id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20409 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x0000000201d6b100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 122 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 555 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 584 in use_shared_context File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 146 in render File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 115 in _redraw File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 153 in resizeEvent File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 in event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c26a4ca659ccf786d750a9018fa39da11d127601"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000536 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > runscript /Users/sconnell/local/chimerax-trimmings/chimerax_trimmings.py > camera ortho > cofr centerOfView > mousemode alt rightMode ""contour level"" > mousemode rightMode clip > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot 7,0.25 > alias usage cofron synopsis ""Center the rotation point on the view and show > the pivot"" > alias cofroff cofr centerofview showpivot false > alias usage cofroff synopsis ""Recenter the rotation point on the view and > hide the pivot marker"" > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias usage symclip synopsis ""Set symmetric clip planes around the center of > rotation"" $1 half-distance > alias selmodel sel ##num_residues > alias usage selmodel synopsis ""Select atomic models"" > alias selmap sel ~##num_residues > alias usage selmap synopsis ""Select non-atomic models such as maps"" > alias selside sel sidechain & $1 | ~backbone & nucleic & $1 > alias usage selside synopsis ""Select protein sidechains and nucleic-acid > bases"" $1 atom-spec > alias dispside sel sidechain & $1 | ~backbone & nucleic & $1; disp sel > alias usage dispside synopsis ""Display protein sidechains and nucleic-acid > bases"" $1 atom-spec > alias cootmode_white set bgColor white; surface cap false; surface style > solid; nucleotides #* atoms; lighting flat; graphics silhouettes false; > style stick; ~rib; color ##num_residues orange; color byhet ; disp > ##num_residues & ##display; ~disp @H*; style ions sphere; style solvent > ball; size ballscale 0.2; size stickradius 0.07; transparency 85; cofr > centerofview; clip near -10 far 10 position cofr; color ~##num_residues > medium blue > alias usage cootmode_white synopsis ""Apply the white-background Coot-style > display preset"" > alias cootmode set bgColor black; surface cap false; surface style solid; > nucleotides #* atoms; lighting flat; graphics silhouettes false; style > stick; ~rib; color ##num_residues gold; color byhet ; disp ##num_residues & > ##display; ~disp @H*; style ions sphere; style solvent ball; size ballscale > 0.2; size stickradius 0.07; transparency 70; cofr centerofview; clip near > -10 far 10 position cofr; color ~##num_residues cornflower blue > alias usage cootmode synopsis ""Apply the dark-background Coot-style display > preset"" > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > nucleotides #* atoms; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp ##num_residues & ##display; ~disp > @H*; style solvent ball; style ions sphere; size ballscale 0.2; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ~##num_residues #3d60ffff; transparency 50 > alias usage cootmode_mesh synopsis ""Apply the mesh Coot-style display > preset"" > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias usage ca_and_sidechains synopsis ""Show CA or phosphate trace plus > sidechains or bases"" $1 model-spec > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias usage ca_trace synopsis ""Show a CA or phosphate trace"" $1 model-spec > alias expand_sym ~disp $1; rib $1; sym $1 assembly 1 copies false newModel > true > alias usage expand_sym synopsis ""Expand an asymmetric unit to biological > assembly 1 as ribbon copies"" $1 model-spec > alias map_sphere_15 volume unzone ~##num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias usage map_sphere_15 synopsis ""Zone maps to a 15 A sphere around the > center of rotation"" > alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask > #10000 spacing 1 border -0.5 > alias usage cubic_map synopsis ""Create a spherical mask map on a cubic grid"" > $1 ""sphere radius"" > alias map_unsphere volume unzone ~##num_residues > alias usage map_unsphere synopsis ""Remove map zoning from all maps"" > alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine > $1.