id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15070 Crash in garbage collection haaris.safdari@… Eric Pettersen "{{{ 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 Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff85f1a5100 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 334 in _qt_safe File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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All rights reserved. > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs Log from Mon Apr 29 15:45:41 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 > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb Chain information for refined_Ede_Round5-coot-1_withW.pdb #1 --- 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 > 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 > hide #!1 models > show #!1 models > ui tool show Matchmaker > matchmaker #2/A to #1/B 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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 5lmv, chain A (#2), sequence alignment score = 2553.7 RMSD between 463 pruned atom pairs is 1.372 angstroms; (across all 1023 pairs: 39.083) > hide #!2 models > select add #1 36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > show #!2 models > show #!2 cartoons > hide #!2 atoms > show #!1 models > hide #!2 models > open 1i95 1i95 title: Crystal structure of the 30S ribosomal subunit from thermus thermophilus In complex with edeine [more info...] Chain information for 1i95 #3 --- 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 #3 --- EDE — edeine B MG — magnesium ion WO2 — octadecatungstenyl diphosphate ZN — zinc ion > select add #3 36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected > show sel cartoons > hide sel atoms > select subtract #3 Nothing selected > ui tool show Matchmaker > matchmaker #3/A to #1/B 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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 1i95, chain A (#3), sequence alignment score = 2559.4 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 #!2 models > hide #!2 models > open /Users/Haaris/Desktop/Figures_Ksg_Edeine/4u4n_model.pdb Summary of feedback from opening /Users/Haaris/Desktop/Figures_Ksg_Edeine/4u4n_model.pdb --- warnings | Cannot find LINK/SSBOND residue ZN (500 ) Cannot find LINK/SSBOND residue ZN (500 ) Cannot find LINK/SSBOND residue ZN (500 ) Cannot find LINK/SSBOND residue ZN (500 ) Cannot find LINK/SSBOND residue ZN (101 ) 33 messages similar to the above omitted Chain information for 4u4n_model.pdb #4 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available C0 | No description available C1 | No description available C2 | No description available C3 | No description available C4 | No description available C5 | No description available C6 | No description available C7 | No description available C8 | No description available C9 | No description available D0 | No description available D1 | No description available D2 | No description available D3 | No description available D4 | No description available D5 | No description available D6 | No description available D7 | No description available D8 | No description available D9 | No description available E0 | No description available E1 | No description available L2 | No description available L3 | No description available L4 | No description available L5 | No description available L6 | No description available L7 | No description available L8 | No description available L9 | No description available M0 | No description available M1 | No description available M3 | No description available M4 | No description available M5 | No description available M6 | No description available M7 | No description available M8 | No description available M9 | No description available N0 | No description available N1 | No description available N2 | No description available N3 | No description available N4 | No description available N5 | No description available N6 | No description available N7 | No description available N8 | No description available N9 | No description available O0 | No description available O1 | No description available O2 | No description available O3 | No description available O4 | No description available O5 | No description available O6 | No description available O7 | No description available O8 | No description available O9 | No description available Q0 | No description available Q1 | No description available Q2 | No description available Q3 | No description available S0 | No description available S1 | No description available S2 | No description available S3 | No description available S4 | No description available S5 | No description available