11/A
> select clear
> select #11/A
1364 atoms, 1403 bonds, 176 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #3/C:2046
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:2046-2047
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4.11/A:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.11/A:46-56
98 atoms, 101 bonds, 11 residues, 1 model selected
> show #!5 models
> hide #!11 models
> show #!11 models
> hide #!1 models
> select #4.11/A:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4.11/A:65-76
87 atoms, 88 bonds, 12 residues, 1 model selected
> select #4.11/A:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.11/A:46-49
31 atoms, 30 bonds, 4 residues, 1 model selected
> mmaker #5 to #11
Computing secondary structure
[Repeated 1 time(s)] 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 7kjp, chain A (#11) with 6ouu, chain A (#5), sequence alignment
score = 971.6
RMSD between 141 pruned atom pairs is 1.008 angstroms; (across all 174 pairs:
1.673)
> mmaker #5/B to #11/A
Computing secondary structure
[Repeated 1 time(s)] 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 7kjp, chain A (#11) with 6ouu, chain B (#5), sequence alignment
score = 925.5
RMSD between 146 pruned atom pairs is 1.118 angstroms; (across all 169 pairs:
1.596)
> mmaker #5/C to #11/A
Computing secondary structure
[Repeated 1 time(s)] 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 7kjp, chain A (#11) with 6ouu, chain C (#5), sequence alignment
score = 932.7
RMSD between 130 pruned atom pairs is 1.176 angstroms; (across all 174 pairs:
2.070)
> show #!4 models
> hide #!5 models
> show #3 models
> mmaker #3 to #11
Computing secondary structure
[Repeated 1 time(s)] 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 7kjp, chain C (#11) with 7mry, chain C (#3), sequence alignment
score = 989.1
RMSD between 136 pruned atom pairs is 0.896 angstroms; (across all 165 pairs:
1.951)
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> hide #3 models
> select #1/GA:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/GA:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/FA:114
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/GA:112
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel target ab
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 19 atom styles
> select #10:174
315 atoms, 315 bonds, 45 residues, 1 model selected
> select #11:174
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1:174
315 atoms, 315 bonds, 45 residues, 1 model selected
> show #!5 models
> hide #!11 models
> select #1:114
495 atoms, 495 bonds, 45 residues, 1 model selected
> ui tool show Distances
> select #1/GA:112@CB
1 atom, 1 residue, 1 model selected
> select #1/GA:112@CB
1 atom, 1 residue, 1 model selected
> select add #1/FA:114@CB
2 atoms, 2 residues, 1 model selected
> distance #1/GA:112@CB #1/FA:114@CB
Distance between 7k6v #1/GA ASN 112 CB and /FA PHE 114 CB: 5.770Å
> select #1/FA:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #3 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> save "/Users/jl209164/OneDrive -
> GSK/OneDrive_Documents/Norovirus/structures/VLP-structures_20250922.cxs"
——— End of log from Mon Sep 22 14:32:25 2025 ———
opened ChimeraX session
> select #1:135-142
2790 atoms, 2880 bonds, 360 residues, 1 model selected
> select #3:135-142
62 atoms, 64 bonds, 8 residues, 1 model selected
> select #3:1135-1142
62 atoms, 64 bonds, 8 residues, 1 model selected
> select #5:135-142
248 atoms, 256 bonds, 32 residues, 1 model selected
> show #!2 models
> select #2:135-142
3720 atoms, 3840 bonds, 480 residues, 60 models selected
> hide #3 models
> hide #!2 models
> select #2:112,189
780 atoms, 660 bonds, 120 residues, 60 models selected
> select #1:112,189
600 atoms, 525 bonds, 75 residues, 1 model selected
> show #!1 models
> show #3 models
> hide #!1 models
> select #2:112,189
780 atoms, 660 bonds, 120 residues, 60 models selected
> show #!2 models
> show sel target ab
> color sel byhetero
> select #2.19/A:189@CB
1 atom, 1 residue, 1 model selected
> select subtract #2.19/A:189@CB
Nothing selected
> ui tool show Distances
> select add #2.19/A:189@CB
1 atom, 1 residue, 1 model selected
> select add #2.20/A:112@CB
2 atoms, 2 residues, 2 models selected
> distance #2.19/A:189@CB #2.20/A:112@CB
Distance between 7MRY.pdb1 #2.19/A ASN 189 CB and 7MRY.pdb1 #2.20/A ASN 112
CB: 11.086Å
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #2:105-120
6780 atoms, 6780 bonds, 960 residues, 60 models selected
> select #3:105-120
113 atoms, 113 bonds, 16 residues, 1 model selected
> show #!2 models
> select #2:105-120
6780 atoms, 6780 bonds, 960 residues, 60 models selected
> select #2:105-120, 181-196
13560 atoms, 13680 bonds, 1 pseudobond, 1920 residues, 61 models selected
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/emd_23960.map
Opened emd_23960.map as #7, grid size 500,500,500, pixel 1.24, shown at level
0.653, step 2, values float32
> volume #7 step 1
> close #2
> open 7mry
7mry title:
Norovirus T=3 GII.4 HOV VLP [more info...]
