![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 20 months ago
Closed 20 months ago
#14758 closed defect (duplicate)
Help Viewer: No module named 'pyqt'
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Help System | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Noort/OneDrive/Bureaublad/Uni/Ma1/Semester 2/Stage/Scaffold
> pdb Files/Convex_Cys.pdb"
> "C:/Users/Noort/OneDrive/Bureaublad/Uni/Ma1/Semester 2/Stage/Scaffold pdb
> Files/Convex_FLYYP.pdb" "C:/Users/Noort/OneDrive/Bureaublad/Uni/Ma1/Semester
> 2/Stage/Scaffold pdb Files/Convex_GPL.pdb"
Chain information for Convex_Cys.pdb #1
---
Chain | Description
A | No description available
Chain information for Convex_FLYYP.pdb #2
---
Chain | Description
A | No description available
Chain information for Convex_GPL.pdb #3
---
Chain | Description
A | No description available
> select #2/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select
> #1/A:3-8,10-12,18-25,33-39,46-51,58-60,68-73,78-83,92-99,112-115,119-123
965 atoms, 967 bonds, 62 residues, 1 model selected
> select #1/A:100
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:100-103
44 atoms, 43 bonds, 4 residues, 1 model selected
> select #1/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:99-111
142 atoms, 141 bonds, 13 residues, 1 model selected
> color sel yellow
> select add #1
1782 atoms, 1798 bonds, 125 residues, 1 model selected
> select subtract #1
Nothing selected
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:99-108
138 atoms, 139 bonds, 10 residues, 1 model selected
> select #2/A:114
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:110-114
76 atoms, 77 bonds, 5 residues, 1 model selected
> select #2/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:99-114
228 atoms, 232 bonds, 16 residues, 1 model selected
> color sel blue
> select
> #1/A:3-8,10-12,18-25,33-39,46-51,58-60,68-73,78-83,92-99,112-115,119-123
965 atoms, 967 bonds, 62 residues, 1 model selected
> select #1/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:99-114
196 atoms, 197 bonds, 16 residues, 1 model selected
> color sel yellow
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:99-114
208 atoms, 210 bonds, 16 residues, 1 model selected
> color sel pink
> color sel purple
> select add #3
1788 atoms, 1804 bonds, 125 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #1 models
> hide #2 models
> hide #3 models
> show #1 models
> show #2 models
> show #3 models
> hide #1 models
> hide #2 models
> hide #3 models
> save "C:/Users/Noort/OneDrive/Bureaublad/Uni/Ma1/Semester
> 2/Stage/convex_sample_analysis.cxs"
> set bgColor white
> set bgColor #ffffff00
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> open 2x89
Summary of feedback from opening 2x89 fetched from pdb
---
note | Fetching compressed mmCIF 2x89 from
http://files.rcsb.org/download/2x89.cif
2x89 title:
Structure of the Beta2_microglobulin involved in amyloidogenesis [more
info...]
Chain information for 2x89 #4
---
Chain | Description | UniProt
A B C | ANTIBODY |
D E F G | BETA-2-MICROGLOBULIN | B2MG_HUMAN 7-99
2x89 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
5| author_and_software_defined_assembly
> hide #!4 atoms
> show #!4 cartoons
> select #4/A:1-128
986 atoms, 1007 bonds, 128 residues, 1 model selected
> log metadata #4
Metadata for 2x89 #4
---
Title | Structure of the Beta2_microglobulin involved in amyloidogenesis
Citation | Domanska, K., Vanderhaegen, S., Srinivasan, V., Pardon, E., Dupeux,
F., Marquez, J.A., Giorgetti, S., Stoppini, M., Wyns, L., Bellotti, V.,
Steyaert, J. (2011). Atomic Structure of a Nanobody-Trapped Domain-Swapped
Dimer of an Amyloidogenic {Beta}2-Microglobulin Variant.
