id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14456 Crash in garbage collection haaris.safdari@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-x86_64-i386-64bit ChimeraX Version: 1.7.dev202307312254 (2023-07-31 22:54:15 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 0x00007ff848b9eb80 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py"", line 580 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py"", line 580 in summarize_msgs File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py"", line 569 in log_summary File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/logger.py"", line 682 in __exit__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 482 in collated_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 195 in provider_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 38 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 162 in _qt_safe File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1044 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, 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""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000361 }, { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > mousemode shift leftMode ""translate selected models"" > mousemode shift middleMode ""rotate selected models"" > mousemode rightMode zoom > mousemode control wheelMode ""contour level"" > mousemode setting ""contour level"" speed 0.1 > mousemode shift wheelMode ""rotate selected models"" > camera ortho > set bgColor grey > lighting shadows false > lighting depthCue false > graphics silhouettes true > lighting simple > functionkey F1 cofr sel > functionkey F2 mousemode rightMode 'mark surface' > functionkey F3 mousemode rightMode 'move markers' > functionkey F4 mk 3 1 > functionkey F5 view > functionkey F6 view sel pad 0.92 clip false > functionkey F7 mousemode rightMode 'delete markers' > functionkey F8 mousemode rightMode zoom > functionkey F9 sequence chain sel > functionkey F10 transparency sel 65 > functionkey F11 transparency sel 0 > functionkey F12 tool show 'Fit in Map' > color name f01graublau #BADBED Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed > color name f02silber #F6FAFC Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc > color name f03muschel #FFFFE5 Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5 > color name f04beige #F3F3A9 Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9 > color name f05gelb #f2b701 Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701 > color name f06orange #e68310 Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310 > color name f07rotorange #FF6A25 Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25 > color name f08rot #dd3d2d Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d > color name f09lachs #f97b72 Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72 > color name f10flieder #D57AD5 Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5 > color name f11violett #cf1c90 Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90 > color name f12lila #4b148f Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f > color name f13dunkelblau #2E2EF7 Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7 > color name f14blau #00AAFF Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff > color name f15cyan #60e2d6 Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6 > color name f16blaugrün #30ffa6 Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6 > color name f17grün #00FF00 Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00 > color name f18dunkelgrün #228B22 Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 > color name f19hellgrau #DCDCDC Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc > color name f20grau #B2B2B2 Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2 > color name f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.1 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001.mrc Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00588, step 2, values float32 > set bgColor white > volume #1 step 1 > volume #1 level 0.003733 > volume #1 level 0.004176 > open > /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_class3.mrc Opened run_class001_class3.mrc as #2, grid size 400,400,400, pixel 0.832, shown at level 0.00811, step 2, values float32 > 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 > volume #2 step 1 > volume #2 level 0.004326 > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > open /Users/Haaris/Desktop/Edeine/Edeine_Comparsion_maps.cxs Opened run_it100_class001.mrc as #1.1, grid size 200,200,200, pixel 1.66, shown at level 0.0136, step 1, values float32 Opened run_it100_class002.mrc as #1.2, grid size 200,200,200, pixel 1.66, shown at level 0.0181, step 1, values float32 Opened run_it100_class003.mrc as #1.3, grid size 200,200,200, pixel 1.66, shown at level 0.017, step 1, values float32 Opened run_it100_class004.mrc as #1.4, grid size 200,200,200, pixel 1.66, shown at level 0.0256, step 1, values float32 Opened run_it100_class005.mrc as #1.5, grid size 200,200,200, pixel 1.66, shown at level 0.0165, step 1, values float32 opened ChimeraX session > hide #!1.4 models > hide #!4 models > show #!4 models > hide #!4.1 models > show #!4.1 models > show #!2 models > hide #!2 models > show #!2 models > show #!1.3 models > hide #!4 models > hide #!4.1 models > hide #!2 models > volume #1.3 level 0.01056 > volume #1.3 level 0.01099 > show #!4 models > hide #!4 models > show #!4.1 models > volume #1.3 level 0.02218 > volume #1.3 level 0.02261 > show #!1.2 models > hide #!1.3 models > color #1.2 #b2b2b2b1 models > show #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.4 models > hide #!1.1 models > show #!1.3 models > hide #!1.4 