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Opened 9 months ago
Closed 9 months ago
#16770 closed defect (limitation)
Restore new session in old ChimeraX
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202210050721 (2022-10-05 07:21:30 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5.dev202210050721 (2022-10-05)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Oct 27 21:22:03 2024UCSF ChimeraX version: 1.7.dev202310270152
(2023-10-27)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/yyy/Desktop/bamAK534-E650.cxs
Log from Sun Oct 27 20:44:36 2024UCSF ChimeraX version: 1.7.dev202310270152
(2023-10-27)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/yyy/Desktop/bAL534K.cxs format session
Log from Fri Oct 25 00:36:44 2024UCSF ChimeraX version: 1.7.dev202310270152
(2023-10-27)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5D0O
Summary of feedback from opening 5D0O fetched from pdb
---
note | Fetching compressed mmCIF 5d0o from
http://files.rcsb.org/download/5d0o.cif
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> show atoms
> hide atoms
> show atoms
> show cartoons
> hide cartoons
> style stick
Changed 22815 atom styles
> style stick
Changed 22815 atom styles
> style ball
Changed 22815 atom styles
> style sphere
Changed 22815 atom styles
> style ball
Changed 22815 atom styles
> show atoms
> hide atoms
> hide cartoons
> show atoms
> hide cartoons
> show cartoons
> style stick
Changed 22815 atom styles
> style ball
Changed 22815 atom styles
> style sphere
Changed 22815 atom styles
> style sphere
Changed 22815 atom styles
> show atoms
[Repeated 1 time(s)]
> hide atoms
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> szqppq lys #0: 534.a
Unknown command: szqppq lys #0: 534.a
> swappa lys #0: 534.a
Unknown command: swappa lys #0: 534.a
> select clear
> select :45.A
Expected an objects specifier or a keyword
> select :45.A
Expected an objects specifier or a keyword
> help select
> select N534K.A
Expected an objects specifier or a keyword
> select :534.A
Expected an objects specifier or a keyword
> select
> /A:29-32,72-79,84-90,93-100,150-158,162-170,176-183,239-247,253-261,271-274,321-327,336-342,348-355,398-404,411-418,424-433,437-446,454-462,466-475,488-495,505-518,523-537,564-579,590-600,608-620,628-630,632-640,710-720,734-745,767-777,782-784,787-789
4461 atoms, 4479 bonds, 280 residues, 1 model selected
> select clear
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
/A ASN 534: phi -106.2, psi 131.8 trans
Changed 438 bond radii
> swapaa interactive sel LYS rotLib Dunbrack
5d0o #!1/A ASN 534: phi -106.2, psi 131.8 trans
Changed 438 bond radii
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> hbonds #!1 & ~#!1/A:534 & ~solvent reveal true restrict #1.3 & ~@c,ca,n
29 hydrogen bonds found
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> style sel sphere
Changed 14 atom styles
> style sel sphere
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:535
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #!1/A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
5d0o #!1/A ASN 534: phi -106.2, psi 131.8 trans
Changed 438 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
[Repeated 1 time(s)]
> swapaa #!1/A:534 LYS criteria 16 rotLib Dunbrack
Using Dunbrack library
5d0o #!1/A ASN 534: phi -106.2, psi 131.8 trans
Applying LYS rotamer (chi angles: -62.9 -177.5 -75.1 -68.8) to 5d0o #!1/A LYS
534
> hide sel cartoons
> show sel cartoons
> style sel sphere
Changed 6 atom styles
> select clear
> style sphere
Changed 23834 atom styles
> style sphere
Changed 23834 atom styles
> select clear
[Repeated 1 time(s)]
> style sphere
Changed 23834 atom styles
> style ball
Changed 23834 atom styles
> style stick
Changed 23834 atom styles
> style sphere
Changed 23834 atom styles
> style sphere
Changed 23834 atom styles
> show atoms
[Repeated 1 time(s)]
> hide atoms
> select #!1/A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel atoms
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> color sel red
> select clear
> select #!1/A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> view clip false
> show target m
[Repeated 2 time(s)]
> view clip false
> log metadata #!1
Metadata for 5d0o #!1
---
Title | BamABCDE complex, outer membrane β barrel assembly machinery entire
complex
Citation | Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z., Paterson, N.G.,
Stansfeld, P.J., Wang, Z., Zhang, Y., Wang, W., Dong, C. (2016). Structural
basis of outer membrane protein insertion by the BAM complex. Nature, 531,
47-52. PMID: 26901871. DOI: 10.1038/nature17199
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #!1
Chain information for 5d0o #!1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> log metadata #1.2.1
The model has no metadata
> log chains #1.2.1
> log metadata #1.2.2
The model has no metadata
> log chains #1.2.2
> log metadata #1.2.3
The model has no metadata
> log chains #1.2.3
> log metadata #1.2.4
The model has no metadata
> log chains #1.2.4
> log metadata #1.2.5
The model has no metadata
> log chains #1.2.5
> log metadata #1.2.6
The model has no metadata
> log chains #1.2.6
> log metadata #1.2.7
The model has no metadata
> log chains #1.2.7
> log metadata #1.2.8
The model has no metadata
> log chains #1.2.8
> log metadata #1.2.9
The model has no metadata
> log chains #1.2.9
> log metadata #1.2.10
The model has no metadata
> log chains #1.2.10
> log metadata #1.2.11
The model has no metadata
> log chains #1.2.11
> log metadata #1.2.12
The model has no metadata
> log chains #1.2.12
> log metadata #1.2.13
The model has no metadata
> log chains #1.2.13
> log metadata #1.2.14
The model has no metadata
> log chains #1.2.14
> log metadata #1.2.15
The model has no metadata
> log chains #1.2.15
> log metadata #1.2.16
The model has no metadata
> log chains #1.2.16
> log metadata #1.2.17
The model has no metadata
> log chains #1.2.17
> log metadata #1.2.18
The model has no metadata
> log chains #1.2.18
> log metadata #1.2.19
The model has no metadata
> log chains #1.2.19
> log metadata #1.2.20
The model has no metadata
> log chains #1.2.20
> log metadata #1.2.21
The model has no metadata
> log chains #1.2.21
> log metadata #1.2.22
The model has no metadata
> log chains #1.2.22
> log metadata #1.2.23
The model has no metadata
> log chains #1.2.23
> log metadata #1.2.24