Proc.Natl.Acad.Sci.USA, 108, 1314. PMID: 21220305. DOI:
10.1073/PNAS.1008560108
Gene sources | Homo sapiens (human)
Camelus dromedarius (arabian camel)
Experimental method | X-ray diffraction
Resolution | 2.16Å
> show #1 models
> hide #1 models
> mmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Convex_Cys.pdb, chain A (#1) with 2x89, chain B (#4), sequence
alignment score = 438.5
RMSD between 104 pruned atom pairs is 0.812 angstroms; (across all 125 pairs:
2.076)
> show #1 models
> mmaker #4 to #2
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 Convex_FLYYP.pdb, chain A (#2) with 2x89, chain C (#4), sequence
alignment score = 450.2
RMSD between 103 pruned atom pairs is 0.830 angstroms; (across all 119 pairs:
3.490)
> show #2 models
> hide #1 models
> mmaker #4 to #3
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 Convex_GPL.pdb, chain A (#3) with 2x89, chain A (#4), sequence
alignment score = 447.1
RMSD between 107 pruned atom pairs is 0.879 angstroms; (across all 125 pairs:
1.574)
> show #3 models
> hide #2 models
> show #2 models
> show #1 models
> mmaker #4 to #3 & #2 & #1
No 'to' model specified
> sequence align #4/A,#1,#2,#3
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 2x89 chain A to chain A with 0 mismatches
Associated 2x89 chain B to chain A with 0 mismatches
Associated 2x89 chain C to chain A with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 2x89 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: 0J892EWNGAGUNCQ0
> select #4/A-C:104
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #4/A-C:104
18 atoms, 15 bonds, 3 residues, 1 model selected
> mmaker #4/A to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Convex_Cys.pdb, chain A (#1) with 2x89, chain A (#4), sequence
alignment score = 438.3
RMSD between 102 pruned atom pairs is 0.836 angstroms; (across all 125 pairs:
2.091)
> hide #2 models
> hide #3 models
> select add #4
6225 atoms, 6081 bonds, 2 pseudobonds, 1039 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
6225 atoms, 6081 bonds, 2 pseudobonds, 1039 residues, 2 models selected
> hide #1 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces
16 buried areas: #2/A #3/A 3249, #1/A #4/A 3224, #3/A #4/A 3049, #2/A #4/A
3042, #3/A #1/A 2932, #2/A #1/A 2831, #4/F #4/G 1563, #4/E #4/D 1556, #4/B
#4/F 716, #4/C #4/E 681, #4/B #4/D 648, #4/A #4/D 645, #1/A #4/D 478, #4/C
#4/G 477, #3/A #4/D 416, #2/A #4/D 406
> select #4/A-C:104
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A:104 #2/A:104 #3/A:104 #4/A:104 #4/B:104 #4/C:104
50 atoms, 44 bonds, 6 residues, 4 models selected
> select #1/A:104
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:104
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 4/A
> select add #4
6225 atoms, 6081 bonds, 2 pseudobonds, 1039 residues, 2 models selected
> hide #!4 models
> select subtract #4
Nothing selected
> open 7e53
Summary of feedback from opening 7e53 fetched from pdb
---
warning | Atom H1 is not in the residue template for GLN /B:1
note | Fetching compressed mmCIF 7e53 from
http://files.rcsb.org/download/7e53.cif
7e53 title:
Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron
resolution [more info...]
Chain information for 7e53 #5
---
Chain | Description | UniProt
A | Green fluorescent protein | A0A059PIQ0_AEQVI 3-232
B | Green fluorescent protein's nanobody nb2 |
Non-standard residues in 7e53 #5
---
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)
> sequence align #5/B,#1,#2,#
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align #5/B,#1,#2,#3
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 7e53 chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 7e53 #5/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: LO8FBA813LHDR3SA
> select add #5
5550 atoms, 5525 bonds, 445 residues, 1 model selected
> select subtract #5
Nothing selected
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> mmaker #5/B to #3
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 Convex_GPL.pdb, chain A (#3) with 7e53, chain B (#5), sequence
alignment score = 468
RMSD between 109 pruned atom pairs is 0.823 angstroms; (across all 123 pairs:
1.811)
> show #3 models
> show #2 models
> hide #3 models
> hide #2 models
> show #1 models
> hide #1 models
> select add #5
5550 atoms, 5525 bonds, 445 residues, 1 model selected
> interfaces
28 buried areas: #2/A #3/A 3249, #5/B #2/A 3226, #1/A #4/A 3224, #5/B #3/A
3206, #5/B #4/A 3175, #3/A #4/A 3049, #2/A #4/A 3042, #5/B #1/A 3026, #3/A
#1/A 2932, #2/A #1/A 2831, #5/A #4/E 1935, #4/F #4/G 1563, #4/E #4/D 1556,
#5/A #4/D 1164, #5/A #5/B 817, #4/B #4/F 716, #5/A #4/A 708, #4/C #4/E 681,
#4/B #4/D 648, #4/A #4/D 645, #5/B #4/D 546, #5/A #2/A 509, #1/A #4/D 478,
#4/C #4/G 477, #5/A #3/A 462, #3/A #4/D 416, #2/A #4/D 406, #5/A #1/A 355
> interfaces #5
1 buried areas: A B 817
> select add #5
5550 atoms, 5525 bonds, 445 residues, 1 model selected
> select subtract #5
Nothing selected
> hide #5 models
> open 3g9a
Summary of feedback from opening 3g9a fetched from pdb
---
note | Fetching compressed mmCIF 3g9a from
http://files.rcsb.org/download/3g9a.cif
3g9a title:
Green fluorescent protein bound to minimizer nanobody [more info...]