Chain information for 7mry #2
---
Chain | Description | UniProt
A B C | VP1 | A9YYE4_9CALI 1-540 1001-1540 2001-2540
7mry mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> volume #7 color #b2b2b268
> volume #7 color #8efa00
> volume #7 color #ff8ad8
> volume #7 color #424242
> volume #7 color #42424268
> volume #7 color #42424259
> open 7mry
7mry title:
Norovirus T=3 GII.4 HOV VLP [more info...]
Chain information for 7mry #13
---
Chain | Description | UniProt
A B C | VP1 | A9YYE4_9CALI 1-540 1001-1540 2001-2540
7mry mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_S.pdb
Chain information for 7mry_S.pdb #14
---
Chain | Description
A B C | No description available
> hide #14 models
> show #14 models
> close #14
> close #13
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/7MRY.pdb1
7MRY.pdb1 title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7MRY.pdb1
---
Chain | Description
13.1/A 13.1/B 13.1/C | No description available
13.2/A 13.3/A 13.4/A 13.5/A 13.6/A 13.7/A 13.8/A 13.9/A 13.10/A 13.11/A 13.12/A 13.13/A 13.14/A 13.15/A 13.16/A 13.17/A 13.18/A 13.19/A 13.20/A 13.21/A 13.22/A 13.23/A 13.24/A 13.25/A 13.26/A 13.27/A 13.28/A 13.29/A 13.30/A 13.31/A 13.32/A 13.33/A 13.34/A 13.35/A 13.36/A 13.37/A 13.38/A 13.39/A 13.40/A 13.41/A 13.42/A 13.43/A 13.44/A 13.45/A 13.46/A 13.47/A 13.48/A 13.49/A 13.50/A 13.51/A 13.52/A 13.53/A 13.54/A 13.55/A 13.56/A 13.57/A 13.58/A 13.59/A 13.60/A | No description available
13.2/B 13.3/B 13.4/B 13.5/B 13.6/B 13.7/B 13.8/B 13.9/B 13.10/B 13.11/B 13.12/B 13.13/B 13.14/B 13.15/B 13.16/B 13.17/B 13.18/B 13.19/B 13.20/B 13.21/B 13.22/B 13.23/B 13.24/B 13.25/B 13.26/B 13.27/B 13.28/B 13.29/B 13.30/B 13.31/B 13.32/B 13.33/B 13.34/B 13.35/B 13.36/B 13.37/B 13.38/B 13.39/B 13.40/B 13.41/B 13.42/B 13.43/B 13.44/B 13.45/B 13.46/B 13.47/B 13.48/B 13.49/B 13.50/B 13.51/B 13.52/B 13.53/B 13.54/B 13.55/B 13.56/B 13.57/B 13.58/B 13.59/B 13.60/B 13.2/C 13.3/C 13.4/C 13.5/C 13.6/C 13.7/C 13.8/C 13.9/C 13.10/C 13.11/C 13.12/C 13.13/C 13.14/C 13.15/C 13.16/C 13.17/C 13.18/C 13.19/C 13.20/C 13.21/C 13.22/C 13.23/C 13.24/C 13.25/C 13.26/C 13.27/C 13.28/C 13.29/C 13.30/C 13.31/C 13.32/C 13.33/C 13.34/C 13.35/C 13.36/C 13.37/C 13.38/C 13.39/C 13.40/C 13.41/C 13.42/C 13.43/C 13.44/C 13.45/C 13.46/C 13.47/C 13.48/C 13.49/C 13.50/C 13.51/C 13.52/C 13.53/C 13.54/C 13.55/C 13.56/C 13.57/C 13.58/C 13.59/C 13.60/C | No description available
> color #13 #0433ffff models
> color #13 silver models
> color #13 #919191ff models
> select #13:222-540
144120 atoms, 148380 bonds, 18660 residues, 60 models selected
> cartoon hide sel
[Repeated 1 time(s)]
> select #13:2222-2540
143400 atoms, 147660 bonds, 18540 residues, 60 models selected
> cartoon hide sel
> select #13:105-120, 181-196
13560 atoms, 13680 bonds, 1920 residues, 60 models selected
> color sel orange red
> view #13:105-120, 181-196
> hide #!13 models
> show #!13 models
> hide #!5 models
> hide #3 models
> hide #2 models
> select #7
3 models selected
> color #7 #4242429a models
> color #7 #424242b2 models
> color #7 #424242de models
> volume #7 level 0.4554
> volume #7 level 0.2356
> volume #7 level 0.3308
> volume #7 level 0.4041
> view #13:105-120, 181-196
No visible atoms or bonds selected
> select #13:105-120, 181-196
13560 atoms, 13680 bonds, 1920 residues, 60 models selected
> show sel target ab
> style sel stick
Changed 13560 atom styles
> color sel byhetero
> select #7
3 models selected
> volume #7 style mesh
> volume #7 level 0.5799
> show #!1 models
> show #!11 models
> hide #!12 models
> hide #12.1 models
> hide #!13 models
> hide #!1 models
> show #!13 models
> show #!7 models
> select subtract #7
Nothing selected
> color #7 #42424275 models
> color #7 #919191ff models
> color #7 #91919194 models
> volume #7 style surface
> select #13:1222-1540
143400 atoms, 147660 bonds, 18540 residues, 60 models selected
> cartoon hide sel
> volume #7 level 0.4188
> select 13.1
Expected an objects specifier or a keyword
> select #13.1
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> select #13.1,13.2
Nothing selected
> select #13.2
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> select #13
679800 atoms, 700560 bonds, 87900 residues, 61 models selected
> cartoon hide sel
> hide sel target a
> cartoon sel
> cartoon hide sel
> select #13.2
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> /A,B,C
Unknown command: /A,B,C
