id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15064 Mouse wheel: no Qt.KeyboardModifier.CtrlModifier haaris.safdari@… Tom Goddard "{{{ 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 }}} " defect closed normal UI can't reproduce all ChimeraX