The model has no metadata
> log chains #1.2.24
> log metadata #1.2.25
The model has no metadata
> log chains #1.2.25
> log metadata #1.2.26
The model has no metadata
> log chains #1.2.26
> log metadata #1.2.27
The model has no metadata
> log chains #1.2.27
> log metadata #1.2.28
The model has no metadata
> log chains #1.2.28
> log metadata #1.2.29
The model has no metadata
> log chains #1.2.29
> log metadata #1.2.30
The model has no metadata
> log chains #1.2.30
> log metadata #1.2.31
The model has no metadata
> log chains #1.2.31
> log metadata #1.2.32
The model has no metadata
> log chains #1.2.32
> log metadata #1.2.33
The model has no metadata
> log chains #1.2.33
> log metadata #1.2.34
The model has no metadata
> log chains #1.2.34
> log metadata #1.2.35
The model has no metadata
> log chains #1.2.35
> log metadata #1.2.36
The model has no metadata
> log chains #1.2.36
> log metadata #1.2.37
The model has no metadata
> log chains #1.2.37
> log metadata #1.2.38
The model has no metadata
> log chains #1.2.38
> log metadata #1.2.39
The model has no metadata
> log chains #1.2.39
> log metadata #1.2.40
The model has no metadata
> log chains #1.2.40
> log metadata #1.2.41
The model has no metadata
> log chains #1.2.41
> log metadata #1.2.42
The model has no metadata
> log chains #1.2.42
> log metadata #1.2.43
The model has no metadata
> log chains #1.2.43
> log metadata #1.2.44
The model has no metadata
> log chains #1.2.44
> log metadata #1.2.45
The model has no metadata
> log chains #1.2.45
> log metadata #1.2.46
The model has no metadata
> log chains #1.2.46
> log metadata #1.2.47
The model has no metadata
> log chains #1.2.47
> log metadata #1.2.48
The model has no metadata
> log chains #1.2.48
> log metadata #1.2.49
The model has no metadata
> log chains #1.2.49
> log metadata #1.2.50
The model has no metadata
> log chains #1.2.50
> log metadata #1.2.51
The model has no metadata
> log chains #1.2.51
> log metadata #1.2.52
The model has no metadata
> log chains #1.2.52
> log metadata #1.2.53
The model has no metadata
> log chains #1.2.53
> log metadata #1.2.54
The model has no metadata
> log chains #1.2.54
> log metadata #1.2.55
The model has no metadata
> log chains #1.2.55
> log metadata #1.2.56
The model has no metadata
> log chains #1.2.56
> log metadata #1.2.57
The model has no metadata
> log chains #1.2.57
> log metadata #1.2.58
The model has no metadata
> log chains #1.2.58
> log metadata #1.2.59
The model has no metadata
> log chains #1.2.59
> log metadata #1.2.60
The model has no metadata
> log chains #1.2.60
> log metadata #1.2.61
The model has no metadata
> log chains #1.2.61
> log metadata #1.2.62
The model has no metadata
> log chains #1.2.62
> log metadata #1.2.63
The model has no metadata
> log chains #1.2.63
> log metadata #1.2.64
The model has no metadata
> log chains #1.2.64
> log metadata #1.2.65
The model has no metadata
> log chains #1.2.65
> log metadata #1.2.66
The model has no metadata
> log chains #1.2.66
> log metadata #1.2.67
The model has no metadata
> log chains #1.2.67
> log metadata #1.2.68
The model has no metadata
> log chains #1.2.68
> log metadata #1.2.69
The model has no metadata
> log chains #1.2.69
> log metadata #1.2.70
The model has no metadata
> log chains #1.2.70
> log metadata #1.2.71
The model has no metadata
> log chains #1.2.71
> log metadata #1.2.72
The model has no metadata
> log chains #1.2.72
> log metadata #1.2.73
The model has no metadata
> log chains #1.2.73
> log metadata #1.3.1
The model has no metadata
> log chains #1.3.1
> log metadata #1.3.2
The model has no metadata
> log chains #1.3.2
> log metadata #1.3.3
The model has no metadata
> log chains #1.3.3
> log metadata #1.3.4
The model has no metadata
> log chains #1.3.4
> log metadata #1.3.5
The model has no metadata
> log chains #1.3.5
> log metadata #1.3.6
The model has no metadata
> log chains #1.3.6
> log metadata #1.3.7
The model has no metadata
> log chains #1.3.7
> log metadata #1.3.8
The model has no metadata
> log chains #1.3.8
> log metadata #1.3.9
The model has no metadata
> log chains #1.3.9
> log metadata #1.3.10
The model has no metadata
> log chains #1.3.10
> log metadata #1.3.11
The model has no metadata
> log chains #1.3.11
> log metadata #1.3.12
The model has no metadata
> log chains #1.3.12
> log metadata #1.3.13
The model has no metadata
> log chains #1.3.13
> log metadata #1.3.14
The model has no metadata
> log chains #1.3.14
> log metadata #1.3.15
The model has no metadata
> log chains #1.3.15
> log metadata #1.3.16
The model has no metadata
> log chains #1.3.16
> log metadata #1.3.17
The model has no metadata
> log chains #1.3.17
> log metadata #1.3.18
The model has no metadata
> log chains #1.3.18
> log metadata #1.3.19
The model has no metadata
> log chains #1.3.19
> log metadata #1.3.20
The model has no metadata
> log chains #1.3.20
> log metadata #1.3.21
The model has no metadata
> log chains #1.3.21
> log metadata #1.3.22
The model has no metadata
> log chains #1.3.22
> log metadata #1.3.23
The model has no metadata
> log chains #1.3.23
> log metadata #1.3.24
The model has no metadata
> log chains #1.3.24
> log metadata #1.3.25
The model has no metadata
> log chains #1.3.25
> log metadata #1.3.26
The model has no metadata
> log chains #1.3.26
> log metadata #1.3.27
The model has no metadata
> log chains #1.3.27
> log metadata #1.3.28
The model has no metadata
> log chains #1.3.28
> log metadata #1.3.29
The model has no metadata
> log chains #1.3.29
> log metadata #1.3.30
The model has no metadata
> log chains #1.3.30
> log metadata #1.3.31
The model has no metadata
> log chains #1.3.31
> log metadata #1.3.32
The model has no metadata
> log chains #1.3.32
> log metadata #1.3.33
The model has no metadata
> log chains #1.3.33
> log metadata #1.3.34
The model has no metadata
> log chains #1.3.34
> log metadata #1.3.35
The model has no metadata
> log chains #1.3.35
> log metadata #1.3.36
The model has no metadata
> log chains #1.3.36
> log metadata #1.3.37
The model has no metadata
> log chains #1.3.37
> log metadata #1.3.38
The model has no metadata
> log chains #1.3.38
> log metadata #1.3.39
The model has no metadata
> log chains #1.3.39
> log metadata #1.3.40
The model has no metadata
> log chains #1.3.40
> log metadata #1.3.41
The model has no metadata
> log chains #1.3.41
> log metadata #1.3.42