> select #13.2/A,B,C
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> select #13.2/A,B,C:222-540
2402 atoms, 2473 bonds, 311 residues, 1 model selected
> surface hidePatches sel
> select #13.2/A:222-540
2402 atoms, 2473 bonds, 311 residues, 1 model selected
> delete #13.2/A:222-540
> delete #13.2/B:1222-1540
> delete #13.2/C:1222-1540
> delete #13.2/C:2222-2540
> select #13.42
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> select clear
> select #13.43
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> select #13.44
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> select #13.22
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> select #13.23
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> select #13.3/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> cartoon sel
> select #13.4/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> cartoon sel
> select #13.5/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> cartoon sel
> select #13.1/A
3776 atoms, 3892 bonds, 489 residues, 1 model selected
> cartoon sel
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!11 models
> open 7mry
7mry title:
Norovirus T=3 GII.4 HOV VLP [more info...]
Chain information for 7mry #14
---
Chain | Description | UniProt
A B C | VP1 | A9YYE4_9CALI 1-540 1001-1540 2001-2540
7mry mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> close #14
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/7MRY.pdb1
7MRY.pdb1 title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7MRY.pdb1
---
Chain | Description
14.1/A 14.1/B 14.1/C | No description available
14.2/A 14.3/A 14.4/A 14.5/A 14.6/A 14.7/A 14.8/A 14.9/A 14.10/A 14.11/A 14.12/A 14.13/A 14.14/A 14.15/A 14.16/A 14.17/A 14.18/A 14.19/A 14.20/A 14.21/A 14.22/A 14.23/A 14.24/A 14.25/A 14.26/A 14.27/A 14.28/A 14.29/A 14.30/A 14.31/A 14.32/A 14.33/A 14.34/A 14.35/A 14.36/A 14.37/A 14.38/A 14.39/A 14.40/A 14.41/A 14.42/A 14.43/A 14.44/A 14.45/A 14.46/A 14.47/A 14.48/A 14.49/A 14.50/A 14.51/A 14.52/A 14.53/A 14.54/A 14.55/A 14.56/A 14.57/A 14.58/A 14.59/A 14.60/A | No description available
14.2/B 14.3/B 14.4/B 14.5/B 14.6/B 14.7/B 14.8/B 14.9/B 14.10/B 14.11/B 14.12/B 14.13/B 14.14/B 14.15/B 14.16/B 14.17/B 14.18/B 14.19/B 14.20/B 14.21/B 14.22/B 14.23/B 14.24/B 14.25/B 14.26/B 14.27/B 14.28/B 14.29/B 14.30/B 14.31/B 14.32/B 14.33/B 14.34/B 14.35/B 14.36/B 14.37/B 14.38/B 14.39/B 14.40/B 14.41/B 14.42/B 14.43/B 14.44/B 14.45/B 14.46/B 14.47/B 14.48/B 14.49/B 14.50/B 14.51/B 14.52/B 14.53/B 14.54/B 14.55/B 14.56/B 14.57/B 14.58/B 14.59/B 14.60/B 14.2/C 14.3/C 14.4/C 14.5/C 14.6/C 14.7/C 14.8/C 14.9/C 14.10/C 14.11/C 14.12/C 14.13/C 14.14/C 14.15/C 14.16/C 14.17/C 14.18/C 14.19/C 14.20/C 14.21/C 14.22/C 14.23/C 14.24/C 14.25/C 14.26/C 14.27/C 14.28/C 14.29/C 14.30/C 14.31/C 14.32/C 14.33/C 14.34/C 14.35/C 14.36/C 14.37/C 14.38/C 14.39/C 14.40/C 14.41/C 14.42/C 14.43/C 14.44/C 14.45/C 14.46/C 14.47/C 14.48/C 14.49/C 14.50/C 14.51/C 14.52/C 14.53/C 14.54/C 14.55/C 14.56/C 14.57/C 14.58/C 14.59/C 14.60/C | No description available
> hide #!14 models
> select #13.3
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> show #!14 models
> hide #!14 models
> select #13.3
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> cartoon sel
> show #!14 models
> hide #!13 models
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_14.1.pdb models #14.1
> relModel #13
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_14.1.pdb
7mry_14.1.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_14.1.pdb #15
---
Chain | Description
A B C | No description available
> hide #!14 models
> delete #15/A:222-540
> delete #15/B:1222-1540
> delete #15/C:2222-2540
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_1_S.pdb models #15 relModel
> #13
> show #!7 models
> view #15
> hide #15 models
> hide #!11 models
> show #!14 models
> show #!13 models
> hide #!14 models
> hide #!7 models
> select #13.4
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> select #13.42
11330 atoms, 11676 bonds, 1465 residues, 1 model selected
> open "/Users/jl209164/Downloads/ranked_0 (3).pdb"
Chain information for ranked_0 (3).pdb #16
---
Chain | Description
A B | No description available
Computing secondary structure
> mmaker #16 to #13.42
Computing secondary structure
[Repeated 1 time(s)] 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 7MRY.pdb1, chain B (#13.42) with ranked_0 (3).pdb, chain B (#16),
