![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 18 months ago
#15064 closed defect (can't reproduce)
Mouse wheel: no Qt.KeyboardModifier.CtrlModifier
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
Log from Fri Apr 26 17:08:38 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> 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 0.0 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 width 5500 supersample 4
> transparentBackground false
> alias durch save browse format tiff height 4000 width 5500 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 dust surface dust #$2 size $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
> alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ;
> camera ortho; cartoon style width 2.4 thickness 0.4; lighting
> ambientintensity 1.2 fillIntensity 0.4
> alias abbild sel zone sel 1 #$1 residues true extend true
> alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel
> intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues
> true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel
> intersect :MG; style sel ball; size sel ballscale 0.5
> alias network sel zone sel $1 #$2 residues true extend true
> alias network34 sel zone sel 3.4 #$1 residues true extend true
> alias network4 sel zone sel 4 #$1 residues true extend true
> alias network10 sel zone sel 10 #$1 residues true extend true
> alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect
> #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true
> alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH
> alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 &
> protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel
> f17; sel #$1:K; color sel f15
> alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect
> #$1@o*:HOH:MG
> alias upsplit color zone #$1 near #$3 sharpEdges true distance $2
> alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel
> intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2
> residues true extend true; sel subtract badwaters
> alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel
> ballscale 0.5
> alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel
> ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect
> ##name="K"; color sel blueviolet
> alias pixel zoom pixelsize 0.04
> alias da sel #$1 @@display
> alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix
> Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2;
> abbild+ $1
> alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet;
> hbonds sel color f05 restrict both interModel false intraMol false intraRes
> false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel
> intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; del pbonds sel; sel temp; show sel; da $2; sel
> intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect
> ##name="hydrogen bonds"; hide sel; da $2; sel intersect protein; sel
> intersect ##name="hydrogen bonds"; hide sel; da $1; sel intersect
> ##name="hydrogen bonds"; color sel f15
> alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale
> 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect
> @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K
> log true
> alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale
> 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp
> overlapCutoff -0.8 color #00FF00 name Mg log true
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1I95
1i95 title:
Crystal structure of the 30S ribosomal subunit from thermus thermophilus In
complex with edeine [more info...]
Chain information for 1i95 #1
---
Chain | Description | UniProt
A | 16S RRNA |
B | 30S RIBOSOMAL PROTEIN S2 |
C | 30S RIBOSOMAL PROTEIN S3 |
D | 30S RIBOSOMAL PROTEIN S4 | RS4_THETH 2-209
E | 30S RIBOSOMAL PROTEIN S5 | RS5_THETH 2-162
F | 30S RIBOSOMAL PROTEIN S6 | RS6_THETH 1-101
G | 30S RIBOSOMAL PROTEIN S7 | P17291 2-156
H | 30S RIBOSOMAL PROTEIN S8 | RS8_THETH 1-138
I | 30S RIBOSOMAL PROTEIN S9 |
J | 30S RIBOSOMAL PROTEIN S10 | RS10_THETH 2-105
K | 30S RIBOSOMAL PROTEIN S11 |
L | 30S RIBOSOMAL PROTEIN S12 | RS12_THETH 5-135
M | 30S RIBOSOMAL PROTEIN S13 |
N | 30S RIBOSOMAL PROTEIN S14 | RS14_THETH 2-61
O | 30S RIBOSOMAL PROTEIN S15 | RS15_THETH 2-89
P | 30S RIBOSOMAL PROTEIN S16 |
Q | 30S RIBOSOMAL PROTEIN S17 | RS17_THETH 2-105
R | 30S RIBOSOMAL PROTEIN S18 |
S | 30S RIBOSOMAL PROTEIN S19 | RS19_THETH 2-93
T | 30S RIBOSOMAL PROTEIN S20 |
U | 30S RIBOSOMAL PROTEIN THX |
Non-standard residues in 1i95 #1
---
EDE — edeine B
MG — magnesium ion
WO2 — octadecatungstenyl diphosphate
ZN — zinc ion
> set bgColor white
> show cartoons
> hide atoms
> open 5lmv
5lmv title:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation
complex(state-III) [more info...]