The model has no metadata
> log chains #1.3.42
> log metadata #1.3.43
The model has no metadata
> log chains #1.3.43
> log metadata #1.3.44
The model has no metadata
> log chains #1.3.44
> log metadata #1.3.45
The model has no metadata
> log chains #1.3.45
> log metadata #1.3.46
The model has no metadata
> log chains #1.3.46
> log metadata #1.3.47
The model has no metadata
> log chains #1.3.47
> log metadata #1.3.48
The model has no metadata
> log chains #1.3.48
> log metadata #1.3.49
The model has no metadata
> log chains #1.3.49
> log metadata #1.3.50
The model has no metadata
> log chains #1.3.50
> log metadata #1.3.51
The model has no metadata
> log chains #1.3.51
> log metadata #1.3.52
The model has no metadata
> log chains #1.3.52
> log metadata #1.3.53
The model has no metadata
> log chains #1.3.53
> log metadata #1.3.54
The model has no metadata
> log chains #1.3.54
> log metadata #1.3.55
The model has no metadata
> log chains #1.3.55
> log metadata #1.3.56
The model has no metadata
> log chains #1.3.56
> log metadata #1.3.57
The model has no metadata
> log chains #1.3.57
> log metadata #1.3.58
The model has no metadata
> log chains #1.3.58
> log metadata #1.3.59
The model has no metadata
> log chains #1.3.59
> log metadata #1.3.60
The model has no metadata
> log chains #1.3.60
> log metadata #1.3.61
The model has no metadata
> log chains #1.3.61
> log metadata #1.3.62
The model has no metadata
> log chains #1.3.62
> log metadata #1.3.63
The model has no metadata
> log chains #1.3.63
> log metadata #1.3.64
The model has no metadata
> log chains #1.3.64
> log metadata #1.3.65
The model has no metadata
> log chains #1.3.65
> log metadata #1.3.66
The model has no metadata
> log chains #1.3.66
> log metadata #1.3.67
The model has no metadata
> log chains #1.3.67
> log metadata #1.3.68
The model has no metadata
> log chains #1.3.68
> log metadata #1.3.69
The model has no metadata
> log chains #1.3.69
> log metadata #1.3.70
The model has no metadata
> log chains #1.3.70
> log metadata #1.3.71
The model has no metadata
> log chains #1.3.71
> log metadata #1.3.72
The model has no metadata
> log chains #1.3.72
> log metadata #1.3.73
The model has no metadata
> log chains #1.3.73
> log metadata #!1
Metadata for 5d0o #!1
---
Title | BamABCDE complex, outer membrane β barrel assembly machinery entire
complex
Citation | Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z., Paterson, N.G.,
Stansfeld, P.J., Wang, Z., Zhang, Y., Wang, W., Dong, C. (2016). Structural
basis of outer membrane protein insertion by the BAM complex. Nature, 531,
47-52. PMID: 26901871. DOI: 10.1038/nature17199
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #!1
Chain information for 5d0o #!1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> log metadata #1.2.1
The model has no metadata
> log chains #1.2.1
> log metadata #1.2.2
The model has no metadata
> log chains #1.2.2
> log metadata #1.2.3
The model has no metadata
> log chains #1.2.3
> log metadata #1.2.4
The model has no metadata
> log chains #1.2.4
> log metadata #1.2.5
The model has no metadata
> log chains #1.2.5
> log metadata #1.2.6
The model has no metadata
> log chains #1.2.6
> log metadata #1.2.7
The model has no metadata
> log chains #1.2.7
> log metadata #1.2.8
The model has no metadata
> log chains #1.2.8
> log metadata #1.2.9
The model has no metadata
> log chains #1.2.9
> log metadata #1.2.10
The model has no metadata
> log chains #1.2.10
> log metadata #1.2.11
The model has no metadata
> log chains #1.2.11
> log metadata #1.2.12
The model has no metadata
> log chains #1.2.12
> log metadata #1.2.13
The model has no metadata
> log chains #1.2.13
> log metadata #1.2.14
The model has no metadata
> log chains #1.2.14
> log metadata #1.2.15
The model has no metadata
> log chains #1.2.15
> log metadata #1.2.16
The model has no metadata
> log chains #1.2.16
> log metadata #1.2.17
The model has no metadata
> log chains #1.2.17
> log metadata #1.2.18
The model has no metadata
> log chains #1.2.18
> log metadata #1.2.19
The model has no metadata
> log chains #1.2.19
> log metadata #1.2.20
The model has no metadata
> log chains #1.2.20
> log metadata #1.2.21
The model has no metadata
> log chains #1.2.21
> log metadata #1.2.22
The model has no metadata
> log chains #1.2.22
> log metadata #1.2.23
The model has no metadata
> log chains #1.2.23
> log metadata #1.2.24
The model has no metadata
> log chains #1.2.24
> log metadata #1.2.25
The model has no metadata
> log chains #1.2.25
> log metadata #1.2.26
The model has no metadata
> log chains #1.2.26
> log metadata #1.2.27
The model has no metadata
> log chains #1.2.27
> log metadata #1.2.28
The model has no metadata
> log chains #1.2.28
> log metadata #1.2.29
The model has no metadata
> log chains #1.2.29
> log metadata #1.2.30
The model has no metadata
> log chains #1.2.30
> log metadata #1.2.31
The model has no metadata
> log chains #1.2.31
> log metadata #1.2.32
The model has no metadata
> log chains #1.2.32
> log metadata #1.2.33
The model has no metadata
> log chains #1.2.33
> log metadata #1.2.34
The model has no metadata
> log chains #1.2.34
> log metadata #1.2.35
The model has no metadata
> log chains #1.2.35
> log metadata #1.2.36
The model has no metadata
> log chains #1.2.36
> log metadata #1.2.37
The model has no metadata
> log chains #1.2.37
> log metadata #1.2.38
The model has no metadata
> log chains #1.2.38
> log metadata #1.2.39
The model has no metadata
> log chains #1.2.39
> log metadata #1.2.40
The model has no metadata
> log chains #1.2.40
> log metadata #1.2.41
The model has no metadata
> log chains #1.2.41
> log metadata #1.2.42
The model has no metadata
> log chains #1.2.42
> log metadata #1.2.43
The model has no metadata
> log chains #1.2.43
> log metadata #1.2.44
The model has no metadata
> log chains #1.2.44
> log metadata #1.2.45
The model has no metadata
> log chains #1.2.45
> log metadata #1.2.46
The model has no metadata
> log chains #1.2.46
> log metadata #1.2.47
The model has no metadata
> log chains #1.2.47
> log metadata #1.2.48
The model has no metadata
> log chains #1.2.48
> log metadata #1.2.49
The model has no metadata
> log chains #1.2.49
> log metadata #1.2.50
The model has no metadata
> log chains #1.2.50
> log metadata #1.2.51
The model has no metadata
> log chains #1.2.51