Chain information for 3g9a #6
---
Chain | Description | UniProt
A | Green fluorescent protein | GFP_AEQVI 1-238
B | Minimizer |
Non-standard residues in 3g9a #6
---
GYS —
[(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid (chromophore (ser-tyr-gly))
> sequence chain #6/B
Alignment identifier is 6/B
> log metadata #6
Metadata for 3g9a #6
---
Title | Green fluorescent protein bound to minimizer nanobody
Citation | Kirchhofer, A., Helma, J., Schmidthals, K., Frauer, C., Cui, S.,
Karcher, A., Pellis, M., Muyldermans, S., Deulcci, C.C., Cardoso, M.C.,
Leonhardt, H., Hopfner, K.-P., Rothbauer, U. (2010). Modulation of protein
properties in living cells using nanobodies. Nat.Struct.Mol.Biol., 17,
133-138. PMID: 20010839. DOI: 10.1038/nsmb.1727
Non-standard residue | GYS —
[(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid (chromophore (ser-tyr-gly))
Gene sources | Aequorea victoria (jellyfish)
Camelus dromedarius (alpaca)
Experimental method | X-ray diffraction
Resolution | 1.61Å
> sequence align #1,#2,#3,#6/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 3g9a chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 3g9a #6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: FTIQG3DV4HX2FXQG
> mmaker #6/B to #2
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 Convex_FLYYP.pdb, chain A (#2) with 3g9a, chain B (#6), sequence
alignment score = 452.6
RMSD between 103 pruned atom pairs is 0.646 angstroms; (across all 122 pairs:
2.978)
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> interfaces #6
1 buried areas: A B 1275
> select add #6
3457 atoms, 2832 bonds, 1041 residues, 1 model selected
> select subtract #6
Nothing selected
> hide #6 models
> open 3jbc
Summary of feedback from opening 3jbc fetched from pdb
---
note | Fetching compressed mmCIF 3jbc from
http://files.rcsb.org/download/3jbc.cif
3jbc title:
Complex of Poliovirus with VHH PVSP29F [more info...]
Chain information for 3jbc #7
---
Chain | Description | UniProt
1 | Capsid protein VP1 | POLG_POL1M 1-302
2 | Capsid protein VP2 | POLG_POL1M 1-272
3 | Capsid protein VP3 | POLG_POL1M 1-237
4 | Capsid protein VP4 | POLG_POL1M 2-69
7 | nanobody VHH PVSP29F |
Non-standard residues in 3jbc #7
---
MYR — myristic acid
PLM — palmitic acid
3jbc 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 #7 atoms
> hide #7 cartoons
> show #7 cartoons
> select #7/7:1-129
960 atoms, 979 bonds, 129 residues, 1 model selected
> sequence align #1,#2,#3,#7/7
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 3jbc chain 7 to chain 7 with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 3jbc #7/7
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: TSPK2WHQFQG6Y8CF
> mmaker #7/7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Convex_Cys.pdb, chain A (#1) with 3jbc, chain 7 (#7), sequence
alignment score = 398.4
RMSD between 96 pruned atom pairs is 0.786 angstroms; (across all 123 pairs:
2.450)
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> hide #1 models
> interfaces #7
6 buried areas: 1 3 3811, 1 2 2344, 2 3 1658, 1 4 1203, 3 4 829, 2 4 567
> interfaces #7
6 buried areas: 1 3 3811, 1 2 2344, 2 3 1658, 1 4 1203, 3 4 829, 2 4 567
> sequence chain #7/7
Alignment identifier is 7/7
> select #7/7:1-129
960 atoms, 979 bonds, 129 residues, 1 model selected
> interfaces #7/7
0 buried areas:
> open 4i13
Summary of feedback from opening 4i13 fetched from pdb
---
notes | Fetching compressed mmCIF 4i13 from
http://files.rcsb.org/download/4i13.cif
Fetching CCD FOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FOL/FOL.cif
4i13 title:
Nanobody ca1697 binding to the DHFR.folate binary complex [more info...]