sequence alignment score = 2327.1
RMSD between 440 pruned atom pairs is 1.035 angstroms; (across all 486 pairs:
1.441)
> hide #16 models
> show #16 models
> show #!1 models
> show #12.1 models
> hide #!13 models
> hide #12.1 models
> hide #!12 models
> hide #16 models
> show #2 models
> hide #2 models
> show #!5 models
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!5 models
> hide #!4 models
> view #1
> show #3 models
> show #15 models
> show #16 models
> mmaker #16 to #1
Computing secondary structure
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 7k6v, chain FB (#1) with ranked_0 (3).pdb, chain A (#16), sequence
alignment score = 2176.2
RMSD between 181 pruned atom pairs is 0.891 angstroms; (across all 211 pairs:
4.125)
> hide #!1 models
> show #!1 models
> hide #3 models
> select #1:168,127
900 atoms, 855 bonds, 90 residues, 1 model selected
> select #1:69
495 atoms, 450 bonds, 45 residues, 1 model selected
> show #!14 models
> hide #16 models
> hide #!14 models
> select #1:58,136
675 atoms, 585 bonds, 90 residues, 1 model selected
> show (#!1 & sel) target ab
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select ::name="CYS"
24054 atoms, 20064 bonds, 3999 residues, 189 models selected
> select #1:131
405 atoms, 360 bonds, 45 residues, 1 model selected
> select #1/AA:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/AA:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> open /Users/jl209164/Documents/hPV/35-Fab/HPV_20250922.cxs
> To restore session:
>
> * install ISOLDE bundle version 1.8 or newer
>
Failed opening file /Users/jl209164/Documents/hPV/35-Fab/HPV_20250922.cxs:
Unable to restore session: need to install missing bundle
> show #16 models
> hide #16 models
> show #!14 models
> hide #15 models
> show #15 models
> hide #15 models
> show #16 models
> hide #16 models
> hide #!14 models
> show #15 models
> hide #!1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #15 models
> show #15 models
> show #3 models
> hide #!13 models
> hide #15 models
> open /Users/jl209164/Downloads/HPV-68_68H6_P311_J394_005_volume_map.mrc
Opened HPV-68_68H6_P311_J394_005_volume_map.mrc as #17, grid size 320,320,320,
pixel 0.894, shown at level 0.0183, step 2, values float32
> close #17
> open "/Users/jl209164/Downloads/ranked_0 (4).pdb"
Chain information for ranked_0 (4).pdb #17
---
Chain | Description
A B C D E F | No description available
> open
> /Users/jl209164/Documents/hPV/59-Fab/HPV-59_59H30_P311_J121_003_volume_map_sharp.mrc
Opened HPV-59_59H30_P311_J121_003_volume_map_sharp.mrc as #18, grid size
256,256,256, pixel 0.894, shown at level 0.0513, step 1, values float32
> close #18
> open
> /Users/jl209164/Downloads/cryosparc_P228_J33_004_volume_map_sharp_hexa_z_flip_resample.mrc
Opened cryosparc_P228_J33_004_volume_map_sharp_hexa_z_flip_resample.mrc as
#18, grid size 400,400,400, pixel 0.894, shown at level 4.15, step 2, values
float32
> volume #18 level 2.933
> close #18
> hide #17 models
> show #17 models
> close #16-17
> show #15 models
> show #!14 models
> hide #15 models
> show #15 models
> hide #!14 models
> show #!14 models
> hide #15 models
> show #!13 models
> hide #!14 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> close #6
> show #!8 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> select #13:1-41
Nothing selected
> select #13:221-540
142258 atoms, 146446 bonds, 18409 residues, 60 models selected
> delete #13:221-540
> delete #13:1221-1540
> delete #13:2221-2540
> show #15 models
> hide #15 models
> hide #3 models
> show #!14 models
> hide #!14 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #3 models
> show #15 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #!14 models
> hide #!14 models
> hide #3 models
> delete #13.6,13.7,13.8,13.9,13.10,13.11, 13.12
> select #13
247260 atoms, 255060 bonds, 31980 residues, 61 models selected
> cartoon sel
> delete #13.6
> delete #13.7, #13.7
Missing or invalid "atoms" argument: only initial part "#13.7" of atom
specifier valid
> delete #13.7
> delete #13.8
> delete #13.9
> delete #13.10
> delete #13.11
> delete #13.12
> delete #13.13
> delete #13.14
> delete #13.15
> delete #13.16
> delete #13.17
> delete #13.18
> delete #13.19
> delete #13.20
> delete #13.21
> delete #13.24
> delete #13.25
> delete #13.26
> delete #13.27
> delete #13.28
> delete #13.29
> delete #13.30
> delete #13.31