> log metadata #1.2.52
The model has no metadata
> log chains #1.2.52
> log metadata #1.2.53
The model has no metadata
> log chains #1.2.53
> log metadata #1.2.54
The model has no metadata
> log chains #1.2.54
> log metadata #1.2.55
The model has no metadata
> log chains #1.2.55
> log metadata #1.2.56
The model has no metadata
> log chains #1.2.56
> log metadata #1.2.57
The model has no metadata
> log chains #1.2.57
> log metadata #1.2.58
The model has no metadata
> log chains #1.2.58
> log metadata #1.2.59
The model has no metadata
> log chains #1.2.59
> log metadata #1.2.60
The model has no metadata
> log chains #1.2.60
> log metadata #1.2.61
The model has no metadata
> log chains #1.2.61
> log metadata #1.2.62
The model has no metadata
> log chains #1.2.62
> log metadata #1.2.63
The model has no metadata
> log chains #1.2.63
> log metadata #1.2.64
The model has no metadata
> log chains #1.2.64
> log metadata #1.2.65
The model has no metadata
> log chains #1.2.65
> log metadata #1.2.66
The model has no metadata
> log chains #1.2.66
> log metadata #1.2.67
The model has no metadata
> log chains #1.2.67
> log metadata #1.2.68
The model has no metadata
> log chains #1.2.68
> log metadata #1.2.69
The model has no metadata
> log chains #1.2.69
> log metadata #1.2.70
The model has no metadata
> log chains #1.2.70
> log metadata #1.2.71
The model has no metadata
> log chains #1.2.71
> log metadata #1.2.72
The model has no metadata
> log chains #1.2.72
> log metadata #1.2.73
The model has no metadata
> log chains #1.2.73
> log metadata #1.3.1
The model has no metadata
> log chains #1.3.1
> log metadata #1.3.2
The model has no metadata
> log chains #1.3.2
> log metadata #1.3.3
The model has no metadata
> log chains #1.3.3
> log metadata #1.3.4
The model has no metadata
> log chains #1.3.4
> log metadata #1.3.5
The model has no metadata
> log chains #1.3.5
> log metadata #1.3.6
The model has no metadata
> log chains #1.3.6
> log metadata #1.3.7
The model has no metadata
> log chains #1.3.7
> log metadata #1.3.8
The model has no metadata
> log chains #1.3.8
> log metadata #1.3.9
The model has no metadata
> log chains #1.3.9
> log metadata #1.3.10
The model has no metadata
> log chains #1.3.10
> log metadata #1.3.11
The model has no metadata
> log chains #1.3.11
> log metadata #1.3.12
The model has no metadata
> log chains #1.3.12
> log metadata #1.3.13
The model has no metadata
> log chains #1.3.13
> log metadata #1.3.14
The model has no metadata
> log chains #1.3.14
> log metadata #1.3.15
The model has no metadata
> log chains #1.3.15
> log metadata #1.3.16
The model has no metadata
> log chains #1.3.16
> log metadata #1.3.17
The model has no metadata
> log chains #1.3.17
> log metadata #1.3.18
The model has no metadata
> log chains #1.3.18
> log metadata #1.3.19
The model has no metadata
> log chains #1.3.19
> log metadata #1.3.20
The model has no metadata
> log chains #1.3.20
> log metadata #1.3.21
The model has no metadata
> log chains #1.3.21
> log metadata #1.3.22
The model has no metadata
> log chains #1.3.22
> log metadata #1.3.23
The model has no metadata
> log chains #1.3.23
> log metadata #1.3.24
The model has no metadata
> log chains #1.3.24
> log metadata #1.3.25
The model has no metadata
> log chains #1.3.25
> log metadata #1.3.26
The model has no metadata
> log chains #1.3.26
> log metadata #1.3.27
The model has no metadata
> log chains #1.3.27
> log metadata #1.3.28
The model has no metadata
> log chains #1.3.28
> log metadata #1.3.29
The model has no metadata
> log chains #1.3.29
> log metadata #1.3.30
The model has no metadata
> log chains #1.3.30
> log metadata #1.3.31
The model has no metadata
> log chains #1.3.31
> log metadata #1.3.32
The model has no metadata
> log chains #1.3.32
> log metadata #1.3.33
The model has no metadata
> log chains #1.3.33
> log metadata #1.3.34
The model has no metadata
> log chains #1.3.34
> log metadata #1.3.35
The model has no metadata
> log chains #1.3.35
> log metadata #1.3.36
The model has no metadata
> log chains #1.3.36
> log metadata #1.3.37
The model has no metadata
> log chains #1.3.37
> log metadata #1.3.38
The model has no metadata
> log chains #1.3.38
> log metadata #1.3.39
The model has no metadata
> log chains #1.3.39
> log metadata #1.3.40
The model has no metadata
> log chains #1.3.40
> log metadata #1.3.41
The model has no metadata
> log chains #1.3.41
> log metadata #1.3.42
The model has no metadata
> log chains #1.3.42
> log metadata #1.3.43
The model has no metadata
> log chains #1.3.43
> log metadata #1.3.44
The model has no metadata
> log chains #1.3.44
> log metadata #1.3.45
The model has no metadata
> log chains #1.3.45
> log metadata #1.3.46
The model has no metadata
> log chains #1.3.46
> log metadata #1.3.47
The model has no metadata
> log chains #1.3.47
> log metadata #1.3.48
The model has no metadata
> log chains #1.3.48
> log metadata #1.3.49
The model has no metadata
> log chains #1.3.49
> log metadata #1.3.50
The model has no metadata
> log chains #1.3.50
> log metadata #1.3.51
The model has no metadata
> log chains #1.3.51
> log metadata #1.3.52
The model has no metadata
> log chains #1.3.52
> log metadata #1.3.53
The model has no metadata
> log chains #1.3.53
> log metadata #1.3.54
The model has no metadata
> log chains #1.3.54
> log metadata #1.3.55
The model has no metadata
> log chains #1.3.55
> log metadata #1.3.56
The model has no metadata
> log chains #1.3.56
> log metadata #1.3.57
The model has no metadata
> log chains #1.3.57
> log metadata #1.3.58
The model has no metadata
> log chains #1.3.58
> log metadata #1.3.59
The model has no metadata
> log chains #1.3.59
> log metadata #1.3.60
The model has no metadata
> log chains #1.3.60
> log metadata #1.3.61
The model has no metadata
> log chains #1.3.61
> log metadata #1.3.62
The model has no metadata
> log chains #1.3.62
> log metadata #1.3.63
The model has no metadata
> log chains #1.3.63
> log metadata #1.3.64
The model has no metadata
> log chains #1.3.64
> log metadata #1.3.65
The model has no metadata
> log chains #1.3.65
> log metadata #1.3.66
The model has no metadata
> log chains #1.3.66
> log metadata #1.3.67
The model has no metadata
> log chains #1.3.67
> log metadata #1.3.68
The model has no metadata
> log chains #1.3.68
> log metadata #1.3.69
The model has no metadata
> log chains #1.3.69