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > hide #!1.3 models > show #!1.4 models > show #!1.3 models > hide #!1.3 models > hide #!1.4 models > hide #!4 models > hide #!4.1 models > show #!1.2 models > volume #1.2 level 0.01525 > hide #!1.2 models > close #1.2 > close > open /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001.mrc Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00588, step 2, values float32 > open > /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_class3.mrc Opened run_class001_class3.mrc as #2, grid size 400,400,400, pixel 0.832, shown at level 0.00811, step 2, values float32 > 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 > fitmap #1 inMap #2 Fit map run_class001.mrc in map run_class001_class3.mrc using 79930 points correlation = 0.9679, correlation about mean = 0.8419, overlap = 13.53 steps = 56, shift = 0.903, angle = 1.12 degrees Position of run_class001.mrc (#1) relative to run_class001_class3.mrc (#2) coordinates: Matrix rotation and translation 0.99981252 -0.00322003 0.01909326 -3.36117137 0.00317458 0.99999206 0.00241019 -0.38362619 -0.01910087 -0.00234912 0.99981480 2.78245839 Axis -0.12198018 0.97890759 0.16389257 Axis point 139.77349753 0.00000000 174.27857876 Rotation angle (degrees) 1.11782834 Shift along axis 0.49048597 > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > select ~sel & ##selected Nothing selected > 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 2 Made 1 copies for 4u4n assembly 2 > view > close #3 > select add #4.1 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models selected > show sel cartoons > show sel atoms > hide sel atoms > select subtract #4.1 Nothing selected > select add #4 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models selected > open 1I96 1i96 title: Crystal structure of the 30S ribosomal subunit from thermus thermophilus In complex with the translation initiation factor IF3 (C-terminal domain) [more info...] Chain information for 1i96 #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 | V | TRANSLATION INITIATION FACTOR IF3 | Non-standard residues in 1i96 #3 --- MG — magnesium ion WO2 — octadecatungstenyl diphosphate ZN — zinc ion > select add #3 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models selected > select subtract #4 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected > select subtract #4.1 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected > show sel cartoons > hide sel atoms > select add #4.1 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 8 models selected > view matrix models > #4.1,0.99984,-0.0040773,-0.017182,3.9991,0.0032659,0.99889,-0.046989,9.8597,0.017354,0.046926,0.99875,-4.7723,#3,0.99984,-0.0040773,-0.017182,3.9991,0.0032659,0.99889,-0.046989,9.8597,0.017354,0.046926,0.99875,-4.7723 > select subtract #3 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models selected > select add #4 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models selected > select subtract #4.1 1 model selected > select add #4 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models selected > ui mousemode right ""translate selected models"" > select subtract #4 Nothing selected > select add #4.1 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models selected > select add #3 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 8 models selected > select add #4 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models selected > select subtract #4.1 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 5 models selected > select add #4 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models selected > view matrix models > #4,0.99927,-0.012456,-0.036246,8.8285,0.011052,0.99919,-0.038695,6.9474,0.036698,0.038266,0.99859,-7.0206,#3,0.99844,-0.018218,-0.052784,12.875,0.013642,0.99622,-0.085788,17.028,0.054147,0.084934,0.99491,-11.262 > view matrix models > #4,0.99927,-0.012456,-0.036246,58.641,0.011052,0.99919,-0.038695,-70.422,0.036698,0.038266,0.99859,12.52,#3,0.99844,-0.018218,-0.052784,62.687,0.013642,0.99622,-0.085788,-60.341,0.054147,0.084934,0.99491,8.2785 > select subtract #4.1 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 5 models selected > view matrix models > #4,0.99927,-0.012456,-0.036246,90.05,0.011052,0.99919,-0.038695,-129.17,0.036698,0.038266,0.99859,-219.51,#3,0.99844,-0.018218,-0.052784,94.096,0.013642,0.99622,-0.085788,-119.09,0.054147,0.084934,0.99491,-223.75 > view matrix models > #4,0.99493,0.018263,0.098867,58.862,-0.013864,0.99889,-0.044996,-124.47,-0.099579,0.043397,0.99408,-199.59,#3,0.99655,0.018826,0.080791,62.549,-0.011381,0.99573,-0.091638,-114.46,-0.082171,0.090403,0.99251,-204.3 > view matrix models > #4,0.92117,-0.21364,-0.32527,176.78,-0.040083,0.7793,-0.62537,23.663,0.38709,0.58911,0.70931,-238.4,#3,0.91468,-0.23242,-0.33065,179.91,-0.048385,0.74925,-0.66051,34.171,0.40126,0.62016,0.67408,-234.43 > view matrix models > #4,0.92789,-0.20155,-0.31369,172.34,-0.047071,0.77126,-0.63478,27.433,0.36987,0.60377,0.70616,-235.86,#3,0.92164,-0.21983,-0.31977,175.56,-0.05556,0.74081,-0.66941,37.878,0.38404,0.63473,0.67055,-231.8 > view matrix models > #4,0.92789,-0.20155,-0.31369,168.76,-0.047071,0.77126,-0.63478,-27.963,0.36987,0.60377,0.70616,-228.28,#3,0.92164,-0.21983,-0.31977,171.98,-0.05556,0.74081,-0.66941,-17.518,0.38404,0.63473,0.67055,-224.22 > view matrix models > #4,0.95711,-0.12838,-0.25972,147.38,-0.034838,0.83896,-0.54308,-54.877,0.28761,0.52884,0.7985,-231.48,#3,0.95204,-0.14433,-0.2698,151.18,-0.041518,0.81268,-0.58123,-44.153,0.30315,0.56455,0.76771,-228.93 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99902,0.043649,0.0071443,70.54,-0.041425,0.97999,-0.19469,-141.47,-0.015499,0.19421,0.98084,-207.82,#3,0.99913,0.039862,-0.01208,74.932,-0.041596,0.96993,-0.23979,-131.04,0.0021588,0.24008,0.97075,-210.65 > select add #4 243351 atoms, 253813 bonds, 13856 pseudobonds, 22262 residues, 9 models selected > select subtract #4 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected > view matrix models > #3,0.49949,-0.76092,0.41415,129.97,0.83266,0.55363,0.012952,-156.92,-0.23914,0.33837,0.91012,-202.87 > view matrix models > #3,0.49949,-0.76092,0.41415,321.42,0.83266,0.55363,0.012952,-151.96,-0.23914,0.33837,0.91012,-187.39 > view matrix models > #3,0.57947,-0.76901,0.26988,339.6,0.58014,0.62179,0.52613,-222.68,-0.57241,-0.14831,0.80644,-100.46 > view matrix models > #3,0.57947,-0.76901,0.26988,336.68,0.58014,0.62179,0.52613,-111.19,-0.57241,-0.14831,0.80644,-50.458 > view matrix models > #3,0.40934,-0.73922,0.53479,302.56,0.74155,0.61104,0.27701,-81.204,-0.53155,0.28319,0.79829,-101.91 > view matrix models > #3,0.40934,-0.73922,0.53479,290.78,0.74155,0.61104,0.27701,-229.15,-0.53155,0.28319,0.79829,-169.97 > view matrix models > #3,0.18431,-0.67499,0.71443,267.29,0.89453,0.41638,0.16262,-196.52,-0.40724,0.60911,0.68054,-196.9 > view matrix models > #3,0.18431,-0.67499,0.71443,260.91,0.89453,0.41638,0.16262,-209.99,-0.40724,0.60911,0.68054,-121.09 > view matrix models > #3,0.36953,-0.68929,0.62316,267.55,0.86579,0.49893,0.038469,-200.59,-0.33743,0.52531,0.78115,-128.77 > view matrix models > #3,0.36953,-0.68929,0.62316,286.36,0.86579,0.49893,0.038469,-284.22,-0.33743,0.52531,0.78115,-136.29 > view matrix models > #3,0.54465,-0.7064,0.45205,305.27,0.81273,0.57757,-0.076676,-274.58,-0.20693,0.40916,0.88869,-143.83 > view matrix models > #3,0.58673,-0.67071,0.45376,298.96,0.77004,0.6355,-0.056346,-282.45,-0.25057,0.38247,0.88934,-138.86 > view matrix models > #3,0.58673,-0.67071,0.45376,295.12,0.77004,0.6355,-0.056346,-291.27,-0.25057,0.38247,0.88934,-180.58 > view matrix models > #3,0.59749,-0.67806,0.42807,299.21,0.79979,0.54236,-0.25725,-252.71,-0.057739,0.49607,0.86636,-199.16 > view matrix models > #3,0.59749,-0.67806,0.42807,296.73,0.79979,0.54236,-0.25725,-235.32,-0.057739,0.49607,0.86636,-189.38 > view matrix models > #3,0.59749,-0.67806,0.42807,306.98,0.79979,0.54236,-0.25725,-244.29,-0.057739,0.49607,0.86636,-184.39 > view matrix models > #3,0.62547,-0.66361,0.41038,306.58,0.76412,0.62736,-0.15015,-268.14,-0.15782,0.4075,0.89947,-174.31 > view matrix models > #3,0.62547,-0.66361,0.41038,303.23,0.76412,0.62736,-0.15015,-266.11,-0.15782,0.4075,0.89947,-174.68 > select subtract #3 Nothing selected > hide #!4 models > show #!4 models > hide #!4.1 models > show #!4.1 models > hide #!3 models > hide #!4 models > hide #!4.1 models > show #!3 models > select add #2 2 models selected > select subtract #2 Nothing selected > select add #3 36091 atoms, 36513 bonds, 5230 pseudobonds, 4099 residues, 4 models selected > view matrix models > #3,0.49356,-0.65638,0.57059,285.15,0.68357,-0.11285,-0.72111,-93.241,0.53771,0.74595,0.39298,-172.35 > view matrix models > #3,0.49356,-0.65638,0.57059,224.17,0.68357,-0.11285,-0.72111,99.994,0.53771,0.74595,0.39298,-71.436 > view matrix models > #3,-0.72314,-0.060264,0.68806,190.7,0.4624,-0.78225,0.41746,24.8,0.51308,0.62004,0.59355,-84.373 > view matrix models > #3,-0.72314,-0.060264,0.68806,116.52,0.4624,-0.78225,0.41746,158.4,0.51308,0.62004,0.59355,-0.99605 > view matrix models > #3,-0.80887,-0.41837,0.41316,202.03,0.54148,-0.80389,0.24607,182.12,0.22919,0.42276,0.87678,-5.9877 > view matrix models > #3,-0.80887,-0.41837,0.41316,204.44,0.54148,-0.80389,0.24607,179.83,0.22919,0.42276,0.87678,-9.8855 > view matrix models > #3,-0.80887,-0.41837,0.41316,202.15,0.54148,-0.80389,0.24607,177.86,0.22919,0.42276,0.87678,-16.656 > view matrix models > #3,-0.77858,-0.2824,0.56042,163.62,0.47968,-0.84362,0.24129,185.95,0.40464,0.45668,0.79228,-16.231 > view matrix models > #3,-0.77858,-0.2824,0.56042,166.65,0.47968,-0.84362,0.24129,191,0.40464,0.45668,0.79228,-22.107 > view matrix models > #3,-0.77858,-0.2824,0.56042,156.6,0.47968,-0.84362,0.24129,197.86,0.40464,0.45668,0.79228,-33.091 > view matrix models > #3,-0.77814,-0.276,0.5642,148.74,0.47493,-0.84639,0.24097,199.23,0.41102,0.45546,0.78969,-23.721 > hide #!1 models > fitmap #3 inMap #2 Fit molecule 1i96 (#3) to map run_class001_class3.mrc (#2) using 36091 atoms average map value = 0.01358, steps = 172 shifted from previous position = 7.93 rotated from previous position = 12 degrees atoms outside contour = 14241, contour level = 0.0081123 Position of 1i96 (#3) relative to run_class001_class3.mrc (#2) coordinates: Matrix rotation and translation -0.70372535 -0.40050105 0.58683008 162.16578436 0.51726758 -0.85503386 0.03676081 225.72965937 0.48703685 0.32941769 0.80887521 -11.83435366 Axis 0.30218930 0.10304370 0.94766219 Axis point 53.06833400 133.09158106 0.00000000 Rotation angle (degrees) 151.03811207 Shift along axis 61.04981461 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > show #!4.1 models > select subtract #3 Nothing selected > select add #4.1 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models selected > view matrix models > #4.1,0.99984,-0.0040773,-0.017182,-16.266,0.0032659,0.99889,-0.046989,84.29,0.017354,0.046926,0.99875,76.79 > view matrix models > #4.1,0.38264,-0.42533,0.82017,-100.11,0.85941,-0.16198,-0.48494,59.055,0.33911,0.89043,0.30356,171.1 > view matrix models > #4.1,0.38264,-0.42533,0.82017,-100.79,0.85941,-0.16198,-0.48494,93.958,0.33911,0.89043,0.30356,200.45 > view matrix models > #4.1,0.63319,-0.57684,0.51607,-68.571,0.68103,0.098393,-0.72561,181.31,0.36779,0.81091,0.45515,159.17 > view matrix models > #4.1,0.63319,-0.57684,0.51607,-59.917,0.68103,0.098393,-0.72561,235.27,0.36779,0.81091,0.45515,78.598 > view matrix models > #4.1,0.6069,-0.22179,0.7632,-124.24,0.75247,-0.14877,-0.6416,206.5,0.25584,0.96368,0.076607,190.2 > view matrix models > #4.1,0.6069,-0.22179,0.7632,-145.58,0.75247,-0.14877,-0.6416,281.47,0.25584,0.96368,0.076607,143.55 > view matrix models > #4.1,0.36001,0.061262,0.93094,-147.46,0.78979,-0.55117,-0.26915,190.78,0.49661,0.83214,-0.24681,181.95 > view matrix models > #4.1,0.36001,0.061262,0.93094,-210.89,0.78979,-0.55117,-0.26915,244.14,0.49661,0.83214,-0.24681,188.4 > view matrix models > #4.1,0.38033,-0.74051,0.55407,-103.41,0.89454,0.14244,-0.42368,247.8,0.23482,0.65678,0.71659,1.5881 > view matrix models > #4.1,0.38033,-0.74051,0.55407,-144.85,0.89454,0.14244,-0.42368,266.8,0.23482,0.65678,0.71659,43.895 > view matrix models > #4.1,0.33227,-0.48767,0.80733,-204.39,0.91126,-0.054842,-0.40817,264.17,0.24333,0.87131,0.42617,109.79 > view matrix models > #4.1,0.33227,-0.48767,0.80733,-189.71,0.91126,-0.054842,-0.40817,263.39,0.24333,0.87131,0.42617,106.66 > view matrix models > #4.1,0.41421,-0.23318,0.8798,-228.58,0.83733,-0.28131,-0.46877,297.21,0.3568,0.93086,0.07873,170.56 > view matrix models > #4.1,0.41421,-0.23318,0.8798,-240.32,0.83733,-0.28131,-0.46877,293.11,0.3568,0.93086,0.07873,186.83 > view matrix models > #4.1,0.5362,-0.70048,0.47098,-151.18,0.72059,0.089296,-0.68758,361.12,0.43958,0.70807,0.55264,58.501 > ui tool show Matchmaker > matchmaker #4.1/6 to #3/A pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 4u4n #4.1/6 to 1i96 #3/A 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 1i96, chain A (#3) with 4u4n, chain 6 (#4.1), sequence alignment score = 2337.6 RMSD between 415 pruned atom pairs is 1.120 angstroms; (across all 1462 pairs: 27.040) > hide #!3 models > hide #!4 models > show #!4 models > select add #4 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 5 models selected > select subtract #4 Nothing selected > select add #4.1 207260 atoms, 217300 bonds, 8626 pseudobonds, 18163 residues, 4 models selected > select subtract #4.1 Nothing selected > select ::name=""EDE"" 55 atoms, 55 bonds, 1 residue, 1 model selected > show sel atoms > color #2 #ffffb28a models > volume #2 step 1 > volume #2 level 0.008845 > show #!3 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!4.1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!3 models > show #!1 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > hide #!3 models > show #!4.1 models > volume #1 step 1 > save ""/Users/Haaris/Desktop/Temporary_Processing/Edeine/chimerax_maps_class3 > and withouttrna.cxs"" includeMaps true > open > /Users/Haaris/Desktop/Temporary_Processing/Edeine/run_class001_firstrefine.mrc Opened run_class001_firstrefine.mrc as #5, grid size 200,200,200, pixel 1.66, shown at level 0.0231, step 1, values float32 > hide #!4 models > show #!4 models > hide #!4.1 models > color #5 #b2ffff60 models > hide #!4 models > color #5 #b2ffff61 models > show #!4 models > hide #!2 models > show #!4.1 models > volume #5 level 0.02354 > show #!2 models > hide #!2 models > show #!2 models > hide #!4.1 models > hide #!4 models > hide #!5 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > show #!5 models > hide #!5 models > show #!4.1 models > hide #!3 models > show #!5 models > hide #!5 models > show #!5 models > hide #!2 models > hide #!4 models > hide #!4.1 models > hide #!5 models > show #!5 models > volume #5 level 0.009282 > volume #5 level 0.02116 > show #!2 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!2 models > show #!2 models > show #!5 models > hide #!2 models > volume #5 level 0.01522 > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc Opened run_class001_body.mrc as #6, grid size 400,400,400, pixel 0.832, shown at level 0.00496, step 2, values float32 > hide #!5 models > volume #6 step 1 > volume #6 level 0.007256 > volume #6 level 0.007796 > close #6 > show #!5 models > show #!4.1 models > hide #!4.1 models > hide #!5 models > show #!2 models > show #!4.1 models > save ""/Users/Haaris/Desktop/Temporary_Processing/Edeine/chimerax_maps_class3 > and withouttrna.cxs"" includeMaps true > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc Opened run_class001_body.mrc as #6, grid size 400,400,400, pixel 0.832, shown at level 0.00496, step 2, values float32 > hide #!4.1 models > hide #!4 models > hide #!2 models > volume #5 level 0.01839 > hide #!5 models > volume #6 step 1 > volume #6 level 0.006851 > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb Chain information for Haaris_Kasugamycin_Coot12.pdb #7 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | 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 W | No description available X | No description available > show #!7 cartoons > hide #!7 atoms > close > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc Opened run_class001_body.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00496, step 2, values float32 > volume #1 step 1 > volume #1 level 0.006535 > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb Chain information for Haaris_Kasugamycin_Coot12.pdb #2 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | 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 W | No description available X | No description available > show cartoons > hide atoms > select add #2 35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected > view matrix models #2,1,0,0,20.863,0,1,0,15.292,0,0,1,-5.5963 > fitmap #2 inMap #1 Fit molecule Haaris_Kasugamycin_Coot12.pdb (#2) to map run_class001_body.mrc (#1) using 35059 atoms average map value = 0.006915, steps = 92 shifted from previous position = 5.33 rotated from previous position = 1.75 degrees atoms outside contour = 21787, contour level = 0.0065348 Position of Haaris_Kasugamycin_Coot12.pdb (#2) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99967811 0.02520518 -0.00289489 21.20704341 -0.02525112 0.99953466 -0.01711247 