Chain information for 5lmv #2
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S2 | RS2_THET8 1-256
C | 30S ribosomal protein S3 | RS3_THET8 1-239
D | 30S ribosomal protein S4 | RS4_THET8 1-209
E | 30S ribosomal protein S5 | RS5_THET8 1-162
F | 30S ribosomal protein S6 | RS6_THET8 1-101
G | 30S ribosomal protein S7 | RS7_THET8 1-156
H | 30S ribosomal protein S8 | RS8_THET8 1-138
I | 30S ribosomal protein S9 | RS9_THET8 1-128
J | 30S ribosomal protein S10 | RS10_THET8 1-105
K | 30S ribosomal protein S11 | RS11_THET8 1-129
L | 30S ribosomal protein S12 | RS12_THET8 4-135
M | 30S ribosomal protein S13 | RS13_THET8 1-126
N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
O | 30S ribosomal protein S15 | RS15_THET8 1-89
P | 30S ribosomal protein S16 | RS16_THET8 1-88
Q | 30S ribosomal protein S17 | RS17_THET8 1-105
R | 30S ribosomal protein S18 | RS18_THET8 1-88
S | 30S ribosomal protein S19 | RS19_THET8 1-93
T | 30S ribosomal protein S20 | RS20_THET8 1-106
V | 30S ribosomal protein Thx | RSHX_THET8 1-27
W | Translation initiation factor IF-1 | IF1_THET8 0-71
X | Translation initiation factor IF-3 | IF3_THET8 2-172
Y | mRNA |
Z | tRNAi |
a | Translation initiation factor IF-2 | IF2_THET8 1-571
Non-standard residues in 5lmv #2
---
FME — N-formylmethionine
MG — magnesium ion
ZN — zinc ion
> select add #2
59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected
> hide #!1 models
> show sel cartoons
> hide sel atoms
> view matrix models
> #2,0.48058,0.43954,-0.75884,150.51,0.86599,-0.10151,0.48964,-55.186,0.13819,-0.89247,-0.42943,371.72
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
> show #!1 models
> select add #1
95694 atoms, 100564 bonds, 7135 pseudobonds, 8756 residues, 8 models selected
> view matrix models
> #1,1,0,0,16.05,0,1,0,28.406,0,0,1,-23.457,#2,0.48058,0.43954,-0.75884,166.56,0.86599,-0.10151,0.48964,-26.779,0.13819,-0.89247,-0.42943,348.26
> select subtract #1
59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected
> select add #1
95694 atoms, 100564 bonds, 7135 pseudobonds, 8756 residues, 8 models selected
> select subtract #2
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select subtract #1
Nothing selected
> select add #1
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select subtract #1
Nothing selected
> select add #1
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.039,-0.3043,0.95178,-39.441,0.98487,0.14927,0.088081,72.569,-0.16888,0.94081,0.29387,-25.143
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss matrix Nucleic
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 1i95, chain A (#1) with 5lmv, chain A (#2), sequence alignment
score = 6052.4
RMSD between 1038 pruned atom pairs is 1.093 angstroms; (across all 1511
pairs: 2.576)
> select subtract #1
Nothing selected
> select ::name="EDE"
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open 4u4n
Summary of feedback from opening 4u4n fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue
template for G /5:420
Atom OP2 has no neighbors to form bonds with according to residue template for
G /5:420
4u4n title:
Crystal structure of Edeine bound to the yeast 80S ribosome [more info...]