> log metadata #1.3.70
The model has no metadata
> log chains #1.3.70
> log metadata #1.3.71
The model has no metadata
> log chains #1.3.71
> log metadata #1.3.72
The model has no metadata
> log chains #1.3.72
> log metadata #1.3.73
The model has no metadata
> log chains #1.3.73
> log metadata #!1
Metadata for 5d0o #!1
---
Title | BamABCDE complex, outer membrane β barrel assembly machinery entire
complex
Citation | Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z., Paterson, N.G.,
Stansfeld, P.J., Wang, Z., Zhang, Y., Wang, W., Dong, C. (2016). Structural
basis of outer membrane protein insertion by the BAM complex. Nature, 531,
47-52. PMID: 26901871. DOI: 10.1038/nature17199
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #!1
Chain information for 5d0o #!1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> log metadata #1.2.1
The model has no metadata
> log chains #1.2.1
> log metadata #1.2.2
The model has no metadata
> log chains #1.2.2
> log metadata #1.2.3
The model has no metadata
> log chains #1.2.3
> log metadata #1.2.4
The model has no metadata
> log chains #1.2.4
> log metadata #1.2.5
The model has no metadata
> log chains #1.2.5
> log metadata #1.2.6
The model has no metadata
> log chains #1.2.6
> log metadata #1.2.7
The model has no metadata
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> log metadata #1.2.8
The model has no metadata
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> log metadata #1.2.9
The model has no metadata
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> log metadata #1.2.10
The model has no metadata
> log chains #1.2.10
> log metadata #1.2.11
The model has no metadata
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> log metadata #1.2.12
The model has no metadata
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> log metadata #1.2.13
The model has no metadata
> log chains #1.2.13
> log metadata #1.2.14
The model has no metadata
> log chains #1.2.14
> log metadata #1.2.15
The model has no metadata
> log chains #1.2.15
> log metadata #1.2.16
The model has no metadata
> log chains #1.2.16
> log metadata #1.2.17
The model has no metadata
> log chains #1.2.17
> log metadata #1.2.18
The model has no metadata
> log chains #1.2.18
> log metadata #1.2.19
The model has no metadata
> log chains #1.2.19
> log metadata #1.2.20
The model has no metadata
> log chains #1.2.20
> log metadata #1.2.21
The model has no metadata
> log chains #1.2.21
> log metadata #1.2.22
The model has no metadata
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> log metadata #1.2.23
The model has no metadata
> log chains #1.2.23
> log metadata #1.2.24
The model has no metadata
> log chains #1.2.24
> log metadata #1.2.25
The model has no metadata
> log chains #1.2.25
> log metadata #1.2.26
The model has no metadata
> log chains #1.2.26
> log metadata #1.2.27
The model has no metadata
> log chains #1.2.27
> log metadata #1.2.28
The model has no metadata
> log chains #1.2.28
> log metadata #1.2.29
The model has no metadata
> log chains #1.2.29
> log metadata #1.2.30
The model has no metadata
> log chains #1.2.30
> log metadata #1.2.31
The model has no metadata
> log chains #1.2.31
> log metadata #1.2.32
The model has no metadata
> log chains #1.2.32
> log metadata #1.2.33
The model has no metadata
> log chains #1.2.33
> log metadata #1.2.34
The model has no metadata
> log chains #1.2.34
> log metadata #1.2.35
The model has no metadata
> log chains #1.2.35
> log metadata #1.2.36
The model has no metadata
> log chains #1.2.36
> log metadata #1.2.37
The model has no metadata
> log chains #1.2.37
> log metadata #1.2.38
The model has no metadata
> log chains #1.2.38
> log metadata #1.2.39
The model has no metadata
> log chains #1.2.39
> log metadata #1.2.40
The model has no metadata
> log chains #1.2.40
> log metadata #1.2.41
The model has no metadata
> log chains #1.2.41
> log metadata #1.2.42
The model has no metadata
> log chains #1.2.42
> log metadata #1.2.43
The model has no metadata
> log chains #1.2.43
> log metadata #1.2.44
The model has no metadata
> log chains #1.2.44
> log metadata #1.2.45
The model has no metadata
> log chains #1.2.45
> log metadata #1.2.46
The model has no metadata
> log chains #1.2.46
> log metadata #1.2.47
The model has no metadata
> log chains #1.2.47
> log metadata #1.2.48
The model has no metadata
> log chains #1.2.48
> log metadata #1.2.49
The model has no metadata
> log chains #1.2.49
> log metadata #1.2.50
The model has no metadata
> log chains #1.2.50
> log metadata #1.2.51
The model has no metadata
> log chains #1.2.51
> log metadata #1.2.52
The model has no metadata
> log chains #1.2.52
> log metadata #1.2.53
The model has no metadata
> log chains #1.2.53
> log metadata #1.2.54
The model has no metadata
> log chains #1.2.54
> log metadata #1.2.55
The model has no metadata
> log chains #1.2.55
> log metadata #1.2.56
The model has no metadata
> log chains #1.2.56
> log metadata #1.2.57
The model has no metadata
> log chains #1.2.57
> log metadata #1.2.58
The model has no metadata
> log chains #1.2.58
> log metadata #1.2.59
The model has no metadata
> log chains #1.2.59
> log metadata #1.2.60
The model has no metadata
> log chains #1.2.60
> log metadata #1.2.61
The model has no metadata
> log chains #1.2.61
> log metadata #1.2.62
The model has no metadata
> log chains #1.2.62
> log metadata #1.2.63
The model has no metadata
> log chains #1.2.63
> log metadata #1.2.64
The model has no metadata
> log chains #1.2.64
> log metadata #1.2.65
The model has no metadata
> log chains #1.2.65
> log metadata #1.2.66
The model has no metadata
> log chains #1.2.66
> log metadata #1.2.67
The model has no metadata
> log chains #1.2.67
> log metadata #1.2.68
The model has no metadata
> log chains #1.2.68
> log metadata #1.2.69
The model has no metadata
> log chains #1.2.69
> log metadata #1.2.70
The model has no metadata
> log chains #1.2.70
> log metadata #1.2.71
The model has no metadata
> log chains #1.2.71
> log metadata #1.2.72
The model has no metadata
> log chains #1.2.72
> log metadata #1.2.73
The model has no metadata
> log chains #1.2.73
> log metadata #1.3.1
The model has no metadata
> log chains #1.3.1
> log metadata #1.3.2
The model has no metadata
> log chains #1.3.2
> log metadata #1.3.3
The model has no metadata
> log chains #1.3.3
> log metadata #1.3.4