18.95538469 0.00246222 0.01718006 0.99984938 -6.15013976 Axis 0.55995627 -0.08747533 -0.82389140 Axis point 812.67860126 -491.45110025 0.00000000 Rotation angle (degrees) 1.75471226 Shift along axis 15.28393578 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.99968,0.025205,-0.0028949,23.445,-0.025251,0.99953,-0.017112,18.896,0.0024622,0.01718,0.99985,-9.369 > fitmap #2 inMap #1 Fit molecule Haaris_Kasugamycin_Coot12.pdb (#2) to map run_class001_body.mrc (#1) using 35059 atoms average map value = 0.01826, steps = 56 shifted from previous position = 0.928 rotated from previous position = 1.2 degrees atoms outside contour = 2861, contour level = 0.0065348 Position of Haaris_Kasugamycin_Coot12.pdb (#2) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99994116 0.01043734 0.00295644 24.10229484 -0.01042697 0.99993951 -0.00349995 13.69397562 -0.00299279 0.00346892 0.99998950 -6.69780310 Axis 0.30581760 0.26107201 -0.91559653 Axis point 896.17225323 -1803.77974033 0.00000000 Rotation angle (degrees) 0.65283266 Shift along axis 17.07850489 > volume #1 level 0.004305 > volume #1 level 0.00483 > volume #1 level 0.005486 > save /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb > relModel #1 > hide #!1 models > select subtract #2 Nothing selected > select /B 564 atoms, 633 bonds, 26 residues, 1 model selected > select add #2 35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected > select subtract #2 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 2/B > show #!1 models > hide #!2 models > volume #1 level 0.006797 > volume #1 level 0.007059 > show #!2 models > open ""/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1 > (1).pdb"" Chain information for 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb #3 --- 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available > hide #!2 models > hide #!3 models > show #!3 models > show #!3 cartoons > hide #!3 atoms > close #3 > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > open /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb Chain information for 6vwm_aligned.pdb #3 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available A | No description available AA | No description available AB | No description available AC | No description available B | No description available C | No description available D | No description available E | 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 > select add #3 140044 atoms, 152352 bonds, 74 pseudobonds, 9975 residues, 3 models selected > show sel cartoons > hide sel atoms > view matrix models > #3,0.92864,-0.17248,0.32844,-16.243,0.16405,0.985,0.053435,-32.583,-0.33273,0.0042566,0.94301,61.642 > view matrix models > #3,0.92864,-0.17248,0.32844,7.5618,0.16405,0.985,0.053435,-26.046,-0.33273,0.0042566,0.94301,47.096 > view matrix models > #3,0.9918,0.12535,-0.024996,14.511,-0.12484,0.99195,0.021003,24.645,0.027428,-0.01771,0.99947,-16.902 > view matrix models > #3,0.99137,-0.065524,0.11356,16.259,0.060068,0.9969,0.050816,-10.173,-0.11653,-0.043556,0.99223,10.398 > view matrix models > #3,0.99137,-0.065524,0.11356,14.086,0.060068,0.9969,0.050816,-7.8441,-0.11653,-0.043556,0.99223,14.225 > view matrix models > #3,0.9854,-0.065548,0.15713,8.7703,0.047105,0.99185,0.11835,-14.914,-0.16361,-0.10922,0.98046,31.003 > fitmap #3 inMap #1 Fit molecule 6vwm_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 140044 atoms average map value = 0.003391, steps = 304 shifted from previous position = 6.27 rotated from previous position = 12 degrees atoms outside contour = 115070, contour level = 0.0070593 Position of 6vwm_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99993638 0.01097084 0.00262103 24.09129339 -0.01096138 0.99993346 -0.00359628 13.77834458 -0.00266031 0.00356732 0.99999010 -6.76724154 Axis 0.30265489 0.22313070 -0.92661357 Axis point 928.85137536 -1731.60218196 0.00000000 Rotation angle (degrees) 0.67808919 Shift along axis 16.63633736 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > save /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb models #3 relModel > #1 > close #3 > open /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb Chain information for 5np6_aligned.pdb #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 v | No description available w | No description available x | No description available y | No description available z | No description available > select add #3 146883 atoms, 159526 bonds, 10662 residues, 1 model selected > show sel cartoons > hide sel atoms > hide #!1 models > show #!1 models > view matrix models > #3,0.95304,-0.11333,0.28086,-21.011,0.10609,0.99352,0.040896,-22.544,-0.28367,-0.0091798,0.95888,53.208 > view matrix models > #3,0.95304,-0.11333,0.28086,-11.174,0.10609,0.99352,0.040896,-20.315,-0.28367,-0.0091798,0.95888,46.249 > view matrix models > #3,0.94898,0.26305,0.1739,-37.161,-0.25673,0.96472,-0.058305,56.533,-0.1831,0.010684,0.98304,24.102 > view matrix models > #3,0.94898,0.26305,0.1739,-35.242,-0.25673,0.96472,-0.058305,57.7,-0.1831,0.010684,0.98304,11.757 > view matrix models > #3,0.93908,0.31552,0.13627,-33.997,-0.31176,0.94891,-0.048673,67.007,-0.14466,0.0032251,0.98948,5.3991 > fitmap #3 inMap #1 Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 146883 atoms average map value = 0.003255, steps = 728 shifted from previous position = 20.9 rotated from previous position = 19.4 degrees atoms outside contour = 121667, contour level = 0.0070593 Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99991637 0.01257933 0.00300382 23.76375413 -0.01256970 0.99991587 -0.00320224 13.95056368 -0.00304385 0.00316422 0.99999036 -6.66117709 Axis 0.23899962 0.22703247 -0.94410563 Axis point 847.16032451 -1595.91193628 0.00000000 Rotation angle (degrees) 0.76314323 Shift along axis 