Chain information for 4u4n #3
---
Chain | Description | UniProt
1 5 | 25S ribosomal RNA |
2 6 | 18S ribosomal RNA |
3 7 | 5S ribosomal RNA |
4 8 | 5.8S ribosomal RNA |
C0 c0 | 40S ribosomal protein S10-A | RS10A_YEAST 1-105
C1 c1 | 40S ribosomal protein S11-A | RS11A_YEAST 2-156
C2 c2 | 40S ribosomal protein S12 | RS12_YEAST 2-143
C3 c3 | 40S ribosomal protein S13 | RS13_YEAST 2-151
C4 c4 | 40S ribosomal protein S14-A | RS14A_YEAST 2-137
C5 c5 | 40S ribosomal protein S15 | RS15_YEAST 2-142
C6 c6 | 40S ribosomal protein S16-A | RS16A_YEAST 2-143
C7 c7 | 40S ribosomal protein S17-A | RS17A_YEAST 1-136
C8 c8 | 40S ribosomal protein S18-A | RS18A_YEAST 2-146
C9 c9 | 40S ribosomal protein S19-A | RS19A_YEAST 2-144
D0 d0 | 40S ribosomal protein S20 | RS20_YEAST 2-121
D1 d1 | 40S ribosomal protein S21-A | RS21A_YEAST 1-87
D2 d2 | 40S ribosomal protein S22-A | RS22A_YEAST 2-130
D3 d3 | 40S ribosomal protein S23-A | RS23A_YEAST 2-145
D4 d4 | 40S ribosomal protein S24-A | RS24A_YEAST 2-135
D5 d5 | 40S ribosomal protein S25-A | RS25A_YEAST 2-108
D6 d6 | 40S ribosomal protein S26-B | RS26B_YEAST 2-98
D7 d7 | 40S ribosomal protein S27-A | RS27_YEAST 2-82
D8 d8 | 40S ribosomal protein S28-A | RS28A_YEAST 2-67
D9 d9 | 40S ribosomal protein S29-A | RS29A_YEAST 2-56
E0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-61
E1 e1 | Ubiquitin-40S ribosomal protein S31 | RS27A_YEAST 77-152
L2 l2 | 60S ribosomal protein L2-A | RL2A_YEAST 2-254
L3 l3 | 60S ribosomal protein L3 | RL3_YEAST 2-387
L4 l4 | 60S ribosomal protein L4-A | RL4A_YEAST 2-362
L5 l5 | 60S ribosomal protein L5 | RL5_YEAST 2-297
L6 l6 | 60S ribosomal protein L6-A | RL6A_YEAST 2-176
L7 l7 | 60S ribosomal protein L7-A | RL7A_YEAST 2-244
L8 l8 | 60S ribosomal protein L8-A | RL8A_YEAST 2-256
L9 l9 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
M0 m0 | 60S ribosomal protein L10 | RL10_YEAST 2-221
M1 m1 | 60S ribosomal protein L11-B | RL11B_YEAST 2-174
M3 m3 | 60S ribosomal protein L13-A | RL13A_YEAST 2-199
M4 m4 | 60S ribosomal protein L14-A | RL14A_YEAST 2-138
M5 m5 | 60S ribosomal protein L15-A | RL15A_YEAST 2-204
M6 m6 | 60S ribosomal protein L16-A | RL16A_YEAST 2-199
M7 m7 | 60S ribosomal protein L17-A | RL17A_YEAST 2-184
M8 m8 | 60S ribosomal protein L18-A | RL18A_YEAST 2-186
M9 m9 | 60S ribosomal protein L19-A | RL19A_YEAST 2-189
N0 n0 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
N1 n1 | 60S ribosomal protein L21-A | RL21A_YEAST 2-160
N2 n2 | 60S ribosomal protein L22-A | RL22A_YEAST 2-121
N3 n3 | 60S ribosomal protein L23-A | RL23A_YEAST 2-137
N4 n4 | 60S ribosomal protein L24-A | RL24A_YEAST 1-155
N5 n5 | 60S ribosomal protein L25 | RL25_YEAST 2-142
N6 n6 | 60S ribosomal protein L26-A | RL26A_YEAST 2-127
N7 n7 | 60S ribosomal protein L27-A | RL27A_YEAST 2-136
N8 n8 | 60S ribosomal protein L28 | RL28_YEAST 2-149
N9 n9 | 60S ribosomal protein L29 | RL29_YEAST 2-59
O0 o0 | 60S ribosomal protein L30 | RL30_YEAST 2-105
O1 o1 | 60S ribosomal protein L31-A | RL31A_YEAST 2-113
O2 o2 | 60S ribosomal protein L32 | RL32_YEAST 2-130
O3 o3 | 60S ribosomal protein L33-A | RL33A_YEAST 2-107
O4 o4 | 60S ribosomal protein L34-A | RL34A_YEAST 2-120
O5 o5 | 60S ribosomal protein L35-A | RL35A_YEAST 2-120
O6 o6 | 60S ribosomal protein L36-A | RL36A_YEAST 2-100
O7 o7 | 60S ribosomal protein L37-A | RL37A_YEAST 2-88
O8 o8 | 60S ribosomal protein L38 | RL38_YEAST 2-78
O9 o9 | 60S ribosomal protein L39 | RL39_YEAST 2-51
Q0 q0 | Ubiquitin-60S ribosomal protein L40 | RL401_YEAST 77-128
Q1 q1 | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
Q2 q2 | 60S ribosomal protein L42-A | RL44A_YEAST 2-106
Q3 q3 | 60S ribosomal protein L43-A | RL43A_YEAST 2-92
S0 s0 | 40S ribosomal protein S0-A | RSSA1_YEAST 2-252
S1 s1 | 40S ribosomal protein S1-A | RS3A1_YEAST 2-255
S2 s2 | 40S ribosomal protein S2 | RS2_YEAST 2-254
S3 s3 | 40S ribosomal protein S3 | RS3_YEAST 2-240
S4 s4 | 40S ribosomal protein S4-A | RS4A_YEAST 2-261
S5 s5 | 40S ribosomal protein S5 | RS5_YEAST 2-225
S6 s6 | 40S ribosomal protein S6-A | RS6A_YEAST 1-236
S7 s7 | 40S ribosomal protein S7-A | RS7A_YEAST 2-190
S8 s8 | 40S ribosomal protein S8-A | RS8A_YEAST 1-200
S9 s9 | 40S ribosomal protein S9-A | RS9A_YEAST 2-197
SM sM | Suppressor protein STM1 | STM1_YEAST 1-273
SR sR | Guanine nucleotide-binding protein subunit beta-like protein |
GBLP_YEAST 2-319
e0 | 40S ribosomal protein S30-A | RS30A_YEAST 2-63
m2 | Unknown protein m2 |
p0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 2-312
p1 | Unknown protein p1 |
p2 | Unknown protein p2 |
Non-standard residues in 4u4n #3
---
EDE — edeine B
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
4u4n mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> sym #3 assembly 1
Made 1 copies for 4u4n assembly 1
> view
> close #3
> hide #!4 models
> show #!4 models
> select add #4
203998 atoms, 214099 bonds, 8467 pseudobonds, 17698 residues, 5 models
selected
> select subtract #4.1
1 model selected
> show #!2#!4.1 cartoons
> hide #!2#!4.1 atoms
> select add #4
203998 atoms, 214099 bonds, 8467 pseudobonds, 17698 residues, 5 models
selected
> select subtract #4.1
1 model selected
> select add #4
203998 atoms, 214099 bonds, 8467 pseudobonds, 17698 residues, 5 models
selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #4.1/2 to #1/A pairing ss matrix Nucleic
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 1i95, chain A (#1) with 4u4n, chain 2 (#4.1), sequence alignment
score = 2307
RMSD between 368 pruned atom pairs is 1.119 angstroms; (across all 1438 pairs:
26.088)
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select ::name="EDE"
110 atoms, 110 bonds, 2 residues, 2 models selected
> show sel & #!4.1 atoms
> select add #4.1
204053 atoms, 214154 bonds, 8467 pseudobonds, 17699 residues, 5 models
selected
> select subtract #4.1
55 atoms, 55 bonds, 1 residue, 1 model selected
> select add #1
36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected
> select subtract #1
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
203943 atoms, 214044 bonds, 8467 pseudobonds, 17697 residues, 4 models
selected
> delete sel
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> hide #!4.1 models
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb
Chain information for refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb #3
---
Chain | Description
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
Y | No description available
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #3/B to #1/A pairing ss matrix Nucleic
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 1i95, chain A (#1) with
refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb, chain B (#3), sequence alignment
score = 2567.8
RMSD between 662 pruned atom pairs is 1.173 angstroms; (across all 1026 pairs:
39.583)
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
36795 atoms, 37750 bonds, 4 pseudobonds, 4387 residues, 2 models selected
> show sel cartoons
> show sel atoms
> hide #!1 models
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> select add #3
36795 atoms, 37750 bonds, 4 pseudobonds, 4387 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> select #1/A:2001@C2
1 atom, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
36169 atoms, 36529 bonds, 5311 pseudobonds, 4015 residues, 4 models selected
> delete sel
> show #!2 models
> select #2/Y:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
439 atoms, 494 bonds, 20 residues, 1 model selected
> select add #2/Z:36
459 atoms, 515 bonds, 21 residues, 1 model selected
> select up
2085 atoms, 2332 bonds, 97 residues, 1 model selected
> select ~sel & ##selected
57385 atoms, 61648 bonds, 1742 pseudobonds, 4643 residues, 4 models selected
> delete sel
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select ::name="EDE"
165 atoms, 165 bonds, 3 residues, 3 models selected
> show sel & #!1,3 atoms
> hide #!3 models
> show #!3 models
> select add #3
36905 atoms, 37860 bonds, 4 pseudobonds, 4389 residues, 4 models selected
> select subtract #3
110 atoms, 110 bonds, 2 residues, 2 models selected
> select subtract #1
55 atoms, 55 bonds, 1 residue, 1 model selected
> select add #1
110 atoms, 110 bonds, 2 residues, 2 models selected
> hide #!1 models
> select subtract #1
55 atoms, 55 bonds, 1 residue, 1 model selected
> select up
57 atoms, 56 bonds, 2 residues, 2 models selected
> select up
110 atoms, 110 bonds, 2 residues, 2 models selected
> select add #3/Y:21
132 atoms, 134 bonds, 3 residues, 2 models selected
> select up
763 atoms, 845 bonds, 32 residues, 2 models selected
> select ~sel & ##selected
36087 atoms, 36960 bonds, 4 pseudobonds, 4356 residues, 2 models selected
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> color #4 #941100ff models
> select #3/6:2202@C12
1 atom, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> select add #3
708 atoms, 790 bonds, 31 residues, 1 model selected
> color #4 #fffc79ff models
> hide #!3 models
> lighting soft
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #4
55 atoms, 55 bonds, 1 residue, 2 models selected
> select subtract #4
Nothing selected
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
> hide #!4.1 models
> hide #!3 models
> show #!4.1 models
> show #!3 models
> hide #!4 models
> rmsd #3/6 to #4.1/2
RMSD between 55 atom pairs is 1.177
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!4.1 models
> combine #3
> hide #!3 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> rmsd #3/6 to #5/6
RMSD between 55 atom pairs is 0.000
> hide #!5 models
> show #!5 models
> show #!4.1 models
> save /Users/Haaris/Desktop/image1.png supersample 3
> save /Users/Haaris/Desktop/image2.png supersample 3
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
——— End of log from Fri Apr 26 17:08:38 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> select #1/A:2001@C16
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 1 residue, 1 model selected
> select color yellow
Expected an objects specifier or a keyword
> color sel yellow
> color sel byhetero
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> color #1 #f0fe76ff
> color #1 #9dfe20ff
> color #1 #b5fe29ff
> color #1 #feea85ff
> color #1 #feec9dff
> color #1 #daca86ff
> color #1 #dad625ff
> color #1 #dacc47ff
> color #1 #dac830ff
> color sel byhetero
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!5 models
> show #!5 models
> select subtract #1
Nothing selected
> lighting soft
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/Y:37
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
439 atoms, 494 bonds, 20 residues, 1 model selected
> combine sel
> hide #!6 models
> show #!6 models
> hide #!2 models
> select add #2
2085 atoms, 2332 bonds, 82 pseudobonds, 97 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!6 models
> select #6/Z:45
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1646 atoms, 1838 bonds, 77 residues, 1 model selected
> delete sel
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> combine 5
Expected a keyword
> combine #5
> hide #!7 models
> hide #!5 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> select #7/Y:22
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
653 atoms, 735 bonds, 30 residues, 1 model selected
> delete sel
> show #!6 models
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs
> includeMaps true
> foto
> save
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_with_Ada
> format tiff height 4000 width 5500 supersample 4 transparentBackground false
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/run_class001_Edeine_onlybody.mrc
Opened run_class001_Edeine_onlybody.mrc as #8, grid size 400,400,400, pixel
0.832, shown at level 0.00302, step 2, values float32
> close #8
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> show #!3 models
> open
> /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/run_class001_Edeine_onlybody.mrc
Opened run_class001_Edeine_onlybody.mrc as #8, grid size 400,400,400, pixel
0.832, shown at level 0.00302, step 2, values float32
> select add #8
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.89286,0.4442,-0.074029,-44.866,-0.45033,0.88074,-0.14664,120.28,6.2546e-05,0.16427,0.98642,-25.556
> view matrix models
> #8,0.89286,0.4442,-0.074029,-80.844,-0.45033,0.88074,-0.14664,93.786,6.2546e-05,0.16427,0.98642,-28.837
> view matrix models
> #8,0.96599,0.015018,-0.25815,9.2204,0.2263,0.43395,0.87205,-110.98,0.12512,-0.90081,0.4158,222.71
> view matrix models
> #8,0.96599,0.015018,-0.25815,-61.141,0.2263,0.43395,0.87205,-142.45,0.12512,-0.90081,0.4158,154.68
> view matrix models
> #8,0.96599,0.015018,-0.25815,-126.02,0.2263,0.43395,0.87205,-92.781,0.12512,-0.90081,0.4158,167.21
> view matrix models
> #8,0.074988,0.77366,-0.62914,-42.941,0.89035,0.23217,0.39162,-93.064,0.44906,-0.58953,-0.67142,236.52
> view matrix models
> #8,0.074988,0.77366,-0.62914,-13.809,0.89035,0.23217,0.39162,-129.19,0.44906,-0.58953,-0.67142,238.32
> view matrix models
> #8,0.2847,0.5655,-0.77405,9.3989,0.9438,-0.023944,0.32964,-84.895,0.16788,-0.8244,-0.54054,304.35
> view matrix models
> #8,0.2847,0.5655,-0.77405,-5.0169,0.9438,-0.023944,0.32964,-83.636,0.16788,-0.8244,-0.54054,312.14
> view matrix models
> #8,0.2847,0.5655,-0.77405,-3.1863,0.9438,-0.023944,0.32964,-87.321,0.16788,-0.8244,-0.54054,309.38
> color #8 #b2b2b226 models
> view matrix models
> #8,0.2382,0.80003,-0.55066,-71.257,0.84314,-0.45175,-0.29161,103.02,-0.48205,-0.39482,-0.78214,386.17
> view matrix models
> #8,0.2382,0.80003,-0.55066,-57.399,0.84314,-0.45175,-0.29161,97.153,-0.48205,-0.39482,-0.78214,377.23
> view matrix models
> #8,0.2382,0.80003,-0.55066,-70.422,0.84314,-0.45175,-0.29161,89.889,-0.48205,-0.39482,-0.78214,369.41
> view matrix models
> #8,0.2382,0.80003,-0.55066,-67.972,0.84314,-0.45175,-0.29161,88.749,-0.48205,-0.39482,-0.78214,370.73
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,0.2382,0.80003,-0.55066,-69.143,0.84314,-0.45175,-0.29161,88.4,-0.48205,-0.39482,-0.78214,370.41
> view matrix models
> #8,-0.19437,0.87045,-0.45226,-23.765,0.72776,-0.18117,-0.66147,122.37,-0.65771,-0.4577,-0.59826,380.89
> color #8 #b2b2b2ff models
> view matrix models
> #8,-0.15962,0.93417,-0.31915,-62.059,0.76927,-0.084906,-0.63326,94.482,-0.61867,-0.34659,-0.70507,372.87
> view matrix models
> #8,-0.44283,0.79689,-0.41094,24.036,-0.045268,-0.47762,-0.8774,338.51,-0.89546,-0.36993,0.24758,268.81
> view matrix models
> #8,-0.44283,0.79689,-0.41094,36.145,-0.045268,-0.47762,-0.8774,339.73,-0.89546,-0.36993,0.24758,284.76
> view matrix models
> #8,-0.082571,0.8367,-0.5414,-10.398,-0.39438,-0.52634,-0.75328,386.92,-0.91523,0.15132,0.37344,179.57
> view matrix models
> #8,-0.082571,0.8367,-0.5414,-16.86,-0.39438,-0.52634,-0.75328,390.61,-0.91523,0.15132,0.37344,169.84
> view matrix models
> #8,0.018219,0.84909,-0.52793,-38.217,-0.32402,-0.49451,-0.80652,381.97,-0.94587,0.18576,0.26611,186.66
> select subtract #8
Nothing selected
> select add #8
2 models selected
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #8
2 models selected
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.018219,0.84909,-0.52793,-46.004,-0.32402,-0.49451,-0.80652,372.41,-0.94587,0.18576,0.26611,226.7
> view matrix models
> #8,0.03487,0.79354,-0.60752,-26.499,-0.14932,-0.59693,-0.78828,357.15,-0.98817,0.1182,0.097675,272.67
> view matrix models
> #8,-0.29357,0.95513,0.039266,-103.42,-0.34771,-0.068431,-0.9351,325.43,-0.89046,-0.28817,0.3522,283.52
> select subtract #8
Nothing selected
> hide #!3 models
> show #!3 models
> select add #8
2 models selected
> view matrix models
> #8,0.052431,0.86343,-0.50173,-58.58,0.069411,-0.50436,-0.8607,316.32,-0.99621,0.010302,-0.086376,322.31
> view matrix models
> #8,0.052431,0.86343,-0.50173,-146.1,0.069411,-0.50436,-0.8607,256.26,-0.99621,0.010302,-0.086376,376.82
> view matrix models
> #8,0.052431,0.86343,-0.50173,-33.859,0.069411,-0.50436,-0.8607,284.18,-0.99621,0.010302,-0.086376,328.89
> view matrix models
> #8,0.052431,0.86343,-0.50173,-59.256,0.069411,-0.50436,-0.8607,290.89,-0.99621,0.010302,-0.086376,315.39
> view matrix models
> #8,0.052431,0.86343,-0.50173,-61.242,0.069411,-0.50436,-0.8607,293.01,-0.99621,0.010302,-0.086376,317.99
> view matrix models
> #8,0.052431,0.86343,-0.50173,-62.657,0.069411,-0.50436,-0.8607,301.59,-0.99621,0.010302,-0.086376,318.75
> view matrix models
> #8,0.052431,0.86343,-0.50173,-56.449,0.069411,-0.50436,-0.8607,300.55,-0.99621,0.010302,-0.086376,308.24
> hide #!3 models
> show #!3 models
> hide #!1 models
> fitmap #3 inMap #8
Fit molecule refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) to map
run_class001_Edeine_onlybody.mrc (#8) using 708 atoms
average map value = 0.003234, steps = 152
shifted from previous position = 13.5
rotated from previous position = 16.6 degrees
atoms outside contour = 459, contour level = 0.0030202
Position of refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) relative to
run_class001_Edeine_onlybody.mrc (#8) coordinates:
Matrix rotation and translation
0.22159999 0.91568770 -0.33527523 42.43217313
0.97513628 -0.20866734 0.07461356 3.19668773
-0.00163827 -0.34347341 -0.93916097 310.81311902
Axis -0.77684435 -0.61992841 0.11046097
Axis point 0.00000000 12.09526762 158.17476924
Rotation angle (degrees) 164.38968959
Shift along axis -0.61219347
> view matrix models
> #8,0.094159,0.84381,-0.52831,-55.882,0.043931,-0.53367,-0.84455,307.2,-0.99459,0.056312,-0.08732,300.34
> view matrix models
> #8,0.055098,0.80873,-0.58559,-34.024,0.38431,-0.55848,-0.73513,235.94,-0.92156,-0.18454,-0.34157,370.01
> view matrix models
> #8,0.055098,0.80873,-0.58559,-52.193,0.38431,-0.55848,-0.73513,231.89,-0.92156,-0.18454,-0.34157,373.68
> view matrix models
> #8,0.055098,0.80873,-0.58559,-36.667,0.38431,-0.55848,-0.73513,231.52,-0.92156,-0.18454,-0.34157,366.09
> select add #2
2085 atoms, 2332 bonds, 82 pseudobonds, 97 residues, 4 models selected
> select subtract #2
2 models selected
> select subtract #8
Nothing selected
> select add #3
708 atoms, 790 bonds, 31 residues, 1 model selected
> view matrix models
> #3,0.20337,0.028448,0.97869,-131.45,0.048046,-0.99866,0.019045,292.88,0.97792,0.043148,-0.20446,-96.216
> view matrix models
> #3,0.5424,-0.053042,0.83845,-168.25,-0.76325,-0.44817,0.4654,300.54,0.35108,-0.89237,-0.28357,217.49
> view matrix models
> #3,0.5424,-0.053042,0.83845,-166.39,-0.76325,-0.44817,0.4654,301.28,0.35108,-0.89237,-0.28357,217.49
> view matrix models
> #3,0.70911,0.038589,0.70404,-199.97,-0.67813,-0.23616,0.69596,213.48,0.19312,-0.97095,-0.14129,245.78
> view matrix models
> #3,0.70911,0.038589,0.70404,-195.64,-0.67813,-0.23616,0.69596,216.59,0.19312,-0.97095,-0.14129,254.46
> view matrix models
> #3,0.70911,0.038589,0.70404,-195.19,-0.67813,-0.23616,0.69596,217.9,0.19312,-0.97095,-0.14129,256.42
> view matrix models
> #3,0.70911,0.038589,0.70404,-192.72,-0.67813,-0.23616,0.69596,213.88,0.19312,-0.97095,-0.14129,253.43
> fitmap #3 inMap #8
Fit molecule refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) to map
run_class001_Edeine_onlybody.mrc (#8) using 708 atoms
average map value = 0.002582, steps = 144
shifted from previous position = 4.68
rotated from previous position = 5.02 degrees
atoms outside contour = 503, contour level = 0.0030202
Position of refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) relative to
run_class001_Edeine_onlybody.mrc (#8) coordinates:
Matrix rotation and translation