The model has no metadata
> log chains #1.3.4
> log metadata #1.3.5
The model has no metadata
> log chains #1.3.5
> log metadata #1.3.6
The model has no metadata
> log chains #1.3.6
> log metadata #1.3.7
The model has no metadata
> log chains #1.3.7
> log metadata #1.3.8
The model has no metadata
> log chains #1.3.8
> log metadata #1.3.9
The model has no metadata
> log chains #1.3.9
> log metadata #1.3.10
The model has no metadata
> log chains #1.3.10
> log metadata #1.3.11
The model has no metadata
> log chains #1.3.11
> log metadata #1.3.12
The model has no metadata
> log chains #1.3.12
> log metadata #1.3.13
The model has no metadata
> log chains #1.3.13
> log metadata #1.3.14
The model has no metadata
> log chains #1.3.14
> log metadata #1.3.15
The model has no metadata
> log chains #1.3.15
> log metadata #1.3.16
The model has no metadata
> log chains #1.3.16
> log metadata #1.3.17
The model has no metadata
> log chains #1.3.17
> log metadata #1.3.18
The model has no metadata
> log chains #1.3.18
> log metadata #1.3.19
The model has no metadata
> log chains #1.3.19
> log metadata #1.3.20
The model has no metadata
> log chains #1.3.20
> log metadata #1.3.21
The model has no metadata
> log chains #1.3.21
> log metadata #1.3.22
The model has no metadata
> log chains #1.3.22
> log metadata #1.3.23
The model has no metadata
> log chains #1.3.23
> log metadata #1.3.24
The model has no metadata
> log chains #1.3.24
> log metadata #1.3.25
The model has no metadata
> log chains #1.3.25
> log metadata #1.3.26
The model has no metadata
> log chains #1.3.26
> log metadata #1.3.27
The model has no metadata
> log chains #1.3.27
> log metadata #1.3.28
The model has no metadata
> log chains #1.3.28
> log metadata #1.3.29
The model has no metadata
> log chains #1.3.29
> log metadata #1.3.30
The model has no metadata
> log chains #1.3.30
> log metadata #1.3.31
The model has no metadata
> log chains #1.3.31
> log metadata #1.3.32
The model has no metadata
> log chains #1.3.32
> log metadata #1.3.33
The model has no metadata
> log chains #1.3.33
> log metadata #1.3.34
The model has no metadata
> log chains #1.3.34
> log metadata #1.3.35
The model has no metadata
> log chains #1.3.35
> log metadata #1.3.36
The model has no metadata
> log chains #1.3.36
> log metadata #1.3.37
The model has no metadata
> log chains #1.3.37
> log metadata #1.3.38
The model has no metadata
> log chains #1.3.38
> log metadata #1.3.39
The model has no metadata
> log chains #1.3.39
> log metadata #1.3.40
The model has no metadata
> log chains #1.3.40
> log metadata #1.3.41
The model has no metadata
> log chains #1.3.41
> log metadata #1.3.42
The model has no metadata
> log chains #1.3.42
> log metadata #1.3.43
The model has no metadata
> log chains #1.3.43
> log metadata #1.3.44
The model has no metadata
> log chains #1.3.44
> log metadata #1.3.45
The model has no metadata
> log chains #1.3.45
> log metadata #1.3.46
The model has no metadata
> log chains #1.3.46
> log metadata #1.3.47
The model has no metadata
> log chains #1.3.47
> log metadata #1.3.48
The model has no metadata
> log chains #1.3.48
> log metadata #1.3.49
The model has no metadata
> log chains #1.3.49
> log metadata #1.3.50
The model has no metadata
> log chains #1.3.50
> log metadata #1.3.51
The model has no metadata
> log chains #1.3.51
> log metadata #1.3.52
The model has no metadata
> log chains #1.3.52
> log metadata #1.3.53
The model has no metadata
> log chains #1.3.53
> log metadata #1.3.54
The model has no metadata
> log chains #1.3.54
> log metadata #1.3.55
The model has no metadata
> log chains #1.3.55
> log metadata #1.3.56
The model has no metadata
> log chains #1.3.56
> log metadata #1.3.57
The model has no metadata
> log chains #1.3.57
> log metadata #1.3.58
The model has no metadata
> log chains #1.3.58
> log metadata #1.3.59
The model has no metadata
> log chains #1.3.59
> log metadata #1.3.60
The model has no metadata
> log chains #1.3.60
> log metadata #1.3.61
The model has no metadata
> log chains #1.3.61
> log metadata #1.3.62
The model has no metadata
> log chains #1.3.62
> log metadata #1.3.63
The model has no metadata
> log chains #1.3.63
> log metadata #1.3.64
The model has no metadata
> log chains #1.3.64
> log metadata #1.3.65
The model has no metadata
> log chains #1.3.65
> log metadata #1.3.66
The model has no metadata
> log chains #1.3.66
> log metadata #1.3.67
The model has no metadata
> log chains #1.3.67
> log metadata #1.3.68
The model has no metadata
> log chains #1.3.68
> log metadata #1.3.69
The model has no metadata
> log chains #1.3.69
> log metadata #1.3.70
The model has no metadata
> log chains #1.3.70
> log metadata #1.3.71
The model has no metadata
> log chains #1.3.71
> log metadata #1.3.72
The model has no metadata
> log chains #1.3.72
> log metadata #1.3.73
The model has no metadata
> log chains #1.3.73
> log metadata #!1
Metadata for 5d0o #!1
---
Title | BamABCDE complex, outer membrane β barrel assembly machinery entire
complex
Citation | Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z., Paterson, N.G.,
Stansfeld, P.J., Wang, Z., Zhang, Y., Wang, W., Dong, C. (2016). Structural
basis of outer membrane protein insertion by the BAM complex. Nature, 531,
47-52. PMID: 26901871. DOI: 10.1038/nature17199
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #!1
Chain information for 5d0o #!1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
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> log metadata #!1
Metadata for 5d0o #!1
---
Title | BamABCDE complex, outer membrane β barrel assembly machinery entire
complex
Citation | Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z., Paterson, N.G.,
Stansfeld, P.J., Wang, Z., Zhang, Y., Wang, W., Dong, C. (2016). Structural
basis of outer membrane protein insertion by the BAM complex. Nature, 531,
47-52. PMID: 26901871. DOI: 10.1038/nature17199
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #!1
Chain information for 5d0o #!1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
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> log metadata #1.3.52
The model has no metadata
> log chains #1.3.52
> log metadata #1.3.53
The model has no metadata
> log chains #1.3.53
> log metadata #1.3.54
The model has no metadata
> log chains #1.3.54
> log metadata #1.3.55
The model has no metadata