15.13561390 > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > fitmap #3 inMap #1 Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 146883 atoms average map value = 0.003255, steps = 1580 shifted from previous position = 0.0152 rotated from previous position = 0.00125 degrees atoms outside contour = 121656, contour level = 0.0070593 Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99991662 0.01256063 0.00299769 23.76788665 -0.01255100 0.99991608 -0.00321174 13.93475803 -0.00303778 0.00317385 0.99999035 -6.66858997 Axis 0.24001943 0.22685983 -0.94388839 Axis point 846.90457993 -1596.93260426 0.00000000 Rotation angle (degrees) 0.76218367 Shift along axis 15.16039622 > hide #!1 models > show #!1 models > select subtract #3 Nothing selected > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > ui tool show H-Bonds > hbonds sel restrict both saltOnly true select true reveal true log true Atom specifier selects no atoms > select #3/A:14 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 621 atoms, 694 bonds, 29 residues, 1 model selected > ui tool show H-Bonds > hbonds sel restrict both saltOnly true select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 3 5np6_aligned.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select #3/A:17 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 621 atoms, 694 bonds, 29 residues, 1 model selected > ui tool show H-Bonds > hbonds sel saltOnly true select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 Haaris_Kasugamycin_Coot12.pdb 3 5np6_aligned.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): Haaris_Kasugamycin_Coot12.pdb #2/W HIS 43 ND1 5np6_aligned.pdb #3/A U 19 OP1 no hydrogen 1.574 N/A 1 hydrogen bonds found > select add #2 35060 atoms, 37996 bonds, 5 pseudobonds, 2592 residues, 3 models selected > select subtract #2 1 atom, 1 residue, 1 model selected > select add #3 146883 atoms, 159526 bonds, 10662 residues, 1 model selected > hide #3 models > select add #4 146883 atoms, 159526 bonds, 1 pseudobond, 10662 residues, 2 models selected > show #3 models > close #4 > select subtract #3 Nothing selected > hide #3 models > show #3 models > close #3 > open /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb Chain information for 5np6_aligned.pdb #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 v | No description available w | No description available x | No description available y | No description available z | No description available > show #!1 models > select add #3 146883 atoms, 159526 bonds, 10662 residues, 1 model selected > show sel cartoons > hide sel atoms > fitmap #3 inMap #1 Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 146883 atoms average map value = 0.001179, steps = 288 shifted from previous position = 9.77 rotated from previous position = 4.86 degrees atoms outside contour = 138826, contour level = 0.0070593 Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99835362 -0.03346963 0.04658153 3.92921316 0.03631751 0.99743392 -0.06169771 9.89237255 -0.04439700 0.06328785 0.99700730 3.12901804 Axis 0.73688466 0.53638744 0.41144807 Axis point 0.00000000 15.89828662 77.17990237 Rotation angle (degrees) 4.86491126 Shift along axis 9.48894971 > view matrix models > #3,0.98925,-0.10448,0.10227,5.1999,0.097652,0.99278,0.069687,-18.928,-0.10881,-0.058952,0.99231,28.068 > view matrix models > #3,0.98925,-0.10448,0.10227,24.037,0.097652,0.99278,0.069687,-16.564,-0.10881,-0.058952,0.99231,16.159 > view matrix models > #3,0.98048,-0.051195,0.18981,6.5461,0.087367,0.97839,-0.18741,24.644,-0.17612,0.20034,0.96377,2.0857 > view matrix models > #3,0.98048,-0.051195,0.18981,3.2016,0.087367,0.97839,-0.18741,22.35,-0.17612,0.20034,0.96377,-6.2266 > view matrix models > #3,0.98619,-0.025903,0.16355,3.2954,0.058291,0.97878,-0.19646,28.366,-0.15499,0.20329,0.96677,-10.435 > view matrix models > #3,0.98619,-0.025903,0.16355,-3.3241,0.058291,0.97878,-0.19646,36.689,-0.15499,0.20329,0.96677,-6.7037 > fitmap #3 inMap #1 Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 146883 atoms average map value = 0.001115, steps = 280 shifted from previous position = 4.63 rotated from previous position = 7.67 degrees atoms outside contour = 139449, contour level = 0.0070593 Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99468237 0.07143553 0.07418866 14.14805644 -0.05271842 0.97197739 -0.22908670 75.80680390 -0.08847463 0.22395739 0.97057474 -30.96473780 Axis 0.91134818 0.32721515 -0.24974938 Axis point 0.00000000 120.60995147 251.26225221 Rotation angle (degrees) 14.39214450 Shift along axis 45.43236381 > view matrix models > #3,0.99694,0.06522,0.043178,19.055,-0.040567,0.90311,-0.4275,110.85,-0.066875,0.42444,0.90298,-47.103 > view matrix models > #3,0.99694,0.06522,0.043178,8.961,-0.040567,0.90311,-0.4275,109.35,-0.066875,0.42444,0.90298,-44.842 > view matrix models > #3,0.96419,0.25283,-0.080128,11.324,-0.26512,0.9104,-0.31763,128.83,-0.0073582,0.3275,0.94482,-49.76 > view matrix models > #3,0.96419,0.25283,-0.080128,16.466,-0.26512,0.9104,-0.31763,128.88,-0.0073582,0.3275,0.94482,-47.339 > view matrix models > #3,0.99424,-0.046685,-0.096454,47.744,0.049878,0.99828,0.030966,16.363,0.094842,-0.035599,0.99486,-30.407 > fitmap #3 inMap #1 Fit molecule 5np6_aligned.pdb (#3) to map run_class001_body.mrc (#1) using 146883 atoms average map value = 0.003255, steps = 992 shifted from previous position = 21.6 rotated from previous position = 6.98 degrees atoms outside contour = 121658, contour level = 0.0070593 Position of 5np6_aligned.pdb (#3) relative to run_class001_body.mrc (#1) coordinates: Matrix rotation and translation 0.99991627 0.01258777 0.00299901 23.76470096 -0.01257841 0.99991602 -0.00312051 13.92817034 -0.00303804 0.00308253 0.99999063 -6.65277166 Axis 0.23308158 0.22684448 -0.94562919 Axis point 847.69121731 -1604.72460587 0.00000000 Rotation angle (degrees) 0.76243328 Shift along axis 14.98969771 > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > save /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb models #3 relModel > #1 > close #2 > close #3 > close > open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc Opened 30S_IF2_flipped.mrc as #1, grid size 440,440,440, pixel 0.8, shown at level 0.0586, step 2, values float32 > volume #1 step 1 > volume #1 level 0.07981 > open ""/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1 > (1).pdb"" Chain information for 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb #2 --- 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available > select add #2 59485 atoms, 63983 bonds, 20 pseudobonds, 4744 residues, 3 models selected > view matrix models > #2,0.54298,-0.81951,0.18326,173.26,0.30385,-0.011715,-0.95265,267.45,0.78285,0.57295,0.24264,-92.547 > show sel cartoons > hide sel atoms > view matrix models > #2,0.43492,-0.90045,0.0063817,233.38,-0.525,-0.25932,-0.81063,419.81,0.73158,0.34921,-0.58552,89.333 > view matrix models > #2,0.43492,-0.90045,0.0063817,250.43,-0.525,-0.25932,-0.81063,424.56,0.73158,0.34921,-0.58552,101.68 > view matrix models > #2,0.33941,-0.93655,-0.08757,287.61,-0.61993,-0.1527,-0.76965,416.78,0.70745,0.31552,-0.63243,118.78 > view matrix models > #2,0.33941,-0.93655,-0.08757,292.74,-0.61993,-0.1527,-0.76965,429.41,0.70745,0.31552,-0.63243,120.26 > view matrix models > #2,0.26779,-0.87968,-0.393,346.75,-0.81017,0.015169,-0.58599,404,0.52145,0.47532,-0.70863,138.83 > view matrix models > #2,0.26779,-0.87968,-0.393,342.02,-0.81017,0.015169,-0.58599,402.27,0.52145,0.47532,-0.70863,136.96 > fitmap #2 inMap #1 Fit molecule 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb (#2) to map 30S_IF2_flipped.mrc (#1) using 59485 atoms average map value = 0.1923, steps = 220 shifted from previous position = 2.34 rotated from previous position = 15 degrees atoms outside contour = 13557, contour level = 0.079807 Position of 5lmv_aligned_AndreaAUGmap-coot-1 (1).pdb (#2) relative to 30S_IF2_flipped.mrc (#1) coordinates: Matrix rotation and translation 0.16141245 -0.95085759 -0.26422692 348.03537918 -0.69255635 0.08160319 -0.71673330 392.99161741 0.70307306 0.29868171 -0.64535069 122.88646307 Axis 0.71207566 -0.67833425 0.18113779 Axis point 0.00000000 326.28972187 133.53259185 Rotation angle (degrees) 134.52074992 Shift along axis 3.50723285 > select subtract #2 Nothing selected > volume #1 level 0.05152 > volume #1 level 0.08216 > volume #1 level 0.06331 > save ""/Users/Haaris/Desktop/Modelling_Ksg/5lmv_aligned_AndreaAUGmap-coot-1 > (1).pdb"" relModel #1 > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain /Y Alignment identifier is 2/Y > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.07509 > ui tool show ""Show Sequence Viewer"" > sequence chain /Y Destroying pre-existing alignment with identifier 2/Y Alignment identifier is 2/Y > hide #!1 models > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb Chain information for Haaris_Kasugamycin_Coot13.pdb #3 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | 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 W | No description available X | No description available > hide #!2 models > select add #3 35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected > show sel cartoons > hide sel atoms > select subtract #3 Nothing selected > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc Opened run_class001_body.mrc as #4, grid size 400,400,400, pixel 0.832, shown at level 0.00496, step 2, values float32 > volume #4 step 1 > volume #4 level 0.007584 > open 5lmn 5lmn title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A) [more info...] Chain information for 5lmn #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 | Non-standard residues in 5lmn #5 --- MG — magnesium ion ZN — zinc ion > hide #!4 models > select add #5 54149 atoms, 58290 bonds, 1844 pseudobonds, 4286 residues, 4 models selected > show sel cartoons > hide sel atoms > hide #!3 models > select subtract #5 Nothing selected > close #5 > open /Users/Haaris/Desktop/Modelling_Ksg/6vwm_aligned.pdb Chain information for 6vwm_aligned.pdb #5 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available A | No description available AA | No description available AB | No description available AC | No description available B | No description available C | No description available D | No description available E | 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 V | No description available W | No description available X | No description available Y | No description available Z | No description available 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 > show #!5 cartoons > hide #!5 atoms > show #!3 models > hide #!3 models > show #!4 models > volume #4 level 0.002469 > volume #4 level 0.006535 > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > show #!1 models > close #5 > hide #!1 models > show #!1 models > color #1 #b2b2b29a models > color #1 #b2b2b299 models > volume #1 level 0.05388 > volume #1 level 0.08216 > volume #1 level 0.06566 > show #!4 models > hide #!1 models > hide #!2 models > show #!3 models > volume #4 level 0.005092 > close #1 > close #2 > hide #!3 models > show #!3 models > hide #!4 models > select ::name=""KSG"" 26 atoms, 27 bonds, 1 residue, 1 model selected > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001_body.mrc Opened run_class001_body.