Chain information for 4i13 #8
---
Chain | Description | UniProt
A | Dihydrofolate reductase | DYR_ECOLI 1-159
B | Protein ca1697 (nanobody) |
Non-standard residues in 4i13 #8
---
FOL — folic acid
> select add #7
7642 atoms, 7837 bonds, 984 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> sequence align #1,#2,#3,#8/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 4i13 chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 4i13 #8/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: WGFIYRIEREFOVCV8
> select #8/B:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:101-116
139 atoms, 143 bonds, 16 residues, 1 model selected
> interfaces #8
1 buried areas: A B 965
> undo
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> undo
[Repeated 10 time(s)]No undo action is available
> undo
No undo action is available
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select add #8
2656 atoms, 2328 bonds, 672 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
2656 atoms, 2328 bonds, 672 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #7 models
> hide #1 models
> hide #2 models
> select #1/A:102 #2/A:102 #3/A:102 #8/B:102
39 atoms, 35 bonds, 4 residues, 4 models selected
> select add #1
1810 atoms, 1823 bonds, 128 residues, 4 models selected
> select add #2
3620 atoms, 3653 bonds, 252 residues, 4 models selected
> select subtract #1
1838 atoms, 1855 bonds, 127 residues, 3 models selected
> select subtract #2
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #3
1794 atoms, 1809 bonds, 126 residues, 2 models selected
> select subtract #3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> interfaces #8
1 buried areas: A B 965
> select add #8
2656 atoms, 2328 bonds, 672 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #8 models
> sequence align #1,#2,#3,#7/7
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 3jbc chain 7 to chain 7 with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 3jbc #7/7
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: 3C7RSHLM2TMWNXMI
> show #7 models
> interfaces #7
6 buried areas: 1 3 3811, 1 2 2344, 2 3 1658, 1 4 1203, 3 4 829, 2 4 567
> hide #7 models
> show #8 models
> mmaker #8/B to #2
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 Convex_FLYYP.pdb, chain A (#2) with 4i13, chain B (#8), sequence
alignment score = 433.5
RMSD between 104 pruned atom pairs is 0.622 angstroms; (across all 125 pairs:
2.451)
> show #2 models
> hide #2 models
> hide #8 models
> open 4krm
Summary of feedback from opening 4krm fetched from pdb
---
warnings | Atom H1 is not in the residue template for GLN /B:1
Atom H1 is not in the residue template for GLN /D:1
Atom H1 is not in the residue template for GLN /F:1
Atom H1 is not in the residue template for GLN /H:1
Atom H1 is not in the residue template for GLN /J:1
1 messages similar to the above omitted
note | Fetching compressed mmCIF 4krm from
http://files.rcsb.org/download/4krm.cif
4krm title:
Nanobody/VHH domain 7D12 in complex with domain III of the extracellular
region of EGFR, pH 3.5 [more info...]