> delete #13.32
> delete #13.33
> delete #13.34
> delete #13.35
> delete #13.36
> delete #13.37
> delete #13.38
> delete #13.39
> delete #13.40
> delete #13.41
> delete #13.44
[Repeated 1 time(s)]
> delete #13.45
> delete #13.46
> delete #13.47
> delete #13.48
> delete #13.49
> delete #13.50
> delete #13.51
> delete #13.52
> delete #13.53
> delete #13.54
> delete #13.55
> delete #13.56
> delete #13.57
> delete #13.58
> delete #13.59
> delete #13.60
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_pentamer+hexamer.pdb models
> #13 relModel #13
> delete #13.42
> delete #13.43
> delete #13.22
> delete #13.23
> show #!1 models
> hide #!1 models
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_1_S_ISO.pdb
7mry_1_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_1_S_ISO.pdb #6
---
Chain | Description
A B C | No description available
> hide #6 models
> show #6 models
> close #6
> delete #13/B
> delete #13/C
> show #!7 models
> hide #!7 models
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_pentamer_S.pdb models #13
> relModel #7
> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_pentamer+hexamer.pdb
7mry_pentamer+hexamer.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_pentamer+hexamer.pdb
---
Chain | Description
6.1/A 6.1/B 6.1/C | No description available
6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.2/B 6.3/B 6.4/B 6.5/B 6.6/B 6.7/B 6.8/B 6.9/B 6.2/C 6.3/C 6.4/C 6.5/C 6.6/C 6.7/C 6.8/C 6.9/C | No description available
> close #13
> hide #6.1 models
> show #6.1 models
> hide #6.2 models
> show #6.2 models
> hide #6.3 models
> show #6.3 models
> delete #6/A
> delete #6.1
> delete #6.4
> delete #6.5
> delete #6.7/B
> delete #6.2/C
> delete #6.3/B
> delete #6.8/C
> delete #6.9/B
> delete #6.6/C
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_hexamer_S.pdb models #6
> relModel #6
> close session
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_pentamer_S_ISO.pdb
7mry_pentamer_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_pentamer_S_ISO.pdb #1
---
Chain | Description
A | No description available
B C D E | No description available
> hide target a
> cartoon
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select #1
13547 atoms, 13767 bonds, 885 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /A-E:45-220 seqStart 1
704 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select #1/B
2710 atoms, 2754 bonds, 177 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /B:1-176 seqStart 45
176 residues renumbered
> renumber /B:45-220 seqStart 45
0 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> ui tool show "Renumber Residues"
> renumber /C:1-176 seqStart 45
176 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> ui tool show "Renumber Residues"
> renumber /D:1-176 seqStart 45
176 residues renumbered
> renumber /D:45-220 seqStart 45
0 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain /E
Alignment identifier is 1/E
> ui tool show "Renumber Residues"
> renumber /E:1-176 seqStart 45
176 residues renumbered
> renumber /E:45-220 seqStart 45
0 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:45
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:45
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1:58, 136
140 atoms, 130 bonds, 10 residues, 1 model selected
> select #1:112, 116
120 atoms, 110 bonds, 10 residues, 1 model selected
> select /A,B
5417 atoms, 5505 bonds, 354 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 5417 atom styles
> color sel byhetero
> select H
6718 atoms, 885 residues, 1 model selected
> hide sel target a
> select clear
> select :112,116
120 atoms, 110 bonds, 10 residues, 1 model selected
> select :113
50 atoms, 45 bonds, 5 residues, 1 model selected
> ui tool show Distances
> select /B:149@NH2
1 atom, 1 residue, 1 model selected
> select /B:147@OD1
1 atom, 1 residue, 1 model selected
> select add /B:149@NH2
2 atoms, 2 residues, 1 model selected
> distance /B:147@OD1 /B:149@NH2
Distance between /B ASP 147 OD1 and ARG 149 NH2: 5.164Å
> select /B:147@OD2
1 atom, 1 residue, 1 model selected
> select add /B:118@NZ
2 atoms, 2 residues, 1 model selected
> distance /B:147@OD2 /B:118@NZ
Distance between /B ASP 147 OD2 and LYS 118 NZ: 2.733Å
> select :149
120 atoms, 115 bonds, 5 residues, 1 model selected
> select :58,139
155 atoms, 145 bonds, 10 residues, 1 model selected
> select /A:139@CB
1 atom, 1 residue, 1 model selected