-0.45871848 0.79756503 0.39174911 104.42482652
0.88853952 0.41600628 0.19348462 -98.15999097
-0.00865352 0.43683954 -0.89949782 159.85337762
Axis 0.50985182 0.83888180 0.19060024
Axis point 93.55905537 0.00000000 83.59244137
Rotation angle (degrees) 166.19297094
Shift along axis 1.36464920
> view matrix models
> #3,0.69838,0.12457,0.7048,-211.19,-0.66616,-0.24695,0.70374,200.6,0.26172,-0.96099,-0.089482,224.83
> view matrix models
> #3,0.7746,0.029621,0.63176,-199.76,-0.62228,0.21419,0.75292,99.856,-0.11301,-0.97634,0.18434,268.97
> view matrix models
> #3,0.76503,0.052047,0.64189,-203.26,-0.63859,0.19014,0.74569,108.66,-0.083239,-0.98038,0.1787,264.27
> view matrix models
> #3,0.76503,0.052047,0.64189,-202.45,-0.63859,0.19014,0.74569,113.06,-0.083239,-0.98038,0.1787,268.68
> fitmap #3 inMap #8
Fit molecule refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) to map
run_class001_Edeine_onlybody.mrc (#8) using 708 atoms
average map value = 0.003038, steps = 156
shifted from previous position = 1.85
rotated from previous position = 9.44 degrees
atoms outside contour = 464, contour level = 0.0030202
Position of refined_Ede_Round5-coot-1_withW_KSGmRNA.pdb (#3) relative to
run_class001_Edeine_onlybody.mrc (#8) coordinates:
Matrix rotation and translation
-0.01101930 0.99894297 0.04462627 23.00962269
0.99638124 0.00720761 0.08469049 -33.82580862
0.08427933 0.04539801 -0.99540746 231.14383046
Axis -0.70312990 -0.70958219 -0.04584172
Axis point 25.98930207 0.00000000 116.87191456
Rotation angle (degrees) 178.39888286
Shift along axis -2.77259432
> view matrix models
> #3,0.75584,0.034284,0.65385,-201.08,-0.62265,0.3465,0.7016,87.991,-0.20251,-0.93742,0.28325,270.75
> view matrix models
> #3,0.75414,0.044683,0.65519,-202.82,-0.62059,0.37482,0.68875,84.07,-0.2148,-0.92602,0.3104,267.56
> view matrix models
> #3,0.75414,0.044683,0.65519,-202.94,-0.62059,0.37482,0.68875,86.145,-0.2148,-0.92602,0.3104,269.54
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 662, in _wheel_event
f.wheel(MouseEvent(event))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 336, in wheel
a = self.action(event)
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 350, in action
if event.ctrl_down():
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 698, in ctrl_down
return bool(self._event.modifiers() & Qt.KeyboardModifier.CtrlModifier)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
AttributeError: CtrlModifier
AttributeError: CtrlModifier
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py",
line 789, in __getattr__
raise AttributeError(name) from None
See log for complete Python traceback.
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3,7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 32 GB
System Firmware Version: 2020.80.5.0.0
OS Loader Version: 580~1678
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 32 days, 45 minutes
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 0FFXD31242JL
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 months ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Mouse wheel: no Qt.KeyboardModifier.CtrlModifier |
comment:2 by , 18 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
I am not able to reproduce this error. It appears that it happened while using the mouse wheel with the ctrl key pressed. That does not produce any error for me with the same ChimeraX 1.7.1 and macOS 14.4.1. The error also seems to say that the Qt.KeyboardModifier.CtrlModifier does not exist, but that code is used all the time when the mouse and ctrl key are used (e.g. for selecting atoms). This makes me think ChimeraX maybe encountered memory corruption. The ChimeraX 1.7.1 version is known to have a Python garbage collection bug that might possibly cause that. That bug is fixed in the daily builds.
If you have a way to reproduce this error, tell me and I will try your exact steps.