Chain information for 4krm #9
---
Chain | Description | UniProt
A C E G I K | Epidermal growth factor receptor | EGFR_HUMAN 311-514
B D F H J L | Nanobody/VHH domain 7D12 |
Non-standard residues in 4krm #9
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
4krm mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_defined_assembly
> hide #!9 atoms
> show #!9 cartoons
> sequence align #1,#2,#3,#9/F
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 4krm chain B to chain F with 0 mismatches
Associated 4krm chain D to chain F with 0 mismatches
Associated 4krm chain F to chain F with 0 mismatches
Associated 4krm chain H to chain F with 0 mismatches
Associated 4krm chain J to chain F with 0 mismatches
Associated 4krm chain L to chain F with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 4krm #9/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: Z44PZ3BZGB5MSHXN
> mmaker #9/F to #2
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 Convex_FLYYP.pdb, chain A (#2) with 4krm, chain F (#9), sequence
alignment score = 450.8
RMSD between 112 pruned atom pairs is 0.564 angstroms; (across all 120 pairs:
1.244)
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 4krm #9/F
> show #2 models
> interfaces #9
16 buried areas: G H 755, I J 748, A B 724, E F 722, K L 708, C D 677, E D
343, C B 341, G Q 336, K S 334, E P 329, I R 328, A M 326, C N 326, I L 326, G
J 313
> log metadata #9
Metadata for 4krm #9
---
Title | Nanobody/VHH domain 7D12 in complex with domain III of the
extracellular region of EGFR, pH 3.5
Citation | Schmitz, K.R., Bagchi, A., Roovers, R.C., van Bergen En Henegouwen,
P.M.P., Ferguson, K.M. (2013). Structural Evaluation of EGFR Inhibition
Mechanisms for Nanobodies/VHH Domains. Structure, 21, 1214-1224. PMID:
23791944. DOI: 10.1016/j.str.2013.05.008
Non-standard residues | BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose;
mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Gene sources | Homo sapiens (human)
Lama glama (llama)
Experimental method | X-ray diffraction
Resolution | 2.650Å
> select add #9
28686 atoms, 28948 bonds, 1 pseudobond, 2051 residues, 2 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> hide #2 models
> open 4krp
Summary of feedback from opening 4krp fetched from pdb
---
warnings | Atom H1 is not in the residue template for GLU /B:1
Atom H1 is not in the residue template for ASP /C:1
Atom H1 is not in the residue template for GLN /D:1
note | Fetching compressed mmCIF 4krp from
http://files.rcsb.org/download/4krp.cif
4krp title:
Nanobody/VHH domain 9G8 in complex with the extracellular region of EGFR [more
info...]
Chain information for 4krp #10
---
Chain | Description | UniProt
A | Epidermal growth factor receptor | EGFR_HUMAN 1-619
B | Nanobody/VHH domain 9G8 |
C | Cetuximab light chain |
D | Cetuximab heavy chain |
Non-standard residues in 4krp #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select #10/B:1-124
1473 atoms, 1494 bonds, 1 pseudobond, 116 residues, 2 models selected
> sequence align #1,#2,#3,#10/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 4krp chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 4krp #10/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: B8ARANHB6UX2HJ7V
> mmaker #10/B to #2
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 Convex_FLYYP.pdb, chain A (#2) with 4krp, chain B (#10), sequence
alignment score = 497.9
RMSD between 96 pruned atom pairs is 0.862 angstroms; (across all 114 pairs:
2.456)
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
> 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 #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> interfaces #10
5 buried areas: D C 1586, A B 803, A D 623, A C 383, A E 316
> hide #!10 models
> select add #10
14877 atoms, 15079 bonds, 3 pseudobonds, 1085 residues, 2 models selected
> select subtract #10
Nothing selected
> open 4w6w
Summary of feedback from opening 4w6w fetched from pdb
---
note | Fetching compressed mmCIF 4w6w from
http://files.rcsb.org/download/4w6w.cif
4w6w title:
Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF with
inhibitory nanobody NbFedF6 [more info...]
Chain information for 4w6w #11
---
Chain | Description | UniProt
A | F18 fimbrial adhesin AC | Q47212_ECOLX 15-165
B | NbFedF6 |
> sequence align #1,#2,#3,#11/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 4w6w chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 4w6w #11/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: MAQUL0K85ME5FUQV
> mmaker #11 to #3
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 Convex_GPL.pdb, chain A (#3) with 4w6w, chain B (#11), sequence
alignment score = 452.2
RMSD between 105 pruned atom pairs is 0.562 angstroms; (across all 123 pairs:
1.881)
> show #3 models
> select #11/B:802-925
919 atoms, 938 bonds, 124 residues, 1 model selected
> interfaces #11
1 buried areas: A B 771
> log metadata #11
Metadata for 4w6w #11
---
Title | Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF
with inhibitory nanobody NbFedF6
Citation | Moonens, K., De Kerpel, M., Coddens, A., Cox, E., Pardon, E.,
Remaut, H., De Greve, H. (2014). Nanobody Mediated Inhibition of Attachment of
F18 Fimbriae Expressing Escherichia coli. Plos One, 9, e114691-e114691. PMID:
25502211. DOI: 10.1371/journal.pone.0114691
Gene sources | Escherichia coli
Lama glama (llama)
Experimental method | X-ray diffraction
Resolution | 2.51Å
> interfaces #11
1 buried areas: A B 771
> hide #3 models
> hide #!11 models
> select add #11
2058 atoms, 2047 bonds, 1 pseudobond, 322 residues, 2 models selected
> select subtract #11
Nothing selected
> interfaces #11
1 buried areas: A B 771
> select add #11
2058 atoms, 2047 bonds, 1 pseudobond, 322 residues, 2 models selected
> select subtract #11
Nothing selected
> open 5gxb
Summary of feedback from opening 5gxb fetched from pdb
---
note | Fetching compressed mmCIF 5gxb from
http://files.rcsb.org/download/5gxb.cif
5gxb title:
crystal structure of a LacY/Nanobody complex [more info...]