> select add /B:58@CB
2 atoms, 2 residues, 1 model selected
> distance /A:139@CB /B:58@CB
Distance between /A THR 139 CB and /B GLN 58 CB: 4.409Å
> select /A:139@CB
1 atom, 1 residue, 1 model selected
> select add /B:57@CB
2 atoms, 2 residues, 1 model selected
> distance /A:139@CB /B:57@CB
Distance between /A THR 139 CB and /B VAL 57 CB: 4.987Å
> select :184,199
125 atoms, 115 bonds, 10 residues, 1 model selected
> select /A:184@CG2
1 atom, 1 residue, 1 model selected
> select add /B:199@OG
2 atoms, 2 residues, 1 model selected
> distance /A:184@CG2 /B:199@OG
Distance between /A THR 184 CG2 and /B SER 199 OG: 4.583Å
> select :111
35 atoms, 30 bonds, 5 residues, 1 model selected
> cartoon hide sel
> select :147, 151
155 atoms, 145 bonds, 10 residues, 1 model selected
> select /A:147@CB
1 atom, 1 residue, 1 model selected
> select add /B:151@CB
2 atoms, 2 residues, 1 model selected
> distance /A:147@CB /B:151@CB
Distance between /A ASP 147 CB and /B LEU 151 CB: 5.123Å
> select /B:151@CD2
1 atom, 1 residue, 1 model selected
> select add /A:147@OD2
2 atoms, 2 residues, 1 model selected
> distance /B:151@CD2 /A:147@OD2
Distance between /B LEU 151 CD2 and /A ASP 147 OD2: 3.974Å
> select /A:147@OD2
1 atom, 1 residue, 1 model selected
> select add /A:118@NZ
2 atoms, 2 residues, 1 model selected
> distance /A:147@OD2 /A:118@NZ
Distance between /A ASP 147 OD2 and LYS 118 NZ: 2.732Å
> select :109,118
205 atoms, 195 bonds, 10 residues, 1 model selected
> select :187,197
190 atoms, 180 bonds, 10 residues, 1 model selected
> save /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/Norovirus/structures/7mry_pentamer_20250930.cxs
——— End of log from Tue Sep 30 15:26:10 2025 ———
opened ChimeraX session
> select :57,213
175 atoms, 165 bonds, 10 residues, 1 model selected
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_hexamer_S_ISO.pdb
7mry_hexamer_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_hexamer_S_ISO.pdb #3
---
Chain | Description
A B C D E F | No description available
> select add #3
16597 atoms, 16845 bonds, 1078 residues, 2 models selected
> hide sel target a
> cartoon sel
> select :57,213
175 atoms, 165 bonds, 10 residues, 1 model selected
> select :57,213
175 atoms, 165 bonds, 10 residues, 1 model selected
> select #3:57,213
Nothing selected
> ui tool show "Renumber Residues"
> renumber #3/A,C,E:1045-1220/B,D,F:2045-2220 seqStart 1
1056 residues renumbered
> renumber #3/A-F:1-176 seqStart 1
0 residues renumbered
> select #3:57,213
42 atoms, 36 bonds, 6 residues, 1 model selected
> select :57,213
217 atoms, 201 bonds, 16 residues, 2 models selected
> select :57,13
218 atoms, 201 bonds, 17 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/D
Alignment identifier is 3/D
> sequence chain #3/E
Alignment identifier is 3/E
> sequence chain #3/F
Alignment identifier is 3/F
> ui tool show "Renumber Residues"
> renumber #3/A-F:1-176 seqStart 45
1056 residues renumbered
> renumber #3/A-F:45-220 seqStart 45
0 residues renumbered
> renumber #3/A-F:45-220 seqStart 45
0 residues renumbered
> select :57,13
176 atoms, 165 bonds, 11 residues, 2 models selected
> select :57,113
286 atoms, 264 bonds, 22 residues, 2 models selected
> select :57,213
385 atoms, 363 bonds, 22 residues, 2 models selected
> select :57,13
176 atoms, 165 bonds, 11 residues, 2 models selected
> select :57,213
385 atoms, 363 bonds, 22 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #3/B
Alignment identifier is 3/B
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #3/D
Destroying pre-existing alignment with identifier 3/D
Alignment identifier is 3/D
> sequence chain #3/E
Destroying pre-existing alignment with identifier 3/E
Alignment identifier is 3/E
> sequence chain #3/F
Destroying pre-existing alignment with identifier 3/F
Alignment identifier is 3/F
> save /Users/jl209164/Documents/Norovirus/GII.4/7mry_hexamer_S_ISO.pdb models
> #3 relModel #3
> close #3
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /D
Alignment identifier is 1/D
> sequence chain /E
Alignment identifier is 1/E
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_hexamer_S_ISO.pdb
7mry_hexamer_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_hexamer_S_ISO.pdb #3
---
Chain | Description
A B C D E F | No description available
> hide sel target a
> cartoon sel
> select add #3
16597 atoms, 16845 bonds, 1078 residues, 2 models selected
> hide sel target a