> log chains #1.3.55
> log metadata #1.3.56
The model has no metadata
> log chains #1.3.56
> log metadata #1.3.57
The model has no metadata
> log chains #1.3.57
> log metadata #1.3.58
The model has no metadata
> log chains #1.3.58
> log metadata #1.3.59
The model has no metadata
> log chains #1.3.59
> log metadata #1.3.60
The model has no metadata
> log chains #1.3.60
> log metadata #1.3.61
The model has no metadata
> log chains #1.3.61
> log metadata #1.3.62
The model has no metadata
> log chains #1.3.62
> log metadata #1.3.63
The model has no metadata
> log chains #1.3.63
> log metadata #1.3.64
The model has no metadata
> log chains #1.3.64
> log metadata #1.3.65
The model has no metadata
> log chains #1.3.65
> log metadata #1.3.66
The model has no metadata
> log chains #1.3.66
> log metadata #1.3.67
The model has no metadata
> log chains #1.3.67
> log metadata #1.3.68
The model has no metadata
> log chains #1.3.68
> log metadata #1.3.69
The model has no metadata
> log chains #1.3.69
> log metadata #1.3.70
The model has no metadata
> log chains #1.3.70
> log metadata #1.3.71
The model has no metadata
> log chains #1.3.71
> log metadata #1.3.72
The model has no metadata
> log chains #1.3.72
> log metadata #1.3.73
The model has no metadata
> log chains #1.3.73
> save /Users/yyy/Desktop/bAL534K.cxs
——— End of log from Fri Oct 25 00:36:44 2024 ———
opened ChimeraX session
> swapaa #!1/A:534 LYS criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
5d0o #!1/A LYS 534: phi -106.2, psi 131.8 trans
Applying LYS rotamer (chi angles: -64.8 -178.7 -179.5 179.5) to 5d0o #!1/A LYS
534
No rotamers selected
[Repeated 1 time(s)]
> swapaa #!1/A:534 LYS criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
5d0o #!1/A LYS 534: phi -106.2, psi 131.8 trans
Applying LYS rotamer (chi angles: -64.8 -178.7 -179.5 179.5) to 5d0o #!1/A LYS
534
> style sel ball
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> show sel atoms
> view sel
> select sel :< 5
222 atoms, 222 bonds, 14 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 222 atom styles
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view sel
> close #1
[Repeated 1 time(s)]
> close #2
> open 5D0O
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> style stick
Changed 22815 atom styles
> show cartoons
> hide atoms
> select /A:24-809
12142 atoms, 12286 bonds, 786 residues, 1 model selected
> set bgColor white
> color sel dark gray
> lighting soft
> lighting simple
> lighting full
> swapaa mousemode /A:576 TYR
> swapaa mousemode /A:495 ASP
> hide sel atoms
> select clear
> select /A:576@CD1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 1 atom style
> hide sel atoms
> swapaa mousemode /A:428 PHE
> select /A:590
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> close )(*&±!@#|"@#
Expected a models specifier or a keyword
> close )(*&±!@#|"@#
Expected a models specifier or a keyword
> close )(*&±!@#|"@#
Expected a models specifier or a keyword
> close )(*&±!@#|"@#
Expected a models specifier or a keyword
> close )(*&±!@#|"@#
Expected a models specifier or a keyword
> close #1
> open 5D0Q
Summary of feedback from opening 5D0Q fetched from pdb
---
note | Fetching compressed mmCIF 5d0q from
http://files.rcsb.org/download/5d0q.cif
5d0q title:
BamACDE complex, outer membrane beta-barrel assembly machinery (BAM) complex
[more info...]
Chain information for 5d0q #1
---
Chain | Description | UniProt
A F | Outer membrane protein assembly factor BamA | BAMA_ECOLI 2-810
C G | Outer membrane protein assembly factor BamC | BAMC_ECOLI 2-344
D H | Outer membrane protein assembly factor BamD | BAMD_ECOLI 2-245
E I | Outer membrane protein assembly factor BamE | BAME_ECOLI 2-113
5d0q mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> show atoms
> hide atoms
> show atoms
> style stick
Changed 19900 atom styles
> show cartoons
> hide atoms
> close #1
> open 5D0Q format mmcif fromDatabase pdb
5d0q title:
BamACDE complex, outer membrane beta-barrel assembly machinery (BAM) complex
[more info...]
Chain information for 5d0q #1
---
Chain | Description | UniProt
A F | Outer membrane protein assembly factor BamA | BAMA_ECOLI 2-810
C G | Outer membrane protein assembly factor BamC | BAMC_ECOLI 2-344
D H | Outer membrane protein assembly factor BamD | BAMD_ECOLI 2-245
E I | Outer membrane protein assembly factor BamE | BAME_ECOLI 2-113
5d0q mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #1
> open 5D0O format mmcif fromDatabase pdb
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> hide atoms
> show atoms
> style stick
Changed 22815 atom styles
> show cartoons
> show atoms
> hide atoms
> select /A:24-809
12142 atoms, 12286 bonds, 786 residues, 1 model selected
> color sel cornflower blue
> color sel light gray
> color sel hot pink
> color sel orange
> color sel cyan
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style sel stick
Changed 12142 atom styles
> show sel cartoons
> hide sel atoms
> select clear
> style stick
Changed 22815 atom styles
> hide atoms
> show cartoons
> select /A:24-809
12142 atoms, 12286 bonds, 786 residues, 1 model selected
> color sel cyan
> set bgColor black
> swapaa mousemode /A:716 LYS
> set bgColor white
> lighting full
> lighting simple
> color sel light sea green
> swapaa mousemode /A:712 ALA
> color sel dark gray
> select clear
> swapaa mousemode /A:488 ASP
> swapaa mousemode /A:439 PHE
> swapaa mousemode /A:651 GLU
> select down
Nothing selected
> move -y 20
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> view sel
> swapaa mousemode /A:534 ASN
> undo
> close #1
> open 5D0O format mmcif fromDatabase pdb
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> style stick
Changed 22815 atom styles
> show atoms
> show cartoons
> hide atoms
> select /A:24-809
12142 atoms, 12286 bonds, 786 residues, 1 model selected
> color sel dark gray
> move -y20
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move -y 20
> select clear
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> view sel
> color sel blue
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> swapaa mousemode /A:534 ASN
[Repeated 8 time(s)]Drag select of 1 residues
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> close #1
> open 5D0O format mmcif fromDatabase pdb
5d0o title:
BamABCDE complex, outer membrane β barrel assembly machinery entire complex
[more info...]