Chain information for 5gxb #12
---
Chain | Description | UniProt
A | Lactose permease | LACY_ECOLI 1-417
B | nanobody |
> select #12/B:0-131
1035 atoms, 1059 bonds, 132 residues, 1 model selected
> sequence align #1,#2,#3,#12/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 5gxb chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 5gxb #12/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: REDRFJLB5ML55EP5
> select #1/A:78 #2/A:78 #3/A:78 #12/B:78
49 atoms, 45 bonds, 4 residues, 4 models selected
> select #12/B:15-16
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/A:15-72 #2/A:15-72 #3/A:15-72 #12/B:15-72
2973 atoms, 3006 bonds, 232 residues, 4 models selected
Clustal Omega Alignment [ID: 1] region chain A..chain B [16-73] RMSD: 52.979
> select #1/A:66-67
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1/A:66-73 #2/A:66-73 #3/A:66-73
393 atoms, 393 bonds, 24 residues, 3 models selected
Clustal Omega Alignment [ID: 1] region chain A..chain A [67-74] RMSD: 5.576
> select #12/B:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/B:104-105
18 atoms, 18 bonds, 2 residues, 1 model selected
> mmaker #12 to #2
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 Convex_FLYYP.pdb, chain A (#2) with 5gxb, chain B (#12), sequence
alignment score = 456.4
RMSD between 104 pruned atom pairs is 0.616 angstroms; (across all 125 pairs:
3.250)
> show #2 models
> hide #2 models
> interfaces #12
1 buried areas: A B 1008
> hide #!12 models
> select add #12
4121 atoms, 4241 bonds, 1 pseudobond, 519 residues, 2 models selected
> select subtract #12
Nothing selected
> open 5jds
Summary of feedback from opening 5jds fetched from pdb
---
note | Fetching compressed mmCIF 5jds from
http://files.rcsb.org/download/5jds.cif
5jds title:
Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron
resolution [more info...]
Chain information for 5jds #13
---
Chain | Description | UniProt
A | Programmed cell death 1 ligand 1 | PD1L1_HUMAN 18-132
B | Nanobody |
Non-standard residues in 5jds #13
---
CL — chloride ion
NA — sodium ion
SO4 — sulfate ion
> select #13/B:1-127
958 atoms, 976 bonds, 127 residues, 1 model selected
> sequence align #1,#2,#3,#13/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 5jds chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 5jds #13/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: 4WK55KN8L9GRZ2WM
> color #13/B Cys yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #13/B:Cys yellow
> undo
> mmaker #13 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Convex_Cys.pdb, chain A (#1) with 5jds, chain B (#13), sequence
alignment score = 463
RMSD between 102 pruned atom pairs is 0.657 angstroms; (across all 124 pairs:
2.285)
> show #1 models
> hide #1 models
> interfaces #13
1 buried areas: B A 820
> hide #!13 models
> select add #13
2048 atoms, 1917 bonds, 1 pseudobond, 407 residues, 2 models selected
> select subtract #13
Nothing selected
> open 5o02
Summary of feedback from opening 5o02 fetched from pdb
---
note | Fetching compressed mmCIF 5o02 from
http://files.rcsb.org/download/5o02.cif
5o02 title:
GII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4 [more
info...]
