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Opened 2 years ago
Closed 2 years ago
#8938 closed defect (not a bug)
FindHBond: accPhiPsi arguments
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V. natriegens\Karo
> HOMO\03_05_23_Sup_Bac7.cxs" format session
Log from Wed May 3 13:01:05 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V. natriegens\Karo
> HOMO\03_05_23_Sup_Bac7.cxs" format session
Log from Wed May 3 12:46:25 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V.
> natriegens\Figures\ChimeraX files\28_04_23_TT_VN_EC5.cxs" format session
Log from Fri Apr 28 15:32:02 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/27_04_23_Sup_Bac7.cxs"
Log from Thu Apr 27 10:15:46 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/karol/OneDrive/Desktop/PhD HOMO/13_04_23_Sup_Bac7.cxs"
Log from Thu Apr 13 12:47:24 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V.
> natriegens\Figures\ChimeraX files\12_04_23_Sup_Bac7.cxs" format session
Log from Wed Apr 12 15:45:42 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V.
> natriegens\Figures\ChimeraX files\12_04_23_Sup_Bac7.cxs" format session
Log from Wed Apr 12 15:36:17 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V.
> natriegens\Figures\ChimeraX files\06_04_23_Sup_Bac7.cxs" format session
Log from Thu Apr 6 14:50:08 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Karo\Desktop\Karo\Veröffentlichungen\V.
> natriegens\Figures\ChimeraX files\27_03_23_Figure4.cxs" format session
Log from Mon Mar 27 15:28:47 2023
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting simple
> lighting shadows false
> lighting depthCue false
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 mk 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed
> color name f02silber #F6FAFC
Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5
> color name f04beige #F3F3A9
Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9
> color name f05blau #00AAFF
Color 'f05blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> color name f06gelb #f2b701
Color 'f06gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f07orange #e68310
Color 'f07orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f08rotorange #FF6A25
Color 'f08rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f09rot #dd3d2d
Color 'f09rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f10lachs #f97b72
Color 'f10lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f11flieder #D57AD5
Color 'f11flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f12violett #cf1c90
Color 'f12violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f13lila #4b148f
Color 'f13lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f14dunkelblau #1e1edc
Color 'f14dunkelblau' is opaque: rgb(11.8%, 11.8%, 86.3%) hex: #1e1edc
> color name f15cyan #60e2d6
Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6
> color name f16blaugrün #30ffa6
Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6
> color name f17grün #00dc00
Color 'f17grün' is opaque: rgb(0%, 86.3%, 0%) hex: #00dc00
> color name f18hellgrau #DCDCDC
Color 'f18hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f19grau #B2B2B2
Color 'f19grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f20anthrazit #323F45
Color 'f20anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45
> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'
> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias undurch save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground false
> alias foto save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
> alias undust surface undust #$1
> alias dust5 surface dust #$1 size 5
> alias dust6 surface dust #$1 size 6
> alias dust7 surface dust #$1 size 7
> alias dust8 surface dust #$1 size 8
> alias dust9 surface dust #$1 size 9
> alias dust10 surface dust #$1 size 10
> alias dust11 surface dust #$1 size 11
> alias dust12 surface dust #$1 size 12
> alias dust13 surface dust #$1 size 13
> alias dust14 surface dust #$1 size 14
> alias dust15 surface dust #$1 size 15
> alias dust20 surface dust #$1 size 20
> alias dust25 surface dust #$1 size 25
> alias dust30 surface dust #$1 size 30
> alias dust35 surface dust #$1 size 35
> alias dust40 surface dust #$1 size 40
> alias dust45 surface dust #$1 size 45
> alias dust50 surface dust #$1 size 50
> alias spalt volume splitbyzone #$1
> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Vibrio natriegens 50S_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Vibrio natriegens 50S_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 1 in chain
Skipping residue with duplicate label_seq_id 1 in chain
Skipping residue with duplicate label_seq_id 1 in chain
Skipping residue with duplicate label_seq_id 1 in chain
Skipping residue with duplicate label_seq_id 1 in chain
864 messages similar to the above omitted
Expected gap or connection between ALA /Y:63 and A /B:64
Skipping residue with duplicate label_seq_id 66 in chain U
Skipping residue with duplicate label_seq_id 66 in chain U
Skipping residue with duplicate label_seq_id 66 in chain U
Skipping residue with duplicate label_seq_id 66 in chain U
Skipping residue with duplicate label_seq_id 66 in chain U
1026 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Vibrio natriegens 50S_23.cif #1
---
Chain | Description
3 | No description available
A | No description available
B | No description available
V | No description available
Z | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Tyr16_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Tyr16_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Tyr16_23.cif #2
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Arg7_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Arg7_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Arg7_23.cif #3
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Arg8_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Arg8_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Arg8_23.cif #4
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Ile6_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Ile6_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Arg3_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Arg3_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Arg3_23.cif #6
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Arg1_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Arg1_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Arg1_23.cif #7
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/BAC5_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/BAC5_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for BAC5_23.cif #8
---
Chain | Description
9 | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Phe15_1_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Phe15_1_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Phe15_2_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Phe15_2_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Phe15_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Phe15_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Sur_Phe15_23.cif #11
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Sur_Arg7_Arg8_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Sur_Arg7_Arg8_23.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide cartoons
> show atoms
> hide atoms
> show atoms
> style sphere
Changed 68219 atom styles
> style stick
Changed 68219 atom styles
> color #1 #cccccc transparency 0
> set bgColor white
> lighting simple
> lighting gentle
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting gentle
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting gentle
> hide #!1 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting model multishadow true
Missing or invalid "models" argument: invalid models specifier
> lighting multiShadow 0
> lighting multiShadow 25
> lighting multiShadow 20
> color #2 #cccccc transparency 0
> color #2 #aa55aa transparency 0
> color #2 #a5a5a5 transparency 0
> color #3 #a5a5a5 transparency 0
> color #4 #a5a5a5 transparency 0
> color #5 #a5a5a5 transparency 0
> color #6 #a5a5a5 transparency 0
> color #7 #a5a5a5 transparency 0
> lighting multiShadow 10
> color #8 #22ee77 transparency 0
> color #8 #2e7d66 transparency 0
> color #9 #a5a5a5 transparency 0
> color #10 #a5a5a5 transparency 0
> color #11 #a5a5a5 transparency 0
> color #12 #a5a5a5 transparency 0
> lighting flat
> lighting multiShadow 5
> lighting multiShadow 512
> lighting multiShadow 800
> lighting multiShadow 1024
> lighting multiShadow 600
> lighting multiShadow 1
> lighting multiShadow 800
> show #!1 models
> hide #!1 models
> show #!1 models
> lighting multiShadow 512
> lighting multiShadow 1000
> hide #!1 models
> lighting multiShadow 800
> lighting multiShadow 600
> lighting multiShadow 512
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/27_03_23_Figure4.cxs" includeMaps true
> ui tool show H-Bonds
> hbonds intraModel false intraMol false intraRes false reveal true
101 hydrogen bonds found
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/27_03_23_Figure4.cxs" includeMaps true
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
155 atoms, 164 bonds, 17 residues, 1 model selected
> ui tool show Contacts
> ui tool show Matchmaker
> ui tool show H-Bonds
> hbonds intraModel false intraMol false intraRes false reveal true
101 hydrogen bonds found
> hbonds interModel false intraModel false saltOnly true intraMol false
> intraRes false reveal true
0 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false reveal true
101 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false reveal true
101 hydrogen bonds found
> color #13 black models transparency 0
> color #13 #424242 models transparency 0
> color #13 #545454 models transparency 0
> color #13 #343434 models transparency 0
> graphics silhouettes true color black width 1.5
> hbonds sel
29 hydrogen bonds found
> hbonds sel intraModel false
28 hydrogen bonds found
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/27_03_23_Figure4.cxs" includeMaps true
——— End of log from Mon Mar 27 15:28:47 2023 ———
opened ChimeraX session
> ~select #8
Nothing selected
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/BAC7_23.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/BAC7_23.cif
---
warnings | Unknown polymer entity '55' near line 37
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for BAC7_23.cif #14
---
Chain | Description
1y | No description available
> select #14
149 atoms, 152 bonds, 18 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> color #14 #bbee11 transparency 0
> color #14 #be1622 transparency 0
> ~select #14
Nothing selected
> select add #14/1y:101@O
1 atom, 1 residue, 1 model selected
> delete sel
> select add #14/1y:102@O
1 atom, 1 residue, 1 model selected
> delete sel
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/06_04_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Thu Apr 6 14:50:08 2023 ———
opened ChimeraX session
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/A2439.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/A2439.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/C2438.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/C2438.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/C2559.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/C2559.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/G2047.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/G2047.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/G2491.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/G2491.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/U2541.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/U2541.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
> color #15 #a5a5a5 transparency 0
> color #16 #a5a5a5 transparency 0
> color #17 #a5a5a5 transparency 0
> color #18 #a5a5a5 transparency 0
> color #19 #a5a5a5 transparency 0
> color #20 #a5a5a5 transparency 0
> hbonds intraModel false intraMol false intraRes false reveal true
175 hydrogen bonds found
> show #8 models
> hide #8 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> hide #3 models
> hide #4 models
> hide #5 models
> color #13 black models transparency 0
> color #13 #5e5e5e models transparency 0
> color #13 #636363 models transparency 0
> color #13 #7d7d7d models transparency 0
> color #13 #585858 models transparency 0
> color #13 #424242 models transparency 0
> lighting multiShadow 512
> lighting depthCue false
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04_23_Sup_Bac7.cxs" includeMaps true
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> show #4 models
> hide #4 models
> color #2 #f9f9f9 transparency 0
> color #3 #f9f9f9 transparency 0
> color #4 #f9f9f9 transparency 0
> show #4 models
> color #5 #f9f9f9 transparency 0
> show #5 models
> color #6 #f9f9f9 transparency 0
> show #6 models
> hide #6 models
> color #9 #f9f9f9 transparency 0
> show #9 models
> hide #9 models
> color #10 #f9f9f9 transparency 0
> color #11 #f9f9f9 transparency 0
> color #12 #f9f9f9 transparency 0
> show #12 models
> show #11 models
> hide #11 models
> hide #12 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/PDB file/Bac7 Umgebung VN/K_A2439_C2438.cif"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Figures/PDB
file/Bac7 Umgebung VN/K_A2439_C2438.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for K_A2439_C2438.cif #21
---
Chain | Description
A | No description available
> hide #21 models
> show #21 models
> hide #21 models
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Wed Apr 12 15:36:17 2023 ———
opened ChimeraX session
> hbonds intraModel false intraMol false intraRes false reveal true color
> black radius 0.04 dashes 6
184 hydrogen bonds found
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Wed Apr 12 15:45:42 2023 ———
opened ChimeraX session
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Stick.tiff" format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> style #14 sphere
Changed 147 atom styles
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Sphere.tiff" format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> hide #14 models
> show #14 models
> style #14 stick
Changed 147 atom styles
> show #15 models
> show #16 models
> hide #16 models
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Stick_A2439.tiff" format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> show #16 models
> hide #15 models
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Stick_C2438.tiff" format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> hide #16 models
> show #17 models
> show #18 models
> hide #18 models
> show #19 models
> show #20 models
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Stick_Residues in the back.tiff" format tiff width 4000 height 3000
> supersample 4 transparentBackground true
> show #18 models
> hide #19 models
> hide #20 models
> hide #17 models
> foto
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/12_04 2 Figure 4 Draft Only Bac7
> Stick_G2047.tiff" format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> show #19 models
> show #20 models
> show #17 models
> show #16 models
> show #15 models
> show #2 models
> show #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #9 models
> hide #9 models
> show #12 models
> hide #12 models
> show #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #11 models
> hide #3 models
> color #2 #aa55aa transparency 0
> color #2 #a5a5a5 transparency 0
> color #11 #aa55aa transparency 0
> color #11 #a5a5a5 transparency 0
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/13_04_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Thu Apr 13 12:47:24 2023 ———
opened ChimeraX session
> open 7K00
Summary of feedback from opening 7K00 fetched from pdb
---
notes | Fetching compressed mmCIF 7k00 from
http://files.rcsb.org/download/7k00.cif
Fetching CCD PAR from http://ligand-expo.rcsb.org/reports/P/PAR/PAR.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD SPD from http://ligand-expo.rcsb.org/reports/S/SPD/SPD.cif
Fetching CCD SPM from http://ligand-expo.rcsb.org/reports/S/SPM/SPM.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
Fetching CCD G7M from http://ligand-expo.rcsb.org/reports/G/G7M/G7M.cif
Fetching CCD 2MG from http://ligand-expo.rcsb.org/reports/2/2MG/2MG.cif
Fetching CCD 5MC from http://ligand-expo.rcsb.org/reports/5/5MC/5MC.cif
Fetching CCD 4OC from http://ligand-expo.rcsb.org/reports/4/4OC/4OC.cif
Fetching CCD UR3 from http://ligand-expo.rcsb.org/reports/U/UR3/UR3.cif
Fetching CCD MA6 from http://ligand-expo.rcsb.org/reports/M/MA6/MA6.cif
Fetching CCD IAS from http://ligand-expo.rcsb.org/reports/I/IAS/IAS.cif
Fetching CCD D2T from http://ligand-expo.rcsb.org/reports/D/D2T/D2T.cif
Fetching CCD 1MG from http://ligand-expo.rcsb.org/reports/1/1MG/1MG.cif
Fetching CCD 5MU from http://ligand-expo.rcsb.org/reports/5/5MU/5MU.cif
Fetching CCD 6MZ from http://ligand-expo.rcsb.org/reports/6/6MZ/6MZ.cif
Fetching CCD 3TD from http://ligand-expo.rcsb.org/reports/3/3TD/3TD.cif
Fetching CCD OMG from http://ligand-expo.rcsb.org/reports/O/OMG/OMG.cif
Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif
Fetching CCD OMC from http://ligand-expo.rcsb.org/reports/O/OMC/OMC.cif
Fetching CCD 2MA from http://ligand-expo.rcsb.org/reports/2/2MA/2MA.cif
Fetching CCD OMU from http://ligand-expo.rcsb.org/reports/O/OMU/OMU.cif
Fetching CCD MEQ from http://ligand-expo.rcsb.org/reports/M/MEQ/MEQ.cif
Fetching CCD 4D4 from http://ligand-expo.rcsb.org/reports/4/4D4/4D4.cif
Fetching CCD MS6 from http://ligand-expo.rcsb.org/reports/M/MS6/MS6.cif
7k00 title:
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]
Chain information for 7k00 #22
---
Chain | Description | UniProt
0 | 50S ribosomal protein L33 | D7Z9P0_ECOLX
1 | 50S ribosomal protein L34 | RL34_ECO45
2 | 50S ribosomal protein L35 | D7Z814_ECOLX
3 | 50S ribosomal protein L36 | A0A0E2L017_ECOU3
4 | 50S ribosomal protein L31 | D7ZFP6_ECOLX
5 | E-site tRNA |
A | 16S rRNA |
B | 30S ribosomal protein S2 | D7ZK99_ECOLX
C | 30S ribosomal protein S3 | RS3_ECO45
D | 30S ribosomal protein S4 | D7Z9H7_ECOLX
E | 30S ribosomal protein S5 | D7Z9H2_ECOLX
F | 30S ribosomal protein S6 | RS6_ECOLI
G | 30S ribosomal protein S7 | A0A5Q2GFB5_ECOLX
H | 30S ribosomal protein S8 | D7Z9G9_ECOLX
I | 30S ribosomal protein S9 | D7ZES9_ECOLX
J | 30S ribosomal protein S10 | D7Z9F4_ECOLX
K | 30S ribosomal protein S11 | S1ELC2_ECOLX
L | 30S ribosomal protein S12 | I2UHF1_ECOLX
M | 30S ribosomal protein S13 | H4UQ02_ECOLX
N | 30S ribosomal protein S14 | D7Z9G8_ECOLX
O | 30S ribosomal protein S15 | D7ZEL4_ECOLX
P | 30S ribosomal protein S16 | RS16_ECO45
Q | 30S ribosomal protein S17 | D7Z9G4_ECOLX
R | 30S ribosomal protein S18 | A0A0E2KXL3_ECOU3
S | 30S ribosomal protein S19 | D7Z9F9_ECOLX
T | 30S ribosomal protein S20 | D7ZAS2_ECOLX
U | 30S ribosomal protein S21 | A0A0E2L2J1_ECOU3
X | mRNA |
Y | A-site tRNA-val |
Z | P-site tRNA-fMet |
a | 23S rRNA |
b | 5S rRNA |
c | 50S ribosomal protein L2 | RL2_ECOLI
d | 50S ribosomal protein L3 | I2X6U5_ECOLX
e | 50S ribosomal protein L4 | D7Z9F6_ECOLX
f | 50S ribosomal protein L5 | D7Z9G7_ECOLX
g | 50S ribosomal protein L6 | D7Z9H0_ECOLX
h | 50S ribosomal protein L9 | D7ZI15_ECOLX
i | 50S ribosomal protein L13 | D7ZET0_ECOLX
j | 50S ribosomal protein L14 | D7Z9G5_ECOLX
k | 50S ribosomal protein L15 | A0A037Y8L6_ECOLX
l | 50S ribosomal protein L16 | L4V2J8_ECOLX
m | 50S ribosomal protein L17 | D6I1Y5_ECOLX
n | 50S ribosomal protein L18 | D7Z9H1_ECOLX
o | 50S ribosomal protein L19 | D7ZKU3_ECOLX
p | 50S ribosomal protein L20 | RL20_ECO45
q | 50S ribosomal protein L21 | D7ZEN7_ECOLX
r | 50S ribosomal protein L22 | D7Z9G0_ECOLX
s | 50S ribosomal protein L23 | D7X2Z9_ECOLX
t | 50S ribosomal protein L24 | D7Z9G6_ECOLX
u | 50S ribosomal protein L25 | D7XH79_ECOLX
v | 50S ribosomal protein L27 | RL27_ECOLI
w | 50S ribosomal protein L28 | S0YB49_ECOLX
x | 50S ribosomal protein L29 | D7Z9G3_ECOLX
y | 50S ribosomal protein L30 | D7Z9H3_ECOLX
z | 50S ribosomal protein L32 | D7ZGG2_ECOLX
Non-standard residues in 7k00 #22
---
MG — magnesium ion
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
ZN — zinc ion
> hide #2,7,11,14-20#!22 surfaces
> hide #2,7,11,14-20#!22 atoms
> show #2,7,11,14-20#!22 cartoons
> open 5F8K
Summary of feedback from opening 5F8K fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue
template for A /2A:2801A
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2A:2801A
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2B:2
notes | Fetching compressed mmCIF 5f8k from
http://files.rcsb.org/download/5f8k.cif
Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif
Fetching CCD 7MG from http://ligand-expo.rcsb.org/reports/7/7MG/7MG.cif
Fetching CCD M2G from http://ligand-expo.rcsb.org/reports/M/M2G/M2G.cif
Fetching CCD 0TD from http://ligand-expo.rcsb.org/reports/0/0TD/0TD.cif
Fetching CCD 4SU from http://ligand-expo.rcsb.org/reports/4/4SU/4SU.cif
5f8k title:
Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus
thermophilus 70S ribosome [more info...]
Chain information for 5f8k #23
---
Chain | Description | UniProt
10 20 | 50S ribosomal protein L27 | RL27_THET8
11 21 | 50S ribosomal protein L28 | RL28_THET8
12 22 | 50S ribosomal protein L29 | RL29_THET8
13 23 | 50S ribosomal protein L30 | RL30_THET8
14 24 | 50S ribosomal protein L31 | RL31_THET8
15 25 | 50S ribosomal protein L32 | RL32_THET8
16 26 | 50S ribosomal protein L33 | RL33_THET8
17 27 | 50S ribosomal protein L34 | RL34_THET8
18 28 | 50S ribosomal protein L35 | RL35_THET8
19 29 | 50S ribosomal protein L36 | RL36_THET8
1A 2A | 23S ribosomal RNA |
1B 2B | 5S ribosomal RNA |
1D 2D | 50S ribosomal protein L2 | RL2_THET8
1E 2E | 50S ribosomal protein L3 | RL3_THET8
1F 2F | 50S ribosomal protein L4 | RL4_THET8
1G 2G | 50S ribosomal protein L5 | RL5_THET8
1H 2H | 50S ribosomal protein L6 | RL6_THET8
1I 2I | 50S ribosomal protein L9 | RL9_THET8
1N 2N | 50S ribosomal protein L13 | RL13_THET8
1O 2O | 50S ribosomal protein L14 | RL14_THET8
1P 2P | 50S ribosomal protein L15 | RL15_THET8
1Q 2Q | 50S ribosomal protein L16 | RL16_THET8
1R 2R | 50S ribosomal protein L17 | RL17_THET8
1S 2S | 50S ribosomal protein L18 | RL18_THET8
1T 2T | 50S ribosomal protein L19 | RL19_THET8
1U 2U | 50S ribosomal protein L20 | RL20_THET8
1V 2V | 50S ribosomal protein L21 | RL21_THET8
1W 2W | 50S ribosomal protein L22 | RL22_THET8
1X 2X | 50S ribosomal protein L23 | RL23_THET8
1Y 2Y | 50S ribosomal protein L24 | RL24_THET8
1Z 2Z | 50S ribosomal protein L25 | RL25_THET8
1a 2a | 16S ribosomal RNA |
1b 2b | 30S ribosomal protein S2 | RS2_THET8
1c 2c | 30S ribosomal protein S3 | RS3_THET8
1d 2d | 30S ribosomal protein S4 | RS4_THET8
1e 2e | 30S ribosomal protein S5 | RS5_THET8
1f 2f | 30S ribosomal protein S6 | RS6_THET8
1g 2g | 30S ribosomal protein S7 | RS7_THET8
1h 2h | 30S ribosomal protein S8 | RS8_THET8
1i 2i | 30S ribosomal protein S9 | RS9_THET8
1j 2j | 30S ribosomal protein S10 | RS10_THET8
1k 2k | 30S ribosomal protein S11 | RS11_THET8
1l 2l | 30S ribosomal protein S12 | RS12_THET8
1m 2m | 30S ribosomal protein S13 | RS13_THET8
1n 2n | 30S ribosomal protein S14 type Z | RS14Z_THET8
1o 2o | 30S ribosomal protein S15 | RS15_THET8
1p 2p | 30S ribosomal protein S16 | RS16_THET8
1q 2q | 30S ribosomal protein S17 | RS17_THET8
1r 2r | 30S ribosomal protein S18 | RS18_THET8
1s 2s | 30S ribosomal protein S19 | RS19_THET8
1t 2t | 30S ribosomal protein S20 | RS20_THET8
1u 2u | 30S ribosomal protein Thx | RSHX_THET8
1v 2v | mRNA |
1x 2x | tRNAiMet |
1y 2y | Cathelicidin-3 | CTHL3_BOVIN
Non-standard residues in 5f8k #23
---
K — potassium ion
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
5f8k mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #!22 models
> view
> hide #!23 models
> show #!23 models
> select #23
296108 atoms, 313647 bonds, 17182 pseudobonds, 28376 residues, 4 models
selected
> close #23
> open "C:/Users/karol/OneDrive/Desktop/PhD HOMO/Bac7_5F8K_Orientation to
> Overview.cif"
Summary of feedback from opening C:/Users/karol/OneDrive/Desktop/PhD
HOMO/Bac7_5F8K_Orientation to Overview.cif
---
warnings | Unknown polymer entity '1' near line 37
Unknown polymer entity '27' near line 61909
Unknown polymer entity '53' near line 62372
Unknown polymer entity '2' near line 62545
Unknown polymer entity '28' near line 65120
50 messages similar to the above omitted
Skipping residue with duplicate label_seq_id 17 in chain 1x
Skipping residue with duplicate label_seq_id 129 in chain 1a
Skipping residue with duplicate label_seq_id 189 in chain 1a
Skipping residue with duplicate label_seq_id 189 in chain 1a
Skipping residue with duplicate label_seq_id 1001 in chain 1a
4 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for Bac7_5F8K_Orientation to Overview.cif #23
---
Chain | Description
10 | No description available
11 | No description available
12 | No description available
13 | No description available
14 | No description available
15 | No description available
16 | No description available
17 | No description available
18 | No description available
19 | No description available
1A | No description available
1B | No description available
1D | No description available
1E | No description available
1F | No description available
1G | No description available
1H | No description available
1I | No description available
1N | No description available
1O | No description available
1P | No description available
1Q | No description available
1R | No description available
1S | No description available
1T | No description available
1U | No description available
1V | No description available
1W | No description available
1X | No description available
1Y | No description available
1Z | No description available
1a | No description available
1b | No description available
1c | No description available
1d | No description available
1e | No description available
1f | No description available
1g | No description available
1h | No description available
1i | No description available
1j | No description available
1k | No description available
1l | No description available
1m | No description available
1n | No description available
1o | No description available
1p | No description available
1q | No description available
1r | No description available
1s | No description available
1t | No description available
1u | No description available
1v | No description available
1x | No description available
1y | No description available
> hide #2 models
> hide #7 models
> hide #11 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
Drag select of 3355 atoms
> delete sel
Drag select of 382 atoms
> delete sel
Drag select of 28 atoms
> delete sel
> select add #23/2A:3967@MG
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of 1 atoms
> delete sel
> mmaker #23 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 Vibrio natriegens 50S_23.cif, chain 3 (#1) with
Bac7_5F8K_Orientation to Overview.cif, chain 18 (#23), sequence alignment
score = 19.8
RMSD between 5 pruned atom pairs is 0.204 angstroms; (across all 5 pairs:
0.204)
> show #!1 models
> select #23
147924 atoms, 156763 bonds, 8 pseudobonds, 14189 residues, 2 models selected
> hide sel surfaces
> show sel atoms
> hide sel cartoons
> hide #!1 models
> hide sel surfaces
> show sel atoms
> hide sel cartoons
> hide sel surfaces
> style sel stick
Changed 147924 atom styles
> save "C:/Users/karol/OneDrive/Desktop/PhD HOMO/27_04_23_Sup_Bac7.cxs"
> includeMaps true
——— End of log from Thu Apr 27 10:15:46 2023 ———
opened ChimeraX session
> close #23
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/TT Bac7 Sur.pdb"
Chain information for TT Bac7 Sur.pdb #23
---
Chain | Description
1 | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/VN Bac7 Sur.pdb"
Chain information for VN Bac7 Sur.pdb #24
---
Chain | Description
A | No description available
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/EC Bac7 Sur.pdb"
Chain information for EC Bac7 Sur.pdb #25
---
Chain | Description
a | No description available
> show #8 models
> hide #8 models
> delete pseudobonds
> select #23
637 atoms, 721 bonds, 29 residues, 1 model selected
> select #24
528 atoms, 596 bonds, 24 residues, 1 model selected
> select #25
530 atoms, 579 bonds, 25 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> select #24
528 atoms, 596 bonds, 24 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select #23
637 atoms, 721 bonds, 29 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 637 atom styles
> select #24
528 atoms, 596 bonds, 24 residues, 1 model selected
> style sel stick
Changed 528 atom styles
> select #25
530 atoms, 579 bonds, 25 residues, 1 model selected
> style sel stick
Changed 530 atom styles
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 507 atom styles
> hide sel surfaces
> hide sel cartoons
Drag select of 1049 atoms, 1112 bonds, 144 shapes
> style sel stick
Changed 1069 atom styles
> style sel stick
Changed 1069 atom styles
> style sel stick
Changed 1069 atom styles
> hide sel surfaces
> hide sel cartoons
[Repeated 8 time(s)]
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel surfaces
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 942 atom styles
> select #24
528 atoms, 596 bonds, 24 residues, 1 model selected
> select #23
637 atoms, 721 bonds, 29 residues, 1 model selected
> ~select #23
Nothing selected
> color #23 #ffaa7f transparency 0
> color #23 #ffaaff transparency 0
> color #23 #fed8ff transparency 0
> color #23 #e9c6ea transparency 0
> color #23 #d7b7d8 transparency 0
> color #23 #ddbcde transparency 0
> color #24 #cccccc transparency 0
> color #25 #0055ff transparency 0
> color #25 #93c7ff transparency 0
> color #25 #bbd5ff transparency 0
> color #25 #b1c9f1 transparency 0
> color #25 #a0b6da transparency 0
> color #25 #94a9ca transparency 0
> color #25 #7687a1 transparency 0
> color #23 #bca0bd transparency 0
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V.
> natriegens/Figures/ChimeraX files/28_04_23_TT_VN_EC5.cxs" includeMaps true
——— End of log from Fri Apr 28 15:32:02 2023 ———
opened ChimeraX session
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/Spheres.pdb"
> open 5F8K
Summary of feedback from opening 5F8K fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue
template for A /2A:2801A
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2A:2801A
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2B:2
5f8k title:
Crystal structure of the Bac7(1-16) antimicrobial peptide bound to the Thermus
thermophilus 70S ribosome [more info...]
Chain information for 5f8k #27
---
Chain | Description | UniProt
10 20 | 50S ribosomal protein L27 | RL27_THET8
11 21 | 50S ribosomal protein L28 | RL28_THET8
12 22 | 50S ribosomal protein L29 | RL29_THET8
13 23 | 50S ribosomal protein L30 | RL30_THET8
14 24 | 50S ribosomal protein L31 | RL31_THET8
15 25 | 50S ribosomal protein L32 | RL32_THET8
16 26 | 50S ribosomal protein L33 | RL33_THET8
17 27 | 50S ribosomal protein L34 | RL34_THET8
18 28 | 50S ribosomal protein L35 | RL35_THET8
19 29 | 50S ribosomal protein L36 | RL36_THET8
1A 2A | 23S ribosomal RNA |
1B 2B | 5S ribosomal RNA |
1D 2D | 50S ribosomal protein L2 | RL2_THET8
1E 2E | 50S ribosomal protein L3 | RL3_THET8
1F 2F | 50S ribosomal protein L4 | RL4_THET8
1G 2G | 50S ribosomal protein L5 | RL5_THET8
1H 2H | 50S ribosomal protein L6 | RL6_THET8
1I 2I | 50S ribosomal protein L9 | RL9_THET8
1N 2N | 50S ribosomal protein L13 | RL13_THET8
1O 2O | 50S ribosomal protein L14 | RL14_THET8
1P 2P | 50S ribosomal protein L15 | RL15_THET8
1Q 2Q | 50S ribosomal protein L16 | RL16_THET8
1R 2R | 50S ribosomal protein L17 | RL17_THET8
1S 2S | 50S ribosomal protein L18 | RL18_THET8
1T 2T | 50S ribosomal protein L19 | RL19_THET8
1U 2U | 50S ribosomal protein L20 | RL20_THET8
1V 2V | 50S ribosomal protein L21 | RL21_THET8
1W 2W | 50S ribosomal protein L22 | RL22_THET8
1X 2X | 50S ribosomal protein L23 | RL23_THET8
1Y 2Y | 50S ribosomal protein L24 | RL24_THET8
1Z 2Z | 50S ribosomal protein L25 | RL25_THET8
1a 2a | 16S ribosomal RNA |
1b 2b | 30S ribosomal protein S2 | RS2_THET8
1c 2c | 30S ribosomal protein S3 | RS3_THET8
1d 2d | 30S ribosomal protein S4 | RS4_THET8
1e 2e | 30S ribosomal protein S5 | RS5_THET8
1f 2f | 30S ribosomal protein S6 | RS6_THET8
1g 2g | 30S ribosomal protein S7 | RS7_THET8
1h 2h | 30S ribosomal protein S8 | RS8_THET8
1i 2i | 30S ribosomal protein S9 | RS9_THET8
1j 2j | 30S ribosomal protein S10 | RS10_THET8
1k 2k | 30S ribosomal protein S11 | RS11_THET8
1l 2l | 30S ribosomal protein S12 | RS12_THET8
1m 2m | 30S ribosomal protein S13 | RS13_THET8
1n 2n | 30S ribosomal protein S14 type Z | RS14Z_THET8
1o 2o | 30S ribosomal protein S15 | RS15_THET8
1p 2p | 30S ribosomal protein S16 | RS16_THET8
1q 2q | 30S ribosomal protein S17 | RS17_THET8
1r 2r | 30S ribosomal protein S18 | RS18_THET8
1s 2s | 30S ribosomal protein S19 | RS19_THET8
1t 2t | 30S ribosomal protein S20 | RS20_THET8
1u 2u | 30S ribosomal protein Thx | RSHX_THET8
1v 2v | mRNA |
1x 2x | tRNAiMet |
1y 2y | Cathelicidin-3 | CTHL3_BOVIN
Non-standard residues in 5f8k #27
---
K — potassium ion
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
5f8k mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #!27 models
> show #!27 models
> view
> show #14 models
> hide #!27 models
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/TT Bac7 Ribosome.pdb"
Summary of feedback from opening
C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo HOMO/PDB
Files/Bac7 Interaction Partners/TT Bac7 Ribosome.pdb
---
warnings | Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
196104 messages similar to the above omitted
CONECT record from atom to itself: 22522
Chain information for TT Bac7 Ribosome.pdb #28
---
Chain | Description
1 | No description available
1 | No description available
2 | No description available
2 | No description available
> hide #14,26#!23-25,28 surfaces
> select #28
296108 atoms, 313631 bonds, 2898 pseudobonds, 28376 residues, 3 models
selected
> hide sel cartoons
> style sel stick
Changed 296108 atom styles
> color #28 #bca0bd transparency 0
> color #28 #bca0bd96
> ~select #28
Nothing selected
> hide #14 models
> show #14 models
> ui tool show "Side View"
> select #14
147 atoms, 152 bonds, 16 residues, 1 model selected
> ~select #14
Nothing selected
> select add #28@@serial_number=99999
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> ~select #13
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select #28
296108 atoms, 313631 bonds, 2898 pseudobonds, 28376 residues, 3 models
selected
> ~select #28
Nothing selected
> select add #28/1:9869@O
1 atom, 1 residue, 1 model selected
> select add #28@@serial_number=99999
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select down
196110 atoms, 202917 bonds, 126 pseudobonds, 22698 residues, 3 models selected
> select #28
296108 atoms, 313631 bonds, 2898 pseudobonds, 28376 residues, 3 models
selected
> ~select #28
Nothing selected
> select add #28/1:9548@O
1 atom, 1 residue, 1 model selected
> select up
148178 atoms, 156924 bonds, 14205 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
148178 atoms, 156924 bonds, 14205 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select #28
296108 atoms, 313631 bonds, 2898 pseudobonds, 28376 residues, 3 models
selected
> ~select #28
Nothing selected
> hide #26 models
> delete pseudobonds
> color #28 #bca0bd transparency 0
> select add #28@@serial_number=99999
196110 atoms, 202917 bonds, 22698 residues, 1 model selected
> hide #!23 models
> hide #!24 models
> hide #!25 models
> show #!25 models
> select #28
296108 atoms, 313631 bonds, 28376 residues, 1 model selected
> ~select #28
Nothing selected
> select add #28@@serial_number=99999
196110 atoms, 202917 bonds, 22698 residues, 1 model selected
> select down
196110 atoms, 202917 bonds, 22698 residues, 1 model selected
> close #27
> hide #!25 models
> select #28
296108 atoms, 313631 bonds, 28376 residues, 1 model selected
> ~select #28
Nothing selected
> select #28
296108 atoms, 313631 bonds, 28376 residues, 1 model selected
> ~select #28
Nothing selected
> hide target m
> show #!28 models
Drag select of 1 atoms
[Repeated 1 time(s)]
> select up
148178 atoms, 156924 bonds, 14205 residues, 1 model selected
> select down
2 atoms, 2 residues, 1 model selected
> select #28
296108 atoms, 313631 bonds, 28376 residues, 1 model selected
> ~select #28
Nothing selected
> show #26 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/03_05_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Wed May 3 12:46:25 2023 ———
opened ChimeraX session
> open "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/PDB Files/Bac7 Interaction Partners/Waters.pdb"
> show #!25 models
Drag select of 456 atoms
> delete sel
Drag select of 336 atoms
> delete sel
Drag select of 120 atoms
> delete sel
Drag select of 75 atoms
> delete sel
> show #!24 models
> show #!23 models
> show #14 models
> style #14,26-27#!23-25 stick
Changed 2730 atom styles
> show #14,26-27#!23-25 atoms
> hide #14,26-27#!23-25 cartoons
> color #27 #7caeff transparency 0
> color #27 #97bbff transparency 0
> color #27 #78c0ff transparency 0
> color #27 #60b5ff transparency 0
> color #27 #60efff transparency 0
> color #27 #7ccbff transparency 0
> color #27 #93d6ff transparency 0
> color #27 #70a3c2 transparency 0
> color #27 #7db6d9 transparency 0
> color #27 #8cccf3 transparency 0
> color #26 #ffaa7f transparency 0
> color #26 #55aa7f transparency 0
> select #14
147 atoms, 152 bonds, 16 residues, 1 model selected
> hide #!24 models
> hide #!25 models
> hbonds sel intraModel false intraMol false intraRes false reveal true color
> black radius 0.04 dashes 6
TT Bac7 Sur.pdb #23/1 A 2084 O5' has bad number of bonds (4)
TT Bac7 Sur.pdb #23/1 A 2084 O5' has bad number of bonds (3)
TT Bac7 Sur.pdb #23/1 A 2084 O4' has bad number of bonds (4)
VN Bac7 Sur.pdb #24/A U 2490 O4' has bad number of bonds (4)
Skipping possible acceptor with bad geometry: VN Bac7 Sur.pdb #24/A U 2490 O2
Wrong number of grandchild atoms for phi/psi acceptor VN Bac7 Sur.pdb #24/A U
2490 O2
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: VN Bac7
Sur.pdb #24/A U 2490 O4
Wrong number of grandchild atoms for phi/psi acceptor VN Bac7 Sur.pdb #24/A U
2490 O4
donor: Vibrio natriegens 50S_23.cif #1/9 ILE 11 N acceptor: TT Bac7 Sur.pdb
#23/1 A 2084 N1
Traceback (most recent call last):
File "C:\Users\Karo\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Users\Karo\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Users\Karo\ChimeraX 1.3\bin\lib\site-
packages\chimerax\hbonds\cmd.py", line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "C:\Users\Karo\ChimeraX 1.3\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
File "C:\Users\Karo\ChimeraX 1.3\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
See log for complete Python traceback.
> save "C:/Users/Karo/Desktop/Karo/Veröffentlichungen/V. natriegens/Karo
> HOMO/03_05_23_Sup_Bac7.cxs" includeMaps true
——— End of log from Wed May 3 13:01:05 2023 ———
opened ChimeraX session
> select up
516565 atoms, 543808 bonds, 51135 residues, 27 models selected
> hbonds sel intraModel false intraMol false intraRes false reveal true color
> black radius 0.04 dashes 6
TT Bac7 Sur.pdb #23/1 A 2084 O5' has bad number of bonds (4)
TT Bac7 Sur.pdb #23/1 A 2084 O5' has bad number of bonds (3)
TT Bac7 Sur.pdb #23/1 A 2084 O4' has bad number of bonds (4)
VN Bac7 Sur.pdb #24/A U 2490 O4' has bad number of bonds (4)
Skipping possible acceptor with bad geometry: VN Bac7 Sur.pdb #24/A U 2490 O2
Wrong number of grandchild atoms for phi/psi acceptor VN Bac7 Sur.pdb #24/A U
2490 O2
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: VN Bac7
Sur.pdb #24/A U 2490 O4
Wrong number of grandchild atoms for phi/psi acceptor VN Bac7 Sur.pdb #24/A U
2490 O4
donor: Vibrio natriegens 50S_23.cif #1/9 ILE 11 N acceptor: TT Bac7 Sur.pdb
#23/1 A 2084 N1
Traceback (most recent call last):
File "C:\Users\Karo\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute
cmd.run(cmd_text)
File "C:\Users\Karo\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Users\Karo\ChimeraX\bin\lib\site-packages\chimerax\hbonds\cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "C:\Users\Karo\ChimeraX\bin\lib\site-packages\chimerax\hbonds\hbond.py",
line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given
File "C:\Users\Karo\ChimeraX\bin\lib\site-packages\chimerax\hbonds\hbond.py",
line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 432.00
OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 17,021,415,424
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
OSLanguage: de-DE
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
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: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
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
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: 1.1.2
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: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
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
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
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: 5.1.0
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: 5.1.0
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: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
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: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
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: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → FindHBond: accPhiPsi arguments |
comment:2 by , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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