Chain information for 5d0o #1
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI 1-810
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 1-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 1-344
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI 1-245
E | Outer membrane protein assembly factor BamE | BAME_ECOLI 1-113
> style stick
Changed 22815 atom styles
> show cartoons
> show atoms
> hide atoms
> select /A:24-809
12142 atoms, 12286 bonds, 786 residues, 1 model selected
> color sel dim gray
> color sel dark gray
> select clear
> swapaa mousemode /A:443 HIS
> move -y 20
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
Drag select of 2 atoms, 2 residues, 2 bonds
> select /A:534
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
/A ASN 534: phi -106.2, psi 131.8 trans
Changed 438 bond radii
> swapaa #!1/A:534 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
5d0o #!1/A ASN 534: phi -106.2, psi 131.8 trans
Applying LYS rotamer (chi angles: -64.8 -178.7 -179.5 179.5) to 5d0o #!1/A LYS
534
> move -y 20
> view sel
> select sel :< 5
222 atoms, 222 bonds, 14 residues, 1 model selected
> select /A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> select sel :< 5
293 atoms, 293 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> view sel
> hbonds sel reveal true
25 hydrogen bonds found
> color sel hot pink
> color sel byhetero
> color sel lime
> color sel light sea green
> color sel cyan
> color sel orange
> color sel cornflower blue
> color sel forest green
> color sel hot pink
> color sel yellow
> color sel blue
> color sel forest green
> color sel purple
> color sel magenta
> color sel forest green
> color sel yellow
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel medium spring green
> color sel turquoise
> color sel cornflower blue
> color sel blue
> color sel light salmon
> color sel salmon
> color sel peru
> color sel lime
> color sel dark salmon
> color sel light salmon
> color sel salmon
> color sel dark salmon
> color sel light salmon
> color sel tomato
> color sel brown
> color sel coral
> color sel orange
> color sel dark orange
> color sel sandy brown
> ui tool show "Color Actions"
> color sel light salmon
> color sel salmon
> color sel byhetero
> select /A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> color sel forest green
> color sel cyan
> color sel cornflower blue
> color sel lime
> color sel blue
> color sel magenta
> color sel orange
> color sel yellow
> color sel cyan
> view sel
> hbonds sel reveal true
3 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
3 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
3 hydrogen bonds found
> hbonds sel reveal true
3 hydrogen bonds found
> ui tool show H-Bonds
[Repeated 1 time(s)]
> hbonds sel showDist true saltOnly true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5d0o
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 534 NZ /A GLU 650 OE2 no hydrogen 2.210 N/A
1 hydrogen bonds found
> color sel hot pink
> color sel red
> color sel lime
> ui tool show H-Bonds
> select /A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
[Repeated 1 time(s)]
> hbonds sel color #0f26ef showDist true saltOnly true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5d0o
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 534 NZ /A GLU 650 OE2 no hydrogen 2.210 N/A
1 hydrogen bonds found
> select /A:650
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel cyan
> select clear
> save /Users/yyy/Desktop/image1.png supersample 3
> save /Users/yyy/Desktop/bamAK534-E650.cxs
——— End of log from Sun Oct 27 20:44:36 2024 ———
opened ChimeraX session
> select ::name="ASP"
1427 atoms, 1317 bonds, 119 residues, 1 model selected
> ui tool show "Side View"
> show sel atoms
> color sel yellow
> color sel orange
> color sel magenta
> color sel cornflower blue
> color sel magenta
> hbonds sel reveal true
179 hydrogen bonds found
> color sel byhetero
> select /A:534
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select /A:650
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel byhetero
> select ::name="ASP"
1427 atoms, 1317 bonds, 11 pseudobonds, 119 residues, 2 models selected
> color (#!1 & sel) dark gray
> ~hbonds
> select clear
> select /A:650
15 atoms, 14 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
> select /A:610
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel lime
> color sel byhetero
> select /A:610
22 atoms, 21 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /A:650
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
[Repeated 1 time(s)]
> hbonds sel color #0f26ef showDist true saltOnly true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5d0o
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 534 NZ /A GLU 650 OE2 no hydrogen 2.210 N/A
/A LYS 610 NZ /A GLU 650 OE1 /A LYS 610 HZ3 2.716 2.101
2 hydrogen bonds found
> view sel
> move -y 10
> move y 5
[Repeated 1 time(s)]
> save /Users/yyy/Desktop/image2.png supersample 3
> save /Users/yyy/Desktop/bamAK534-Glu.E.650-K610.cxs
——— End of log from Sun Oct 27 21:22:03 2024 ———
opened ChimeraX session
> open "/Users/yangy36/Desktop/ChimeraX Structure Data/bamAN534K and E
> Glu650/bamAK534-Glu.E.650-K610.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Failed opening file /Users/yangy36/Desktop/ChimeraX Structure Data/bamAN534K
and E Glu650/bamAK534-Glu.E.650-K610.cxs:
'list' object has no attribute 'values'
> open "/Users/yangy36/Desktop/ChimeraX Structure Data/bamAN534K and E
> Glu650/bamAK534-E650.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Users/yangy36/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Failed opening file /Users/yangy36/Desktop/ChimeraX Structure Data/bamAN534K
and E Glu650/bamAK534-E650.cxs:
'list' object has no attribute 'values'
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,2
Processor Name: 6-Core Intel Core i7
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.47f3
Software:
System Software Overview:
System Version: macOS 13.7.3 (22H417)
Kernel Version: Darwin 22.6.0
Time since boot: 5 days, 23 hours, 59 minutes
Graphics/Displays:
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C981AA-042
VBIOS Version: 113-C9819A14GP-003
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.8
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.4
ChimeraX-AtomicLibrary: 8.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5.dev202210050721
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.1
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.1.0
filelock: 3.7.1
fonttools: 4.37.4
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.1
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
prompt-toolkit: 3.0.31
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.4
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.2.1
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.5.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.3.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.8.1
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
comment:2 by , 9 months ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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