Chain information for 5o02 #14
---
Chain | Description | UniProt
A | Capsid protein | A0A0A7CJV4_9CALI 225-528
C | Nanobody (VHH) Nano-4 |
Non-standard residues in 5o02 #14
---
EDO — 1,2-ethanediol (ethylene glycol)
IMD — imidazole
> sequence align #1,#2,#3,#14/B
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align #1,#2,#3,#14/C
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 5o02 chain C to chain C with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 5o02 #14/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: G91VK0AF1QLFCJMU
> interfaces #14
1 buried areas: A C 787
> select add #14
3869 atoms, 3442 bonds, 950 residues, 1 model selected
> select subtract #14
Nothing selected
> hide #14 models
> open 5tok
Summary of feedback from opening 5tok fetched from pdb
---
note | Fetching compressed mmCIF 5tok from
http://files.rcsb.org/download/5tok.cif
5tok title:
Crystal structure of the RSV F glycoprotein in complex with the neutralizing
single-domain antibody F-VHH-L66 [more info...]
Chain information for 5tok #15
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0, Fibritin chimera | FUS_HRSVA 1-513
D E F | Single-domain antibody F-VHH-L66 |
Non-standard residues in 5tok #15
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PO4 — phosphate ion
> hide #!15 atoms
> show #!15 cartoons
> show #14 models
> hide #14 models
> sequence align #1,#2,#3,#15/E
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 5tok chain D to chain E with 0 mismatches
Associated 5tok chain E to chain E with 0 mismatches
Associated 5tok chain F to chain E with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 5tok #15/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: EJDS7WPSN5FN2CE6
> select #15/E:Cys
24 atoms, 22 bonds, 4 residues, 1 model selected
> mmaker #15/E to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Convex_Cys.pdb, chain A (#1) with 5tok, chain E (#15), sequence
alignment score = 506.5
RMSD between 111 pruned atom pairs is 0.672 angstroms; (across all 124 pairs:
2.078)
> show #1 models
> hide #1 models
> interfaces #15
9 buried areas: A C 2808, B C 2592, B A 2550, A E 770, C F 768, B D 742, A F
475, C D 466, B E 457
> log metadata #15
Metadata for 5tok #15
---
Title | Crystal structure of the RSV F glycoprotein in complex with the
neutralizing single-domain antibody F-VHH-L66
Citation | Rossey, I., Gilman, M.S., Kabeche, S.C., Sedeyn, K., Wrapp, D.,
Kanekiyo, M., Chen, M., Mas, V., Spitaels, J., Melero, J.A., Graham, B.S.,
Schepens, B., McLellan, J.S., Saelens, X. (2017). Potent single-domain
antibodies that arrest respiratory syncytial virus fusion protein in its
prefusion state. Nat Commun, 8, 14158-14158. PMID: 28194013. DOI:
10.1038/ncomms14158
Non-standard residues | NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
(N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose;
2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-
GLUCOSAMINE)
PO4 — phosphate ion
Gene sources | Human respiratory syncytial virus
Lama glama (llama)
Experimental method | X-ray diffraction
Resolution | 3.800Å
> open 5u4m
Summary of feedback from opening 5u4m fetched from pdb
---
note | Fetching compressed mmCIF 5u4m from
http://files.rcsb.org/download/5u4m.cif
5u4m title:
RTA-V1C7-G29R-no_salt [more info...]
Chain information for 5u4m #16
---
Chain | Description | UniProt
A | Ricin | RICI_RICCO 5-259
B | V1C7 VHH antibody |
Non-standard residues in 5u4m #16
---
CL — chloride ion
> hide #!15 models
> select add #15
13999 atoms, 14268 bonds, 3 pseudobonds, 1810 residues, 2 models selected
> select subtract #15
Nothing selected
> sequence chain #16/B
Alignment identifier is 16/B
> select #16/B:-1-127
994 atoms, 1018 bonds, 129 residues, 1 model selected
> sequence align #1,#2,#3,#16/B
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 5u4m chain B to chain B with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 5u4m #16/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: PYBYDFCHMQJIVV51
> mmaker #16 to #3
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 Convex_GPL.pdb, chain A (#3) with 5u4m, chain B (#16), sequence
alignment score = 467.6
RMSD between 103 pruned atom pairs is 0.704 angstroms; (across all 121 pairs:
2.452)
> show #!4 models
> hide #!4 models
> show #3 models
> hide #3 models
> interfaces #16
1 buried areas: A B 733
> hide #16 models
> select add #16
3062 atoms, 3080 bonds, 432 residues, 1 model selected
> select subtract #16
Nothing selected
> open 6ey6
Summary of feedback from opening 6ey6 fetched from pdb
---
note | Fetching compressed mmCIF 6ey6 from
http://files.rcsb.org/download/6ey6.cif
6ey6 title:
C-terminal part (residues 315-516) of PorM with the llama nanobody nb130 [more
info...]