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00496, step 2, values float32 > volume #1 step 1 > volume #1 level 0.007059 > volume #1 level 0.007453 > open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc Opened 30S_IF2_flipped.mrc as #2, grid size 440,440,440, pixel 0.8, shown at level 0.0586, step 2, values float32 > close #3 > close #1 > close #4 > volume #2 step 1 > volume #2 level 0.04916 > volume #2 level 0.05388 > close > open /Users/Haaris/Desktop/Modelling_Ksg/run_class001.mrc Opened run_class001.mrc as #1, grid size 400,400,400, pixel 0.832, shown at level 0.00636, step 2, values float32 > volume #1 step 1 > volume #1 level 0.004792 > open /Users/Haaris/Desktop/Modelling_Ksg/30S_IF2_flipped.mrc Opened 30S_IF2_flipped.mrc as #2, grid size 440,440,440, pixel 0.8, shown at level 0.0586, step 2, values float32 > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.23487,-0.59138,0.77143,101.3,-0.96393,-0.24394,0.10648,368.37,0.12521,-0.76861,-0.62735,401.01 > view matrix models > #2,0.23487,-0.59138,0.77143,91.476,-0.96393,-0.24394,0.10648,351,0.12521,-0.76861,-0.62735,389.59 > view matrix models > #2,0.35134,-0.63089,0.69176,92.186,-0.93607,-0.2225,0.27251,313.03,-0.018006,-0.74328,-0.66873,417.44 > fitmap #2 inMap #1 Fit map 30S_IF2_flipped.mrc in map run_class001.mrc using 106331 points correlation = 0.912, correlation about mean = 0.7422, overlap = 196 steps = 312, shift = 5.88, angle = 18 degrees Position of 30S_IF2_flipped.mrc (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.16229209 -0.69262641 0.70280149 129.51610375 -0.95060331 0.08124797 0.29958658 262.04742830 -0.26460277 -0.71670596 -0.64522705 452.97789476 Axis -0.71237281 0.67810445 -0.18082956 Axis point 0.00000000 326.19283390 133.61685565 Rotation angle (degrees) 134.49471673 Shift along axis 3.51998480 > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > volume #2 step 1 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > volume #1 level 0.003339 > volume #1 level 0.006134 > show #!2 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 #!1 models > show #!1 models > hide #!2 models > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot13.pdb Chain information for Haaris_Kasugamycin_Coot13.pdb #3 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | 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 W | No description available X | No description available > hide #!3 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > select add #3 35059 atoms, 37996 bonds, 5 pseudobonds, 2591 residues, 2 models selected > show sel cartoons > hide sel atoms > view matrix models > #3,0.99827,-0.045892,-0.03688,13.731,0.045318,0.99884,-0.016241,-4.6294,0.037583,0.014542,0.99919,-8.4134 > view matrix models > #3,0.98299,0.0014204,-0.18368,32.081,-0.00071018,0.99999,0.0039324,-0.51434,0.18368,-0.003735,0.98298,-26.767 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.98299,0.0014204,-0.18368,11.364,-0.00071018,0.99999,0.0039324,-12.761,0.18368,-0.003735,0.98298,-15.25 > view matrix models > #3,0.98299,0.0014204,-0.18368,10.912,-0.00071018,0.99999,0.0039324,-12.66,0.18368,-0.003735,0.98298,-15.791 > fitmap #3 inMap #1 Fit molecule Haaris_Kasugamycin_Coot13.pdb (#3) to map run_class001.mrc (#1) using 35059 atoms average map value = 0.01616, steps = 144 shifted from previous position = 6.18 rotated from previous position = 10.4 degrees atoms outside contour = 2870, contour level = 0.0061341 Position of Haaris_Kasugamycin_Coot13.pdb (#3) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99994195 -0.01035860 -0.00296606 -23.99666021 0.01036889 0.99994021 0.00347345 -13.91681403 0.00292991 -0.00350400 0.99998957 6.67826541 Axis -0.30803884 -0.26029409 0.91507325 Axis point 901.81225901 -1812.37751700 0.00000000 Rotation angle (degrees) 0.64892251 Shift along axis 17.12546993 > select subtract #3 Nothing selected > open /Users/Haaris/Desktop/Modelling_Ksg/1vy4_aligned.pdb ===== Log before crash end ===== Log: > 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 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'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90 > color name f12lila #4b148f Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f > color name f13dunkelblau #2E2EF7 Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7 > color name f14blau #00AAFF Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff > color name f15cyan #60e2d6 Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6 > color name f16blaugrün #30ffa6 Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6 > color name f17grün #00FF00 Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00 > color name f18dunkelgrün #228B22 Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 > color name f19hellgrau #DCDCDC Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc > color name f20grau #B2B2B2 Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2 > color name f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.1 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.2.4 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: 2020.40.3.0.0 OS Loader Version: 580~1053 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 15 days, 4 hours, 3 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: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46.1 ChimeraX-AtomicLibrary: 10.0.8 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: 2.10.4 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202307312254 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 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-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: 1.31.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.41.1 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.7 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 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: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 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 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX