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Opened 2 years ago
Closed 2 years ago
#9568 closed defect (duplicate)
Restore new session in old ChimeraX
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/haaris/Desktop/Barry_Lab.cxs
Log from Fri Aug 11 09:25:46 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Barry_Lab.cxs
Log from Thu Aug 10 14:40:05 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/V5.cxs
Log from Mon Aug 7 17:59:56 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/V5.cxs
Log from Mon Aug 7 16:54:40 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/V5.cxs format session
Opened 7as8 map 5 as #3, grid size 143,159,145, pixel 1.67, shown at level
0.113, step 1, values float32
Log from Mon Aug 7 11:05:47 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/V5.cxs
Log from Thu Aug 3 18:23:46 2023UCSF ChimeraX version: 1.7.dev202307312254
(2023-07-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/v4.cxs format session
Log from Thu Aug 3 13:13:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/v4.cxs format session
Log from Wed Aug 2 12:10:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/Figues_Shura/figure_shura2.cxs
Log from Mon Jul 31 16:36:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/figure_shura2.cxs format session
Log from Mon Jul 31 16:01:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/Haaris/Desktop/figure_shura.cxs format session
Log from Mon Jul 31 15:16:26 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 shadows false
> lighting depthCue false
> graphics silhouettes true
> lighting simple
> 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 f05gelb #f2b701
Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701
> color name f06orange #e68310
Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310
> color name f07rotorange #FF6A25
Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25
> color name f08rot #dd3d2d
Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d
> color name f09lachs #f97b72
Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72
> color name f10flieder #D57AD5
Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5
> color name f11violett #cf1c90
Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90
> color name f12lila #4b148f
Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f
> color name f13dunkelblau #2E2EF7
Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7
> color name f14blau #00AAFF
Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff
> 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 #00FF00
Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00
> color name f18dunkelgrün #228B22
Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
> color name f19hellgrau #DCDCDC
Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc
> color name f20grau #B2B2B2
Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2
> color name f21anthrazit #323F45
Color 'f21anthrazit' 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 foto save browse format tiff height 4000 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 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 spalt volume splitbyzone #$1
> alias undust surface undust #$1
> alias dust1 surface dust #$1 size 1
> alias dust2 surface dust #$1 size 2
> alias dust3 surface dust #$1 size 3
> alias dust4 surface dust #$1 size 4
> 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 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
> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true
> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true
> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3vjr
Summary of feedback from opening 3vjr fetched from pdb
---
note | Fetching compressed mmCIF 3vjr from
http://files.rcsb.org/download/3vjr.cif
3vjr title:
Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex
with the CCA-acceptor-T[PSI]C domain of tRNA [more info...]
Chain information for 3vjr #1
---
Chain | Description | UniProt
A C | Peptidyl-tRNA hydrolase | PTH_ECOLI 4-197
B D | tRNA CCA-acceptor |
> set bgColor white
> select /D:1-36
766 atoms, 854 bonds, 34 pseudobonds, 36 residues, 2 models selected
> delete sel
> select /C:5-197
1480 atoms, 1513 bonds, 193 residues, 1 model selected
> delete sel
> save /Users/Haaris/Desktop/figure_shura.cxs
> nucleotides atoms
> style nucleic stick
Changed 766 atom styles
> nucleotides fill
> style nucleic stick
Changed 766 atom styles
> nucleotides slab
> style nucleic stick
Changed 766 atom styles
> nucleotides tube/slab shape box
> nucleotides tube/slab shape ellipsoid
> nucleotides tube/slab shape muffler
> nucleotides ladder
> nucleotides stubs
> color bynucleotide
> nucleotides stubs
> nucleotides ladder
> nucleotides tube/slab shape muffler
> nucleotides atoms
> style nucleic stick
Changed 766 atom styles
> hide #!1 models
> open 7ASA
Summary of feedback from opening 7ASA fetched from pdb
---
note | Fetching compressed mmCIF 7asa from
http://files.rcsb.org/download/7asa.cif
7asa title:
Bacillus subtilis ribosome-associated quality control complex state B,
multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA,
RqcH, and RqcP/YabO [more info...]
Chain information for 7asa #2
---
Chain | Description | UniProt
0 | Rqc2 homolog RqcH | RQCH_BACSU 1-570
1 | Uncharacterized protein YabO | YABO_BACSU 1-86
2 | tRNA-Ala-1-1 |
A | 23S rRNA |
K | 50S ribosomal protein L11 | RL11_BACSU 1-141
> hide #!2 models
> show #!2 models
> close #2
> close
> open 7ASA
7asa title:
Bacillus subtilis ribosome-associated quality control complex state B,
multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA,
RqcH, and RqcP/YabO [more info...]
Chain information for 7asa #1
---
Chain | Description | UniProt
0 | Rqc2 homolog RqcH | RQCH_BACSU 1-570
1 | Uncharacterized protein YabO | YABO_BACSU 1-86
2 | tRNA-Ala-1-1 |
A | 23S rRNA |
K | 50S ribosomal protein L11 | RL11_BACSU 1-141
> show cartoons
> hide atoms
> close #1
> open 7AS8
7as8 title:
Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S
subunit with P-tRNA, RqcH, and RqcP/YabO [more info...]
Chain information for 7as8 #1
---
Chain | Description | UniProt
0 | Rqc2 homolog RqcH | RQCH_BACSU 1-570
1 | Uncharacterized protein YabO | YABO_BACSU 1-86
2 | tRNA-Ala-1-1 |
A | 23S rRNA |
B | 5s rRNA |
E | 50S ribosomal protein L2 | RL2_BACSU 1-277
F | 50S ribosomal protein L3 | RL3_BACSU 1-209
G | 50S ribosomal protein L4 | RL4_BACSU 1-207
H | 50S ribosomal protein L5 | RL5_BACSU 1-179
I | 50S ribosomal protein L6 | RL6_BACSU 1-179
K | 50S ribosomal protein L11 | RL11_BACSU 1-141
L | 50S ribosomal protein L10 | RL10_BACSU 1-166
N | 50S ribosomal protein L13 | RL13_BACSU 1-145
O | 50S ribosomal protein L14 | RL14_BACSU 1-122
P | 50S ribosomal protein L15 | RL15_BACSU 1-146
Q | 50S ribosomal protein L16 | RL16_BACSU 1-144
R | 50S ribosomal protein L17 | RL17_BACSU 1-120
S | 50S ribosomal protein L18 | RL18_BACSU 1-120
T | 50S ribosomal protein L19 | RL19_BACSU 1-115
U | 50S ribosomal protein L20 | RL20_BACSU 1-119
V | 50S ribosomal protein L21 | RL21_BACSU 1-102
W | 50S ribosomal protein L22 | RL22_BACSU 1-113
X | 50S ribosomal protein L23 | RL23_BACSU 1-95
Y | 50S ribosomal protein L24 | RL24_BACSU 1-103
a | 50S ribosomal protein L27 | RL27_BACSU 1-94
b | 50S ribosomal protein L28 | RL28_BACSU 1-62
c | 50S ribosomal protein L29 | RL29_BACSU 1-66
d | 50S ribosomal protein L30 | RL30_BACSU 1-59
f | 50S ribosomal protein L32 | RL32_BACSU 1-59
g | 50S ribosomal protein L33 1 | RL331_BACSU 1-49
h | 50S ribosomal protein L34 | RL34_BACSU 1-44
i | 50S ribosomal protein L35 | RL35_BACSU 1-66
j | 50S ribosomal protein L36 | RL36_BACSU 1-37
> show cartoons
> hide atoms
> open 7AS9
Summary of feedback from opening 7AS9 fetched from pdb
---
note | Fetching compressed mmCIF 7as9 from
http://files.rcsb.org/download/7as9.cif
7as9 title:
Bacillus subtilis ribosome-associated quality control complex state A.
Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH. [more
info...]
Chain information for 7as9 #2
---
Chain | Description | UniProt
0 | Rqc2 homolog RqcH | RQCH_BACSU 1-570
2 | tRNA-Ala-1-1 |
A | 23S rRNA |
B | 5S rRNA |
E | 50S ribosomal protein L2 | RL2_BACSU 1-277
F | 50S ribosomal protein L3 | RL3_BACSU 1-209
G | 50S ribosomal protein L4 | RL4_BACSU 1-207
H | 50S ribosomal protein L5 | RL5_BACSU 1-179
I | 50S ribosomal protein L6 | RL6_BACSU 1-179
K | 50S ribosomal protein L11 | RL11_BACSU 1-141
L | 50S ribosomal protein L10 | RL10_BACSU 1-166
N | 50S ribosomal protein L13 | RL13_BACSU 1-145
O | 50S ribosomal protein L14 | RL14_BACSU 1-122
P | 50S ribosomal protein L15 | RL15_BACSU 1-146
Q | 50S ribosomal protein L16 | RL16_BACSU 1-144
R | 50S ribosomal protein L17 | RL17_BACSU 1-120
S | 50S ribosomal protein L18 | RL18_BACSU 1-120
T | 50S ribosomal protein L19 | RL19_BACSU 1-115
U | 50S ribosomal protein L20 | RL20_BACSU 1-119
V | 50S ribosomal protein L21 | RL21_BACSU 1-102
W | 50S ribosomal protein L22 | RL22_BACSU 1-113
X | 50S ribosomal protein L23 | RL23_BACSU 1-95
Y | 50S ribosomal protein L24 | RL24_BACSU 1-103
a | 50S ribosomal protein L27 | RL27_BACSU 1-94
b | 50S ribosomal protein L28 | RL28_BACSU 1-62
c | 50S ribosomal protein L29 | RL29_BACSU 1-66
d | 50S ribosomal protein L30 | RL30_BACSU 1-59
f | 50S ribosomal protein L32 | RL32_BACSU 1-59
g | 50S ribosomal protein L33 1 | RL331_BACSU 1-49
h | 50S ribosomal protein L34 | RL34_BACSU 1-44
i | 50S ribosomal protein L35 | RL35_BACSU 1-66
j | 50S ribosomal protein L36 | RL36_BACSU 1-37
> show cartoons
> hide atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> close #2
> open 3vjr
3vjr title:
Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex
with the CCA-acceptor-T[PSI]C domain of tRNA [more info...]
Chain information for 3vjr #2
---
Chain | Description | UniProt
A C | Peptidyl-tRNA hydrolase | PTH_ECOLI 4-197
B D | tRNA CCA-acceptor |
> select #2/D:1-36
766 atoms, 854 bonds, 34 pseudobonds, 36 residues, 2 models selected
> delete sel
> select #2/C:5-197
1480 atoms, 1513 bonds, 193 residues, 1 model selected
> delete sel
> select add #2
2385 atoms, 2367 bonds, 34 pseudobonds, 368 residues, 2 models selected
> view matrix models #2,1,0,0,50.632,0,1,0,186.51,0,0,1,132.98
> view matrix models
> #2,0.92201,-0.35233,-0.1605,55.463,0.27552,0.88834,-0.36736,193.58,0.27201,0.29448,0.91613,132.77
> view matrix models
> #2,0.92201,-0.35233,-0.1605,129.09,0.27552,0.88834,-0.36736,156.71,0.27201,0.29448,0.91613,238.78
> view matrix models
> #2,0.4584,-0.25557,-0.85121,115.3,-0.025931,0.95351,-0.30025,149.15,0.88837,0.15971,0.43047,253.28
> view matrix models
> #2,0.36196,-0.044307,-0.93114,108.83,0.9317,-0.015297,0.3629,190.67,-0.030323,-0.9989,0.035744,255.35
> view matrix models
> #2,0.29962,-0.00646,-0.95404,106.69,0.95108,-0.076919,0.29921,192.12,-0.075316,-0.99702,-0.016902,254.2
> ui tool show Matchmaker
> matchmaker #2/B to #1/2 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match 3vjr #2/B to 7as8 #1/2
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 7as8, chain 2 (#1) with 3vjr, chain B (#2), sequence alignment
score = 113.4
RMSD between 16 pruned atom pairs is 0.783 angstroms; (across all 35 pairs:
19.494)
> hide sel atoms
> save /Users/Haaris/Desktop/figure_shura.cxs includeMaps true
——— End of log from Mon Jul 31 15:16:26 2023 ———
opened ChimeraX session
> show sel atoms
> hide sel cartoons
> style sel sphere
Changed 2385 atom styles
> select ::name="HOH"
139 atoms, 139 residues, 1 model selected
> delete sel
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 atoms
> show #!2 cartoons
> show #!1 models
> select #2/A:79
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
101 atoms, 102 bonds, 14 residues, 1 model selected
> select up
1480 atoms, 1513 bonds, 193 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel sphere
Changed 1480 atom styles
> hide #!2 models
> show #!2 models
> select clear
> open 8ap4
8ap4 title:
Structure of Escherischia coli heat shock protein Hsp15 in complex with
ribosomal 50S subunits bearing peptidyl-tRNA [more info...]
Chain information for 8ap4 #3
---
Chain | Description | UniProt
0 | 50S ribosomal protein L33 | RL33_ECOLI 1-55
1 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
2 | 50S ribosomal protein L35 | RL35_ECOLI 1-65
3 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
4 | 50S ribosomal protein L31 | RL31_ECOLI 1-70
A | Heat shock protein 15 | HSLR_ECOLI 1-133
Z | P-tRNA |
a | 23S rRNA |
b | 5S rRNA |
c | 50S ribosomal protein L2 | RL2_ECOLI 1-273
d | 50S ribosomal protein L3 | RL3_ECOLI 1-209
e | 50S ribosomal protein L4 | RL4_ECOLI 1-201
f | 50S ribosomal protein L5 | RL5_ECOLI 1-179
g | 50S ribosomal protein L6 | RL6_ECOLI 1-177
h | 50S ribosomal protein L9 | RL9_ECOLI 1-149
i | 50S ribosomal protein L13 | RL13_ECOLI 1-142
j | 50S ribosomal protein L14 | RL14_ECOLI 1-123
k | 50S ribosomal protein L15 | RL15_ECOLI 1-144
l | 50S ribosomal protein L16 | RL16_ECOLI 1-136
m | 50S ribosomal protein L17 | RL17_ECOLI 1-127
n | 50S ribosomal protein L18 | RL18_ECOLI 1-117
o | 50S ribosomal protein L19 | RL19_ECOLI 1-115
p | 50S ribosomal protein L20 | RL20_ECOLI 1-118
q | 50S ribosomal protein L21 | RL21_ECOLI 1-103
r | 50S ribosomal protein L22 | RL22_ECOLI 1-110
s | 50S ribosomal protein L23 | RL23_ECOLI 1-100
t | 50S ribosomal protein L24 | RL24_ECOLI 1-104
u | 50S ribosomal protein L25 | RL25_ECOLI 1-94
v | 50S ribosomal protein L27 | RL27_ECOLI 1-85
w | 50S ribosomal protein L28 | RL28_ECOLI 1-78
x | 50S ribosomal protein L29 | RL29_ECOLI 1-63
y | 50S ribosomal protein L30 | RL30_ECOLI 1-59
z | 50S ribosomal protein L32 | RL32_ECOLI 1-57
> select add #3
88614 atoms, 96527 bonds, 3074 pseudobonds, 6206 residues, 3 models selected
> hide #!1 models
> hide #!2 models
> show sel cartoons
> hide sel atoms
> show #!1 models
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-64.489,0,1,0,12.272,0,0,1,285.12
> view matrix models
> #3,0.99177,-0.10855,0.067916,-54.756,0.11192,0.99257,-0.047824,0.17166,-0.062219,0.055031,0.99654,287.72
> view matrix models
> #3,0.99177,-0.10855,0.067916,-54.79,0.11192,0.99257,-0.047824,1.3278,-0.062219,0.055031,0.99654,286.74
> view matrix models
> #3,0.91021,-0.28894,0.29669,-44.222,0.36045,0.90548,-0.224,-2.1887,-0.20393,0.31083,0.92833,279.46
> view matrix models
> #3,0.91021,-0.28894,0.29669,69.048,0.36045,0.90548,-0.224,99.07,-0.20393,0.31083,0.92833,-102.74
> view matrix models
> #3,0.71942,-0.56432,0.40495,135.67,0.46709,-0.03844,-0.88337,347.81,0.51407,0.82466,0.23593,-217.34
> view matrix models
> #3,0.83413,-0.45852,0.30658,111.29,0.37803,0.070478,-0.92311,351.78,0.40166,0.88588,0.23212,-206.36
> view matrix models
> #3,0.84775,-0.45171,0.278,112.05,0.35202,0.087113,-0.93193,355.39,0.39675,0.8879,0.23286,-206.19
> view matrix models
> #3,0.69926,-0.64037,0.31774,166.46,0.43437,0.027598,-0.90031,345.35,0.56776,0.76757,0.29746,-227.43
> view matrix models
> #3,0.73409,-0.54776,0.40132,130.59,0.44927,-0.051373,-0.89192,355,0.50918,0.83505,0.20838,-214.15
> view matrix models
> #3,0.73409,-0.54776,0.40132,148.13,0.44927,-0.051373,-0.89192,232.33,0.50918,0.83505,0.20838,-117.28
> view matrix models
> #3,0.7652,-0.55462,0.32691,155.26,0.39313,0.00042829,-0.91948,238.16,0.50982,0.83211,0.21837,-118.46
> view matrix models
> #3,0.7652,-0.55462,0.32691,128.07,0.39313,0.00042829,-0.91948,212.6,0.50982,0.83211,0.21837,-90.303
> view matrix models
> #3,0.76449,-0.55614,0.32599,86.914,0.3917,-0.0008821,-0.92009,243.47,0.51199,0.83109,0.21717,-89.3
> select subtract #3
Nothing selected
> ui tool show Matchmaker
> matchmaker #!3 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 7as8, chain A (#1) with 8ap4, chain a (#3), sequence alignment
score = 13368.3
RMSD between 2218 pruned atom pairs is 0.939 angstroms; (across all 2674
pairs: 5.722)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> close #3
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/B:35
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
766 atoms, 854 bonds, 36 residues, 1 model selected
> delete sel
> show #!1 models
> save /Users/Haaris/Desktop/figure_shura2.cxs includeMaps true
——— End of log from Mon Jul 31 16:01:09 2023 ———
opened ChimeraX session
> open 6YS3
Summary of feedback from opening 6YS3 fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue
template for A /a:119
Atom OP2 has no neighbors to form bonds with according to residue template for
A /a:119
6ys3 title:
Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled
GBC SecM peptide [more info...]
Chain information for 6ys3 #3
---
Chain | Description | UniProt
0 | 50S ribosomal protein L28 | A0A140N3L9_ECOBD 1-78
1 | 50S ribosomal protein L29 | A0A140N7F5_ECOBD 1-63
2 | 50S ribosomal protein L30 | A0A140N7G4_ECOBD 1-59
3 | 50S ribosomal protein L32 | A0A140NAZ2_ECOBD 1-57
4 | 50S ribosomal protein L33 | A0A140N5Z7_ECOBD 1-55
6 | 50S ribosomal protein L34 | A0A140NHV0_ECOBD 1-46
7 | 50S ribosomal protein L35 | A0A140N9E3_ECOBD 1-65
8 | 50S ribosomal protein L36 | A0A140N5M6_ECOBD 1-38
a | 5S rRNA |
b | 23S rRNA |
c | 50S ribosomal protein L2 | A0A140N7J1_ECOBD 1-273
d | 50S ribosomal protein L3 | A0A140N3G7_ECOBD 1-209
e | 50S ribosomal protein L4 | A0A140N5K8_ECOBD 1-201
f | 50S ribosomal protein L5 | A0A140N5A3_ECOBD 1-179
g | 50S ribosomal protein L6 | A0A140N2T1_ECOBD 1-177
h | 50S ribosomal protein L9 | A0A140NDV1_ECOBD 1-149
j | 50S ribosomal protein L13 | A0A140N598_ECOBD 1-142
k | 50S ribosomal protein L14 | A0A140N3H4_ECOBD 1-123
l | 50S ribosomal protein L15 | A0A140N711_ECOBD 1-144
m | 50S ribosomal protein L16 | A0A140N6Z2_ECOBD 1-136
n | 50S ribosomal protein L17 | A0A140N4M0_ECOBD 1-127
o | 50S ribosomal protein L18 | A0A140N4L0_ECOBD 1-117
p | 50S ribosomal protein L19 | A0A140N6T7_ECOBD 1-115
q | 50S ribosomal protein L20 | A0A140NBS1_ECOBD 1-118
r | 50S ribosomal protein L21 | A0A140N5D7_ECOBD 1-103
s | 50S ribosomal protein L22 | A0A140N2S3_ECOBD 1-110
t | 50S ribosomal protein L23 | C6EGE8_ECOBD 1-100
u | 50S ribosomal protein L24 | A0A140N5L7_ECOBD 1-104
v | glycine-tRNA glyT |
w | 50S ribosomal protein L25 | A0A140N846_ECOBD 1-94
y | 50S ribosomal protein L27 | A0A140N340_ECOBD 1-85
z | Gamma-crystallin B | CRGB_BOVIN 0-154
[lots deleted]
> hide #!3 models
> show #!3 models
> select add #5
107 atoms, 106 bonds, 24 residues, 1 model selected
> color sel orange
> show sel atoms
> hide sel cartoons
> style sel sphere
Changed 107 atom styles
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save /Users/Haaris/Desktop/Figues_Shura/V5.cxs includeMaps true
——— End of log from Mon Aug 7 17:59:56 2023 ———
opened ChimeraX session
> select #3/0:402
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
376 atoms, 381 bonds, 46 residues, 1 model selected
> select up
647 atoms, 658 bonds, 80 residues, 1 model selected
> select up
692 atoms, 702 bonds, 87 residues, 1 model selected
> select up
2200 atoms, 2228 bonds, 304 residues, 1 model selected
> delete sel
> select #3/1:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
93 atoms, 92 bonds, 12 residues, 1 model selected
> select up
659 atoms, 662 bonds, 83 residues, 1 model selected
> select ~sel & ##selected
89379 atoms, 97265 bonds, 3011 pseudobonds, 6347 residues, 3 models selected
> select add #3
90038 atoms, 97927 bonds, 3011 pseudobonds, 6430 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/1:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
93 atoms, 92 bonds, 12 residues, 1 model selected
> select up
659 atoms, 662 bonds, 83 residues, 1 model selected
> delete sel
> select add #3
89379 atoms, 97265 bonds, 3011 pseudobonds, 6347 residues, 3 models selected
> color sel bychain
> show sel atoms
> hide sel cartoons
> select #3/A:2766@P
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
60389 atoms, 67640 bonds, 2812 residues, 1 model selected
> color sel light gray
> select clear
> show #!1 models
> lighting flat
> ui tool show "Side View"
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save /Users/Haaris/Desktop/Barry_Lab.cxs includeMaps true
——— End of log from Thu Aug 10 14:40:05 2023 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> select add #3
89379 atoms, 97265 bonds, 3011 pseudobonds, 6347 residues, 3 models selected
> color (#!3 & sel) light gray
> select clear
> durch
> save /Users/Haaris/Desktop/Figues_Shura/NewStyle_50SCut format tiff height
> 4000 supersample 4 transparentBackground true
> hide #!3 models
> show #!3 models
> show #!1 models
> select add #1
1563 atoms, 1744 bonds, 72 pseudobonds, 73 residues, 3 models selected
> hide #!3 models
> style sel stick
Changed 1563 atom styles
> style sel ball
Changed 1563 atom styles
> hide sel atoms
> lighting flat
> show sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> style sel sphere
Changed 1563 atom styles
> lighting flat
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!5 models
> durch
> save /Users/Haaris/Desktop/Figues_Shura/newstyle_ptrn_nc format tiff height
> 4000 supersample 4 transparentBackground true
> show #!3 models
> show #!2 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> durch
> save /Users/Haaris/Desktop/Figues_Shura/nESTYLE_PTH format tiff height 4000
> supersample 4 transparentBackground true
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save /Users/Haaris/Desktop/Barry_Lab.cxs
——— End of log from Fri Aug 11 09:25:46 2023 ———
opened ChimeraX session
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> ui tool show "Side View"
> lighting soft
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
90942 atoms, 99009 bonds, 3083 pseudobonds, 6420 residues, 6 models selected
> select subtract #1
89379 atoms, 97265 bonds, 3011 pseudobonds, 6347 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select clear
> color #2 red
> open /Users/haaris/Desktop/Barry_Lab.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 465, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 742, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
AttributeError: 'list' object has no attribute 'values'
File
"/Applications/ChimeraX-1.6.1.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():
See log for complete Python traceback.
> open /Users/haaris/Desktop/Barry_Lab.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 368, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 446, in defer
cxcmd(session, topic)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 465, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 742, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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
"/Applications/ChimeraX-1.6.1.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'
AttributeError: 'list' object has no attribute 'values'
File
"/Applications/ChimeraX-1.6.1.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():
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: MGPK3D/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.0.305.0.1
OS Loader Version: 10151.0.305.0.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A5312d)
Kernel Version: Darwin 23.0.0
Time since boot: 2 days, 23 hours, 46 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (1)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Platform: | → all |
| Project: | → ChimeraX |
| Resolution: | → duplicate |
| Status: | new → closed |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
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