> cartoon sel
> select :57,213
385 atoms, 363 bonds, 22 residues, 2 models selected
> select clear
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_1_S.pdb
7mry_1_S.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_1_S.pdb #4
---
Chain | Description
A B C | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_hexamer_S_ISO.pdb
7mry_hexamer_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_hexamer_S_ISO.pdb #5
---
Chain | Description
A B C D E F | No description available
> close #5
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #1/E
Alignment identifier is 1/E
> select :149,151
492 atoms, 468 bonds, 24 residues, 3 models selected
> hide #3 models
> hide #2.1 models
> hide #!2 models
> hide #1 models
> select :149,151
492 atoms, 468 bonds, 24 residues, 3 models selected
> show (#4 & sel) target ab
> show #1 models
> show #3 models
> select add #3
16656 atoms, 16902 bonds, 1080 residues, 3 models selected
> select add #4
20785 atoms, 21163 bonds, 1614 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,4.9878,0,1,0,3.0882,0,0,1,-4.1608,#3,1,0,0,4.9878,0,1,0,3.0882,0,0,1,-4.1608,#4,1,0,0,4.9878,0,1,0,3.0882,0,0,1,-4.1608
> select add #1
34117 atoms, 34725 bonds, 8 pseudobonds, 2489 residues, 4 models selected
> select subtract #1
20570 atoms, 20958 bonds, 1604 residues, 2 models selected
> view matrix models
> #3,1,0,0,-26.29,0,1,0,1.4627,0,0,1,25.444,#4,1,0,0,-26.29,0,1,0,1.4627,0,0,1,25.444
> select subtract #3
4148 atoms, 4278 bonds, 536 residues, 1 model selected
> view matrix models #4,1,0,0,-28.312,0,1,0,-32.427,0,0,1,16.988
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.2724,-0.34642,-0.89766,512.27,0.40881,-0.88622,0.21794,346.25,-0.87102,-0.3076,0.38303,406.52
> view matrix models
> #4,0.0094482,-0.4952,-0.86873,489.25,0.53216,-0.73303,0.42364,236.48,-0.84659,-0.46631,0.2566,471.11
> select add #1
17695 atoms, 18045 bonds, 8 pseudobonds, 1421 residues, 3 models selected
> select subtract #4
13547 atoms, 13767 bonds, 8 pseudobonds, 885 residues, 2 models selected
> view matrix models
> #1,0.90005,0.35022,0.25932,-130.92,-0.21411,0.87371,-0.4368,176.67,-0.37955,0.33762,0.86137,5.8581,#2,1,0,0,0,0,1,0,0,0,0,1,0
> select clear
> select :189, 114
355 atoms, 343 bonds, 24 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 355 atom styles
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> color sel byhetero
> select :189, 114
355 atoms, 343 bonds, 24 residues, 3 models selected
> color sel byhetero
> select :192,191,193
308 atoms, 296 bonds, 36 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 308 atom styles
> color sel byhetero
> select :160-176
3162 atoms, 3210 bonds, 204 residues, 3 models selected
> select :192,191,193
308 atoms, 296 bonds, 36 residues, 3 models selected
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> select :192,191,193
308 atoms, 296 bonds, 36 residues, 3 models selected
> select #3:184-197
1200 atoms, 1206 bonds, 84 residues, 1 model selected
> select #3/A,B:184-197
400 atoms, 402 bonds, 28 residues, 1 model selected
> select #3/A,B:184-197
400 atoms, 402 bonds, 28 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 400 atom styles
> color sel byhetero
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> select #3/A,B:184-199
454 atoms, 456 bonds, 32 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 454 atom styles
> color sel byhetero
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> select clear
> select :51
278 atoms, 290 bonds, 12 residues, 3 models selected
> select :51,91
475 atoms, 487 bonds, 24 residues, 3 models selected
> select :51,140
473 atoms, 473 bonds, 24 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 473 atom styles
> color sel byhetero
> select :51,140,142
634 atoms, 634 bonds, 36 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 634 atom styles
> color sel byhetero
> select :197,187
436 atoms, 412 bonds, 24 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 436 atom styles
> color sel byhetero
> ui tool show Distances
> select #1/B:187@CB
1 atom, 1 residue, 1 model selected
> select add #1/C:197@CB
2 atoms, 2 residues, 1 model selected
> distance #1/B:187@CB #1/C:197@CB
Distance between 7mry_pentamer_S_ISO.pdb #1/B ARG 187 CB and /C THR 197 CB:
8.075Å
Drag select of 2 residues
> select #1/E:182
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:187@NH2
1 atom, 1 residue, 1 model selected