S6 | No description available S7 | No description available S8 | No description available S9 | No description available SM | No description available SR | No description available > select add #4 203998 atoms, 214099 bonds, 3903 pseudobonds, 17698 residues, 3 models selected > hide #!3 models > hide #!1 models > show sel cartoons > hide sel atoms > select subtract #4 Nothing selected > show #!3 models > hide #!4 models > hide #!3 models > show #!1 models > ui tool show Matchmaker > matchmaker #4/2 to #1/B 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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 4u4n_model.pdb, chain 2 (#4), sequence alignment score = 1453 RMSD between 241 pruned atom pairs is 1.093 angstroms; (across all 1014 pairs: 52.158) > 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 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs > includeMaps true > hide #!4 models > select ::name=""EDE"" 165 atoms, 165 bonds, 3 residues, 3 models selected > show sel & #!1 atoms > select add #3 36334 atoms, 36694 bonds, 5311 pseudobonds, 4018 residues, 6 models selected > select add #4 240277 atoms, 250738 bonds, 9214 pseudobonds, 21715 residues, 8 models selected > select subtract #3 204053 atoms, 214154 bonds, 3903 pseudobonds, 17699 residues, 4 models selected > select subtract #4 55 atoms, 55 bonds, 1 residue, 1 model selected > select add #1 36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected > select subtract #1 Nothing selected > select #1/B:770 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 22602 atoms, 25313 bonds, 1051 residues, 1 model selected > select down 20 atoms, 21 bonds, 1 residue, 1 model selected > select down 20 atoms, 21 bonds, 1 residue, 1 model selected > select clear > 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 36087 atoms, 36959 bonds, 4 pseudobonds, 4356 residues, 2 models selected > delete sel > ui mousemode right distance > 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 > style sel sphere Changed 55 atom styles > style sel stick Changed 55 atom styles > ui tool show Clashes > clashes sel restrict both interModel false intraMol false select true reveal > true log true Allowed overlap: 0.6 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: False Detect intra-molecule clashes: False 0 clashes atom1 atom2 overlap distance No clashes > select add #1 55 atoms, 55 bonds, 1 residue, 1 model selected > ui tool show Clashes > clashes sel restrict both interModel false intraRes true intraMol false > select true reveal true log true Allowed overlap: 0.6 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: False 0 clashes atom1 atom2 overlap distance No clashes > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #2 /Y /Z 2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected > select ~sel & ##selected 57375 atoms, 61640 bonds, 1741 pseudobonds, 4641 residues, 4 models selected > delete sel > show #!1 models > hide #!1 models > show #!1 models > lighting soft > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > select ::name=""EDE"" 165 atoms, 165 bonds, 3 residues, 3 models selected > select subtract #1 110 atoms, 110 bonds, 2 residues, 2 models selected > select add #4 204053 atoms, 214154 bonds, 3903 pseudobonds, 17699 residues, 4 models selected > select subtract #4 55 atoms, 55 bonds, 1 residue, 1 model selected > show sel atoms > select ~sel & ##selected 36169 atoms, 36529 bonds, 5311 pseudobonds, 4015 residues, 4 models selected > delete sel > show #!4 models > hide #!3 models > select ::name=""EDE"" 165 atoms, 165 bonds, 3 residues, 3 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 ~sel & ##selected 203943 atoms, 214044 bonds, 3903 pseudobonds, 17697 residues, 3 models selected > delete sel > show #!3 models > show #!2 models > show #!1 models > select #2/Y:34 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 439 atoms, 494 bonds, 20 residues, 1 model selected > color sel saömon Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel salmon > select add #2 2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected > select subtract #2 Nothing selected > select #2/Z:26 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1646 atoms, 1838 bonds, 77 residues, 1 model selected > color sel orange > select add #2 2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected > select subtract #2 Nothing selected > select add #3 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select subtract #3 Nothing selected > color #3 #e9e84cff > color #3 #e5e34bff > color #3 #e0e55fff > color #3 #e4e500ff > color #3 #d8d900ff > color #3 #e8e800ff > color #3 #e3e848ff > color #3 #e2e841ff > color byhetero > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > select #1/6:2202@C35 1 atom, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel f14blau > color sel byhetero > select subtract #1 Nothing selected > foto > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1 > format tiff height 4000 width 5500 supersample 4 transparentBackground false > show #!3 models > foto > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2 > format tiff height 4000 width 5500 supersample 4 transparentBackground false > hide #!2 models > show #!2 models > hide #!1 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > select ::name=""EDE"" 165 atoms, 165 bonds, 3 residues, 3 models selected > show sel & #!4 atoms > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!4 models > show #!4 models > show #!2 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > view name 1 > select subtract #4 110 atoms, 110 bonds, 2 residues, 2 models selected > select add #4 165 atoms, 165 bonds, 3 residues, 3 models selected > hide #!4 models > show #!4 models > hide #!4 models > hide #!1 models > show #!4 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel brown > color #4 #ca544bff > color #4 #a8463eff > color sel byhetero > select subtract #4 Nothing selected > select add #4 55 atoms, 55 bonds, 1 residue, 1 model selected > select subtract #4 Nothing selected > show #!1 models > hide #!1 models > show #!1 models > foto > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3 > format tiff height 4000 width 5500 supersample 4 transparentBackground false > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs > includeMaps true > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > hide #!4 models > hide #!1 models > 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 #5 --- 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 #5 --- FME — N-formylmethionine MG — magnesium ion ZN — zinc ion > select add #5 59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected > show sel cartoons > hide sel atoms > hide #!2 models > select subtract #5 Nothing selected > select #5/Y:36 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 439 atoms, 494 bonds, 20 residues, 1 model selected > select add #5/Z:11 461 atoms, 518 bonds, 21 residues, 1 model selected > select up 2085 atoms, 2332 bonds, 97 residues, 1 model selected > delete sel > close #5 > 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 #5 --- 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 #5 --- FME — N-formylmethionine MG — magnesium ion ZN — zinc ion > select add #5 59470 atoms, 63980 bonds, 1824 pseudobonds, 4740 residues, 4 models selected > show sel cartoons > hide sel atoms > select subtract #5 Nothing selected > ui tool show Matchmaker > matchmaker #5/Y to #2/Y 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 5lmv, chain Y (#2) with 5lmv, chain Y (#5), sequence alignment score = 141.6 RMSD between 20 pruned atom pairs is 0.000 angstroms; (across all 20 pairs: 0.000) > show #!2 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > color #5 silver > select #5/a:562 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 40 atoms, 40 bonds, 5 residues, 1 model selected > select up 692 atoms, 701 bonds, 88 residues, 1 model selected > select up 724 atoms, 732 bonds, 93 residues, 1 model selected > select up 2356 atoms, 2384 bonds, 316 residues, 1 model selected > select up 2384 atoms, 2412 bonds, 319 residues, 1 model selected > delete sel > select #5/X:104 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 163 atoms, 166 bonds, 19 residues, 1 model selected > select up 719 atoms, 729 bonds, 88 residues, 1 model selected > select up 1336 atoms, 1354 bonds, 164 residues, 1 model selected > delete sel > hide #!5 models > show #!5 models > hide #!5 models > hide #!2 models > show #!5 models > select #5 /Y /Z 2095 atoms, 2340 bonds, 83 pseudobonds, 99 residues, 3 models selected > delete sel > select add #5 53655 atoms, 57873 bonds, 1716 pseudobonds, 4158 residues, 4 models selected > select subtract #5 Nothing selected > show #!2 models > view list Named views: 1 > view 1 > view list Named views: 1 > view 1 > ui tool show ""Side View"" > view list Named views: 1 > view 1 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > lighting soft > foto > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1_back > format tiff height 4000 width 5500 supersample 4 transparentBackground false > show #!2 models > hide #!5 models > show #!1 models > lighting soft > durch Command cancelled by user > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > show #!3 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_1 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > view name 2 > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs > includeMaps true > show #!3 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_2 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > hide #!3 models > show #!4 models > durch > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/comparsion_Ede_3 > format tiff height 4000 width 5500 supersample 4 transparentBackground true > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparison_Edeine.cxs > includeMaps true ——— End of log from Mon Apr 29 15:45:41 2024 ——— opened ChimeraX session > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > show #!3 models > hide #!4 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 #!1 models > show #!1 models > ui tool show Matchmaker > matchmaker #!3 to #1 No matrix compatible with both reference structure and all match structures > align #3 toAtoms #1 RMSD between 55 atom pairs is 5.926 angstroms Drag select of 7 atoms, 7 bonds > align #3:sel toAtoms #1:sel No atoms paired for alignment > align sel Missing required ""to_atoms"" argument > ui tool show Matchmaker No reference and/or match structure/chain chosen > matchmaker #!3 & sel to #1 & sel No matrix compatible with both reference structure and all match structures > matchmaker #!3 & sel to #1 & sel No matrix compatible with both reference structure and all match structures > select add #1 62 atoms, 62 bonds, 2 residues, 2 models selected > select add #3 110 atoms, 110 bonds, 2 residues, 2 models selected > select subtract #3 55 atoms, 55 bonds, 1 residue, 1 model selected > select add #3 110 atoms, 110 bonds, 2 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.93896,0.24644,-0.24005,1.5335,-0.23785,0.96915,0.064567,46.238,0.24855,-0.0035302,0.96861,-46.865,#3,-0.12274,-0.79378,0.5957,217.67,-0.36837,-0.52092,-0.77003,328.04,0.92154,-0.31395,-0.22846,168.04 > select subtract #1 55 atoms, 55 bonds, 1 residue, 1 model selected > view matrix models > #3,0.61519,0.047618,0.78694,87.36,0.78051,-0.17753,-0.59941,245.77,0.11116,0.98296,-0.14638,34.031 > view matrix models > #3,0.61519,0.047618,0.78694,86.055,0.78051,-0.17753,-0.59941,245.62,0.11116,0.98296,-0.14638,32.991 > view matrix models > #3,0.45792,-0.22054,0.8612,108.56,0.88878,0.092631,-0.44887,194.88,0.019219,0.97097,0.23843,-13.508 > view matrix models > #3,0.45792,-0.22054,0.8612,104.74,0.88878,0.092631,-0.44887,191.45,0.019219,0.97097,0.23843,-11.289 > view matrix models > #3,-0.24583,-0.63934,0.72857,181.24,0.9182,-0.39446,-0.036338,190.13,0.31062,0.66004,0.68401,-41.156 > view matrix models > #3,-0.24583,-0.63934,0.72857,185.03,0.9182,-0.39446,-0.036338,189.54,0.31062,0.66004,0.68401,-38.528 > view matrix models > #3,0.093225,-0.5029,0.8593,146.6,0.91024,-0.30667,-0.27823,211.45,0.40344,0.80811,0.42917,-23.487 > view matrix models > #3,0.093225,-0.5029,0.8593,146.31,0.91024,-0.30667,-0.27823,208.81,0.40344,0.80811,0.42917,-25.131 > view matrix models > #3,0.095368,0.1061,-0.98977,319.2,-0.87419,-0.46665,-0.13425,243.57,-0.47613,0.87805,0.048245,34.27 > view matrix models > #3,0.095368,0.1061,-0.98977,320.17,-0.87419,-0.46665,-0.13425,251.42,-0.47613,0.87805,0.048245,38.376 > view matrix models > #3,0.29208,-0.015669,-0.95627,325,-0.81297,-0.53072,-0.23961,270.68,-0.50375,0.8474,-0.16775,70.109 > view matrix models > #3,0.29208,-0.015669,-0.95627,320.82,-0.81297,-0.53072,-0.23961,269.41,-0.50375,0.8474,-0.16775,68.83 > view matrix models > #3,0.29208,-0.015669,-0.95627,321.08,-0.81297,-0.53072,-0.23961,270.62,-0.50375,0.8474,-0.16775,69.133 > view matrix models > #3,0.29208,-0.015669,-0.95627,320.38,-0.81297,-0.53072,-0.23961,270.56,-0.50375,0.8474,-0.16775,69.12 > view matrix models > #3,0.19915,-0.0092373,-0.97993,324.62,-0.83064,-0.53218,-0.16379,261.29,-0.51998,0.84658,-0.11366,62.557 > view matrix models > #3,0.19915,-0.0092373,-0.97993,325.17,-0.83064,-0.53218,-0.16379,261.27,-0.51998,0.84658,-0.11366,62.657 > view matrix models > #3,-0.14466,-0.085148,-0.98581,341.06,-0.86504,-0.47281,0.16778,212.78,-0.48039,0.87704,-0.0052584,44.586 > view matrix models > #3,-0.14466,-0.085148,-0.98581,341.56,-0.86504,-0.47281,0.16778,214.25,-0.48039,0.87704,-0.0052584,45.314 > view matrix models > #3,0.14651,-0.12901,-0.98076,339.75,-0.83908,-0.54132,-0.054134,249.74,-0.52392,0.83086,-0.18756,74.695 > view matrix models > #3,0.14651,-0.12901,-0.98076,339.31,-0.83908,-0.54132,-0.054134,248.85,-0.52392,0.83086,-0.18756,73.792 > view matrix models > #3,0.017885,-0.15035,-0.98847,345.21,-0.83519,-0.54575,0.067899,233.5,-0.54967,0.82435,-0.13533,68.276 > view matrix models > #3,0.017885,-0.15035,-0.98847,345.32,-0.83519,-0.54575,0.067899,233.95,-0.54967,0.82435,-0.13533,68.574 