Chain information for 6ey6 #17
---
Chain | Description | UniProt
A B C D E F G H | T9SS component cytoplasmic membrane protein PorM |
A0A1R4DSC1_PORGN 225-516
I J K L M N O P | nb130 |
6ey6 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> hide #17 atoms
> show #17 cartoons
> sequence align #1,#2,#3,#17/K
Alignment identifier is 1
Associated Convex_Cys.pdb chain A to chain A with 0 mismatches
Associated Convex_FLYYP.pdb chain A to chain A with 0 mismatches
Associated Convex_GPL.pdb chain A to chain A with 0 mismatches
Associated 6ey6 chain I to chain K with 0 mismatches
Associated 6ey6 chain J to chain K with 0 mismatches
Associated 6ey6 chain K to chain K with 0 mismatches
Associated 6ey6 chain L to chain K with 0 mismatches
Associated 6ey6 chain M to chain K with 0 mismatches
Associated 6ey6 chain N to chain K with 0 mismatches
Associated 6ey6 chain O to chain K with 0 mismatches
Associated 6ey6 chain P to chain K with 0 mismatches
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 6ey6 #17/N
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Webservices job id: 8PWSP1MLZS72WZAC
> select #17/K:1-113
987 atoms, 1009 bonds, 130 residues, 1 model selected
> mmaker #17/K to #2
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 Convex_FLYYP.pdb, chain A (#2) with 6ey6, chain K (#17), sequence
alignment score = 514.4
RMSD between 111 pruned atom pairs is 0.566 angstroms; (across all 125 pairs:
1.856)
Chains used in RMSD evaluation for alignment 1: Convex_Cys.pdb #1/A,
Convex_FLYYP.pdb #2/A, Convex_GPL.pdb #3/A, 6ey6 #17/K
> show #2 models
> hide #2 models
> show #1 models
> show #3 models
> hide #3 models
> hide #1 models
> interfaces #17
26 buried areas: D C 2753, H G 2745, E F 2421, A B 2389, D L 725, C K 708, E M
692, C M 676, H P 673, F N 661, F P 645, A I 640, D K 613, B J 604, G O 582, C
L 555, A J 534, E N 533, G P 518, F M 516, B I 499, B L 455, H O 413, C F 327,
E A 319, G F 301
> log metadata #17
Metadata for 6ey6 #17
---
Title | C-terminal part (residues 315-516) of PorM with the llama nanobody
nb130
Citations | Leone, P., Roche, J., Vincent, M.S., Tran, Q.H., Desmyter, A.,
Cascales, E., Kellenberger, C., Cambillau, C., Roussel, A. (2018). Type IX
secretion system PorM and gliding machinery GldM form arches spanning the
periplasmic space. Nat Commun, 9, 429-429. PMID: 29382829. DOI:
10.1038/s41467-017-02784-7
Duhoo, Y., Roche, J., Trinh, T.T.N., Desmyter, A., Gaubert, A., Kellenberger,
C., Cambillau, C., Roussel, A., Leone, P. (2017). Camelid nanobodies used as
crystallization chaperones for different constructs of PorM, a component of
the type IX secretion system from Porphyromonas gingivalis. Acta Crystallogr F
Struct Biol Commun, 73, 286-293. PMID: 28471361. DOI:
10.1107/S2053230X17005969
Gene sources | Porphyromonas gingivalis
Lama glama
Experimental method | X-ray diffraction
Resolution | 2.1Å
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
ModuleNotFoundError: No module named 'pyqt'
ModuleNotFoundError: No module named 'pyqt'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\help_viewer\tool.py", line 289, in reject
from pyqt import sip
See log for complete Python traceback.
> save "C:/Users/Noort/OneDrive/Bureaublad/Uni/Ma1/Semester
> 2/Stage/convex_sample_analysis.cxs"
OpenGL version: 3.3.0 NVIDIA 511.69
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: nl_BE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: Zenbook UX535QE
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 16,542,056,448
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics
OSLanguage: nl-NL
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Help System |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Help Viewer: No module named 'pyqt' |
comment:2 by , 20 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