> select add #1/C:197@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/B:187@NH2 #1/C:197@OG1
Distance between 7mry_pentamer_S_ISO.pdb #1/B ARG 187 NH2 and /C THR 197 OG1:
6.900Å
> select #1/C:196
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select :112,116
277 atoms, 253 bonds, 24 residues, 3 models selected
> show sel target ab
> style sel stick
Changed 277 atom styles
> color sel byhetero
> select :111
81 atoms, 69 bonds, 12 residues, 3 models selected
> cartoon sel
> view #3/A,B:112,116
> view #3/A:112
> view #3/B:116
> ui tool show "Side View"
> select #3/B:116@CB
1 atom, 1 residue, 1 model selected
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> select clear
> select #3/B:116@CB
1 atom, 1 residue, 1 model selected
> select add #3/A:112@CG
2 atoms, 2 residues, 1 model selected
> distance #3/B:116@CB #3/A:112@CG
Distance between 7mry_hexamer_S_ISO.pdb #3/B ALA 116 CB and /A ASN 112 CG:
4.569Å
> distance #3/B:116@CB #3/A:112@CG
Distance already exists; modify distance properties with 'distance style'
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> select clear
> select #3/A:111
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.98611,-0.05148,-0.15789,33.73,0.070924,0.99023,0.1201,-39.39,0.15016,-0.12963,0.98013,45.086
> select /B:149
48 atoms, 46 bonds, 2 residues, 2 models selected
> style sel stick
Changed 48 atom styles
> show sel target ab
> color sel byhetero
> select H
14866 atoms, 1953 residues, 2 models selected
> hide sel target a
> select clear
> select #3/A:111
7 atoms, 6 bonds, 1 residue, 1 model selected
> View #1/B:149
Unknown command: View #1/B:149
> View #1
Unknown command: View #1
> show #!2 models
> hide #!2 models
> View #1/A:112
Unknown command: View #1/A:112
> view #1/A:112
> select #1/A:112
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:111
7 atoms, 6 bonds, 1 residue, 1 model selected
> view #1/A:192
> select #1/A:192
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:192,191,193
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel target ab
> select #1/A:192,191,193
24 atoms, 23 bonds, 3 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select #1/E:192,191,193
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #1/E:190
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 7 atom styles
> select #3/A:192,191,193
29 atoms, 28 bonds, 3 residues, 1 model selected
> select #3/A:192,191
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:192,191
17 atoms, 16 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> ui tool show "Find Cavities"
> kvfinder #3
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
See log for complete Python traceback.
No model chosen to save relative to
> save /Users/jl209164/Documents/Norovirus/GII.4/7mry_1_S.pdb models #4
> relModel #4
> close #4
> open /Users/jl209164/Documents/Norovirus/GII.4/7mry_1_S_ISO.pdb
7mry_1_S_ISO.pdb title:
Norovirus T=3 gii.4 hov VLP [more info...]
Chain information for 7mry_1_S_ISO.pdb #4
---
Chain | Description
A B C | No description available
> hide #3 models
> hide #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> ui tool show "Renumber Residues"
> renumber #4/A:45-221/B:1045-1221/C:2045-2221 seqStart 1
354 residues renumbered
> renumber #4/A-C:45-221 seqStart 1
0 residues renumbered
> save /Users/jl209164/Documents/Norovirus/GII.4/7mry_1_S_ISO.pdb models #4
> relModel #4
> show #3 models
> show #1 models
> hide #4 models
> close #1
> close #3
> close #2
> show #4 models
> ui tool show "Find Cavities"
> kvfinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
See log for complete Python traceback.
> ui tool show "Find Cavities"
> kvfinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
ImportError: dlopen(/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/jl209164/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
File "/Users/jl209164/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Model Number: Z14X000HQLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 6 days, 20 hours, 6 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E24u G5:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.1.3
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.1
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 weeks ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib) |
comment:2 by , 5 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Jing,
--Eric