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.23,-0.80839,-0.58713,0.04224,241.18,-0.58591,0.79564,-0.15383,74.79 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.29,-0.80839,-0.58713,0.04224,241.09,-0.58591,0.79564,-0.15383,75.003 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.25,-0.80839,-0.58713,0.04224,240.72,-0.58591,0.79564,-0.15383,74.866 > view matrix models > #3,0.056714,-0.14911,-0.98719,351.37,-0.80839,-0.58713,0.04224,238.87,-0.58591,0.79564,-0.15383,78.146 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.4,-0.80839,-0.58713,0.04224,240.67,-0.58591,0.79564,-0.15383,74.717 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.95,-0.80839,-0.58713,0.04224,240.87,-0.58591,0.79564,-0.15383,75.034 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.34,-0.80839,-0.58713,0.04224,240.63,-0.58591,0.79564,-0.15383,74.857 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.17,-0.80839,-0.58713,0.04224,240.72,-0.58591,0.79564,-0.15383,74.923 > view matrix models > #3,0.056714,-0.14911,-0.98719,344.2,-0.80839,-0.58713,0.04224,240.75,-0.58591,0.79564,-0.15383,74.943 > select subtract #3 Nothing selected > select add #3 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel #FAFF95 > select subtract #3 Nothing selected > select add #3 55 atoms, 55 bonds, 1 residue, 1 model selected > select subtract #3 Nothing selected > select add #3 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel byhetero > select subtract #3 Nothing selected > lighting soft > foto > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/Comparsion_Sup_Edeine- > My_Ada format tiff height 4000 width 5500 supersample 4 > transparentBackground false > close #3 > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome.cxs opened ChimeraX session > close #2 > close #1 > select ::name=""EDE"" 55 atoms, 55 bonds, 1 residue, 1 model selected > show sel atoms > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/postprocess_masked_Edeine_onlybody.mrc Opened postprocess_masked_Edeine_onlybody.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00533, step 2, values float32 > volume #1 step 1 > volume #1 level 0.0132 > fitmap #3 inMap #1 Fit molecule combination (#3) to map postprocess_masked_Edeine_onlybody.mrc (#1) using 36224 atoms average map value = 0.01075, steps = 84 shifted from previous position = 0.107 rotated from previous position = 0.185 degrees atoms outside contour = 24435, contour level = 0.013202 Position of combination (#3) relative to postprocess_masked_Edeine_onlybody.mrc (#1) coordinates: Matrix rotation and translation 0.99999736 -0.00227813 0.00029255 0.43643518 0.00227747 0.99999485 0.00226047 -0.79087533 -0.00029769 -0.00225979 0.99999740 0.50138987 Axis -0.70138787 0.09158511 0.70687143 Axis point 346.70631245 183.74693902 0.00000000 Rotation angle (degrees) 0.18462838 Shift along axis -0.02412457 > select add #3 36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected > select subtract #3 Nothing selected > hide #!1 models > color #2 f02silber > select #1 2 models selected > farben 1 Nothing selected > hide #1 > wasser 1/6:2202 1 No atoms or surfaces specified > close #3 > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.pdb Summary of feedback from opening /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.pdb --- warnings | Cannot find LINK/SSBOND residue IAS (119 ) Cannot find LINK/SSBOND residue IAS (119 ) Chain information for My_edeine_in_Thermus_ribosome.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available > show cartoons > show atoms > select add #1 36224 atoms, 36584 bonds, 3909 pseudobonds, 4016 residues, 3 models selected > show sel cartoons > hide sel atoms > select subtract #1 Nothing selected > lighting soft > select ::name=""EDE"" 55 atoms, 55 bonds, 1 residue, 1 model selected > show sel atoms > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/postprocess_masked_Edeine_onlybody.mrc Opened postprocess_masked_Edeine_onlybody.mrc as #2, grid size 400,400,400, pixel 0.832, shown at level 0.00533, step 2, values float32 > volume #2 step 1 > volume #2 level 0.01283 > surface dust #2 size 8.32 > fitmap #1 inMap #2 Fit molecule My_edeine_in_Thermus_ribosome.pdb (#1) to map postprocess_masked_Edeine_onlybody.mrc (#2) using 36224 atoms average map value = 0.01075, steps = 84 shifted from previous position = 0.105 rotated from previous position = 0.185 degrees atoms outside contour = 24230, contour level = 0.012827 Position of My_edeine_in_Thermus_ribosome.pdb (#1) relative to postprocess_masked_Edeine_onlybody.mrc (#2) coordinates: Matrix rotation and translation 0.99999733 -0.00229160 0.00028743 0.43546268 0.00229094 0.99999483 0.00225797 -0.79294388 -0.00029260 -0.00225730 0.99999741 0.50353530 Axis -0.69902318 0.08979590 0.70943871 Axis point 345.81629974 184.01838732 0.00000000 Rotation angle (degrees) 0.18504831 Shift along axis -0.01837418 > color #2 f02silber > select #1 36224 atoms, 36584 bonds, 3909 pseudobonds, 4016 residues, 3 models selected > farben 1 32534 atoms, 36417 bonds, 1514 residues, 1 model selected 2410 atoms, 2390 pseudobonds, 2410 residues, 2 models selected Nothing selected 75 atoms, 75 residues, 1 model selected Nothing selected > hide #1 > wasser 1/6:2202 1 Selected 184 atoms Nothing selected 55 atoms, 55 bonds, 1 residue, 1 model selected Selected 184 atoms > show sel > style sel stick Changed 184 atom styles > select #1:MG 75 atoms, 75 residues, 1 model selected > style sel ball Changed 75 atom styles > select #1:MG 75 atoms, 75 residues, 1 model selected > size sel ballScale 0.5 Changed 1 ball scales > hide #!2 models > da 1 184 atoms, 194 bonds, 7 residues, 1 model selected > name frozen netzwerk sel > select ~ sel 36040 atoms, 36380 bonds, 3909 pseudobonds, 4009 residues, 5 models selected > select intersect #1 36040 atoms, 36380 bonds, 3909 pseudobonds, 4009 residues, 3 models selected > color sel f02silber > upsplit 2 2 1 > spalt 2 Opened postprocess_masked_Edeine_onlybody.mrc 0 as #3.1, grid size 400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32 Opened postprocess_masked_Edeine_onlybody.mrc 1 as #3.2, grid size 400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32 Opened postprocess_masked_Edeine_onlybody.mrc 2 as #3.3, grid size 400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32 Opened postprocess_masked_Edeine_onlybody.mrc 3 as #3.4, grid size 400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32 > nicemap 3 > volume step 1 > select netzwerk 184 atoms, 194 bonds, 7 residues, 1 model selected > color sel byhetero > hide #!3.1 models > hide #!3.2 models > hide #!3.3 models > hide #!3.4 models > select ~sel & ##selected 36040 atoms, 36390 bonds, 3909 pseudobonds, 4009 residues, 3 models selected > delete sel > close #1.1 > close #1.2 > select add #1 184 atoms, 194 bonds, 7 residues, 1 model selected > show sel atoms > hide sel cartoons > select subtract #1 Nothing selected > select add #1 184 atoms, 194 bonds, 7 residues, 1 model selected > close #3 > color #1 silver > select subtract #1 Nothing selected > select /6:2202@N24 1 atom, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 1 residue, 1 model selected > color sel f14blau > color sel byhetero > select add #1 184 atoms, 194 bonds, 7 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 184 atoms, 194 bonds, 7 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #3afaf9 restrict both interModel false intraMol false > intraRes false log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 My_edeine_in_Thermus_ribosome.pdb 8 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /6 EDE 2202 N46 /A G 1482 OP2 no hydrogen 2.994 N/A /6 EDE 2202 N50 /A U 1483 OP2 no hydrogen 3.213 N/A /6 EDE 2202 O51 /A U 771 O2 no hydrogen 3.551 N/A /A G 676 N1 /A C 778 N3 no hydrogen 3.298 N/A /A G 676 N1 /A C 778 O2 no hydrogen 3.314 N/A /A G 676 N2 /A C 778 O2 no hydrogen 3.059 N/A /A C 778 N4 /A G 676 O6 no hydrogen 3.436 N/A /A G 903 N2 /6 EDE 2202 O44 no hydrogen 3.159 N/A 8 hydrogen bonds found > select add #1.1 184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected > select subtract #1 Nothing selected > select add #1.1 8 pseudobonds, 1 model selected > color sel orange > select add #1 184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected > select subtract #1 Nothing selected > view namw 1 Expected an objects specifier or a view name or a keyword > view name 1 > hide sel pbonds > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.cxs > includeMaps true > view name 1 > view list+ Expected an objects specifier or a view name or a keyword > view list Named views: 1 > view 1 > select /A:903@N2 1 atom, 1 residue, 1 model selected > select add /A:1482@OP2 2 atoms, 2 residues, 1 model selected > select add /A:1483@OP2 3 atoms, 3 residues, 1 model selected > select add /A:676@O6 4 atoms, 4 residues, 1 model selected > select add /A:771@O2 5 atoms, 5 residues, 1 model selected > select add /A:778@N4 6 atoms, 6 residues, 1 model selected > color sel byhetero > select add #1 184 atoms, 194 bonds, 8 pseudobonds, 7 residues, 2 models selected > select subtract #1 Nothing selected > foto Command cancelled by user > foto > save /Users/Haaris/Desktop/Figures_Ksg_Edeine/Ksg_Main_Figures/My_Edeine_On- > Thermus_aligned_16s format tiff height 4000 width 5500 supersample 4 > transparentBackground false > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb Chain information for refined_Ede_Round5-coot-1_withW.pdb #1 --- 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 > show cartoons > hide atoms > color #1 silver > open 5lmn 5lmn title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A) [more info...] Chain information for 5lmn #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 | Non-standard residues in 5lmn #2 --- MG — magnesium ion ZN — zinc ion > hide #!1 models > select add #2 54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected > show sel cartoons > hide sel atoms > show #!1 models > select add #1 90291 atoms, 95304 bonds, 1848 pseudobonds, 8643 residues, 6 models selected > select subtract #1 54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected > select add #1 90291 atoms, 95304 bonds, 1848 pseudobonds, 8643 residues, 6 models selected > select subtract #1 54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected > hide #!1 models > select subtract #2 Nothing selected > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > ui tool show Matchmaker > matchmaker #2/A to #1/B pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 5lmn #2/A to refined_Ede_Round5-coot-1_withW.pdb #1/B 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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 5lmn, chain A (#2), sequence alignment score = 2553.7 RMSD between 432 pruned atom pairs is 1.387 angstroms; (across all 1023 pairs: 39.110) > show #!1 models > hide #!2 models > select ::name=""EDE"" 55 atoms, 55 bonds, 1 residue, 1 model selected > show sel atoms > hide #!1 models > show #!1 models > select add #1 36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected > select subtract #1 Nothing selected > show #!2 models > select #1 /B:790 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > select #2 /A:790 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > save > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome_5lmn.cxs > includeMaps true > select add #2 54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected > select subtract #2 Nothing selected > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/My_edeine_in_Thermus_ribosome.cxs > format session Opened postprocess_masked_Edeine_onlybody.mrc as #2, grid size 400,400,400, pixel 0.832, shown at level 0.0128, step 1, values float32 opened ChimeraX session > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Modelling_Edeine/refined_Ede_Round5-coot-1_withW.pdb Chain information for refined_Ede_Round5-coot-1_withW.pdb #1 --- 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 > show cartoons > hide atoms > lighting soft > oopen 1i95 Unknown command: oopen 1i95 > oopen i195 Unknown command: oopen i195 > oopen 1i95 Unknown command: oopen 1i95 > oopen 1I95 Unknown command: oopen 1I95 > open 1I95 1i95 title: Crystal structure of the 30S ribosomal subunit from thermus thermophilus In complex with edeine [more info...] Chain information for 1i95 #2 --- 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 #2 --- EDE — edeine B MG — magnesium ion WO2 — octadecatungstenyl diphosphate ZN — zinc ion > select add #2 36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected > show sel cartoons > hide sel atoms > select subtract #2 Nothing selected > ui tool show Matchmaker > matchmaker #2/A to #1/B pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 1i95 #2/A to refined_Ede_Round5-coot-1_withW.pdb #1/B 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 refined_Ede_Round5-coot-1_withW.pdb, chain B (#1) with 1i95, chain A (#2), sequence alignment score = 2563.6 RMSD between 662 pruned atom pairs is 1.173 angstroms; (across all 1026 pairs: 39.583) > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > select #1 /B:790 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > show #!2 models > hide #!1 models > select add #1 36142 atoms, 37014 bonds, 4 pseudobonds, 4357 residues, 2 models selected > select add #2 72366 atoms, 73598 bonds, 5315 pseudobonds, 8373 residues, 6 models selected > select subtract #1 36224 atoms, 36584 bonds, 5311 pseudobonds, 4016 residues, 4 models selected > select #1 /A:790 Nothing selected > show #!1 models > select #2 /A:790 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > style sel stick Changed 22 atom styles > show sel atoms > show sel cartoons > close > open > /Users/Haaris/Desktop/Figures_Ksg_Edeine/Edeine_main_figures/My_edeine_in_Thermus_ribosome_5lmn.cxs ===== Log before crash end ===== Log: 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 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: 33 days, 48 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 Core duplicate Tom Goddard all ChimeraX