* close true > alias usage fit_by_chain synopsis ""Split a model by chain, fit each chain > into a map, and recombine"" $1 model-spec $2 map-spec > alias rainbow_new rainbow palette RdYlBu-5 > alias usage rainbow_new synopsis ""Color models by rainbow using the RdYlBu-5 > palette"" > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias usage default_mol_display synopsis ""Restore the default cartoon > molecular display"" > alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; > sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 > minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; > close sel; show $2 > alias usage local_fitmap synopsis ""Fit a model or map into a local zone > around the center of rotation"" $1 ""model or map to fit"" $2 ""target map"" $3 > ""zone radius"" > alias hidemodels hide ##num_residues models > alias usage hidemodels synopsis ""Hide all atomic models"" > alias showmodels show ##num_residues models > alias usage showmodels synopsis ""Show all atomic models"" > alias caps_off surface cap false > alias usage caps_off synopsis ""Turn clipped surface caps off"" > alias caps_on surface cap true > alias usage caps_on synopsis ""Turn clipped surface caps on"" > alias open_vseries ""open browse vseries true"" > alias usage open_vseries synopsis ""Open a file browser with volume series > enabled"" > alias selbetween ks ri > alias usage selbetween synopsis ""Select residues between the current > selection endpoints"" > alias helix setattr $1 res is_helix true > alias usage helix synopsis ""Mark residues as helix"" $1 residue-spec > alias strand setattr $1 res is_strand true > alias usage strand synopsis ""Mark residues as strand"" $1 residue-spec > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias usage coil synopsis ""Clear helix and strand assignment for residues"" > $1 residue-spec > alias rock_movie cofr showpivot false; movie record; rock y 50; wait 600; > movie encode ~/Desktop/rock_movie.mp4; stop > alias usage rock_movie synopsis ""Record a rocking movie and save it to the > default Desktop file"" > alias centersel cofr sel; clip near 10 position cofr; clip far -10 position > cofr; cofr centerOfView showpivot true; view sel > alias usage centersel synopsis ""Center the view on the selection and apply > local clipping"" > alias volume_project set bgColor black; volume $1 step 1 sd_level 0,0 > sd_level 50,1 color white color white style image projection_mode auto > maximum_intensity_projection true bt_correction true linear_interpolation > true; lighting depth_cue false > alias usage volume_project synopsis ""Display a map as a maximum-intensity > projection"" $1 map-spec > alias split_diff_map volume scale $1 rms 1 modelId $2; close $1; volume $2 > capFaces false meshLighting false squareMesh false level -3 color > #da1200000000 level 3 color #0000bda00000; lighting depthCue true; volume $2 > style mesh > alias usage split_diff_map synopsis ""Replace a map with a scaled positive > and negative mesh difference map"" $1 ""input map"" $2 ""output model-id"" > alias local_diff_map view name tmp; close #1001,1002,1003,1004,1005; fitmap > $1 inMap $2; vol zone $2 near $1 range 5 newMap true modelId 1000 > minimalBounds true; fitmap $1 inMap $3; vol zone $3 near $1 range 5 newMap > true modelId 1001 minimalBounds true; volume scale #1000 sd 0.1 modelId > 1002; volume scale #1001 sd 0.1 modelId 1003; fitmap #1003 inMap #1002; > volume resample #1003 onGrid #1002 modelId 1004; volume subtract #1002 #1004 > modelId 1005 minRms true; volume #1005 step 1; split_diff_map #1005 #1006; > close #1000,1001,1002,1003,1004,1005; view tmp > alias usage local_diff_map synopsis ""Build a local difference map between > two fitted maps around a model"" $1 model-spec $2 ""first map"" $3 ""second map"" > alias local_diff_map_sphere ~sel; close > #10000,#1001,#1002,#1003,#1004,#1005; marker #10000 position cofr; sel > #10000; vol zone $1 near sel range $3 newMap true modelId 1000 minimalBounds > true; vol zone $2 near sel range $3 newMap true modelId 1001 minimalBounds > true; volume scale #1000 sd 0.1 modelId 1002; volume scale #1001 sd 0.1 > modelId 1003; fitmap #1003 inMap #1002; volume resample #1003 onGrid #1002 > modelId 1004; volume subtract #1002 #1004 modelId 1005 minRms true; volume > #1005 step 1; split_diff_map #1005 #1006; close > #10000,#1000,#1001,#1002,#1003,#1004,#1005 > alias usage local_diff_map_sphere synopsis ""Build a local difference map > between two maps around the center of rotation"" $1 ""first map"" $2 ""second > map"" $3 radius > alias binary_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum > 1 modelId 2000; volume #2000 level 0.5 > alias usage binary_mask synopsis ""Create a binary mask map at a chosen > contour level"" $1 map-spec $2 ""contour level"" > alias soft_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum 1 > modelId 2000; volume falloff #2000 iterations 20 modelId 2001; volume #2001 > level 0.5; close #2000 > alias usage soft_mask synopsis ""Create a soft-edged mask map at a chosen > contour level"" $1 map-spec $2 ""contour level"" > alias delh delete @H* > alias usage delh synopsis ""Delete all hydrogen atoms"" > alias delh_sel delete sel & @H* > alias usage delh_sel synopsis ""Delete hydrogen atoms from the current > selection"" > alias carve surface zone ~##num_residues nearAtoms sel distance $1 > alias usage carve synopsis ""Carve displayed map surfaces to the current > selection"" $1 distance > alias uncarve surface unzone ~##num_residues > alias usage uncarve synopsis ""Remove surface carving from displayed map > surfaces"" > functionkey F1 prevmodel > functionkey F2 nextmodel > functionkey F3 centersel > functionkey F4 view all > functionkey F5 togglemaps > functionkey F6 togglemodels > functionkey F7 cyclelighting > functionkey F8 cyclemodeldisplay > functionkey F9 prevmap > functionkey F10 nextmap > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr > radius 1"" > buttonpanel Shortcuts add togglemaps command togglemaps > buttonpanel Shortcuts add togglemodels command togglemodels > buttonpanel Shortcuts add reset_mouse_and_help command ""mousemode alt right > contour ; mousemode right clip ; mousemode alt left 'translate selected > models' ; mousemode shift left 'rotate selected models' ; mousemode alt > control left 'pick blobs'; help https://github.com/olibclarke/chimerax- > trimmings/blob/main/default_mousemodes.md"" > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > open /Users/sconnell/local/calc_level_ChimeraX/calc_level.py executed calc_level.py UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/sconnell/Documents/Scans/ICMTB_2026 Current working directory is: /Users/sconnell/Documents/Scans/ICMTB_2026 > open GE81112_assembly_movie.cxc > open 9H9H 9h9h title: Complex 1 30S-IF1-IF2-IF3-GE81112 [more info...] Chain information for 9h9h #1 --- Chain | Description | UniProt 2 | mRNA (5'-R(P*AP*AP*UP*G)-3') | 3 | t-RNA (77-MER) | A | 16S RNA (1534-MER) | B | Small ribosomal subunit protein uS2 | RS2_ECOLI 1-241 C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233 D | Small ribosomal subunit protein uS4 | RS4_ECOLI 1-206 E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167 F | Small ribosomal subunit protein bS6, fully modified isoform | RS6_ECOLI 1-135 G | Small ribosomal subunit protein uS7 | RS7_ECOLI 1-179 H | Small ribosomal subunit protein uS8 | RS8_ECOLI 1-130 I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130 J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103 K | Small ribosomal subunit protein uS11 | RS11_ECOLI 1-129 L | Small ribosomal subunit protein uS12 | RS12_ECOLI 1-124 M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118 N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101 O | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 P | Small ribosomal subunit protein bS16 | RS16_ECOLI 1-82 Q | Small ribosomal subunit protein uS17 | RS17_ECOLI 1-84 R | Small ribosomal subunit protein bS18 | RS18_ECOLI 1-75 S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92 T | Small ribosomal subunit protein bS20 | RS20_ECOLI 1-87 U | Small ribosomal subunit protein bS21 | RS21_ECOLI 1-71 X | Translation initiation factor IF-1 | IF1_ECOLI 1-72 Y | Translation initiation factor IF-2 | IF2_ECO24 1-890 Z | Translation initiation factor IF-3 | IF3_ECOLI 1-180 Non-standard residues in 9h9h #1 --- A1IC4 — (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl- propanoic acid K — potassium ion MG — magnesium ion ZN — zinc ion > delete solvent > delete ions > surface #1 > color #1 & ~(#1/X | #1/Y | #1/Z | #1/2 | #1/3) #b0b0b0 target s > color #1/X #FFD700 target s > color #1/Y #CC2200 target s > color #1/Z #1A5FA8 target s > color #1/2 #00CED1 target s > color #1/3 #FF8C00 target s > select clear > camera ortho > lighting flat > graphics silhouettes true > set bgColor white > windowsize 927 767 > view matrix camera > 0.029709,0.23038,-0.97265,-171.4,-0.86024,0.50144,0.092495,202.3,0.50903,0.83396,0.21308,212.63 > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0 > hide #1/X > hide #1/Y > hide #1/Z > hide #1/2 > hide #1/3 > cofr #1 & ~(#1/X | #1/Y | #1/Z | #1/2 | #1/3) > movie record format PNG > wait 90 > show #1/Z surfaces > transparency #1/Z 100 target s > wait 10 > transparency #1/Z 75 target s > wait 20 > transparency #1/Z 50 target s > wait 20 > transparency #1/Z 25 target s > wait 20 > transparency #1/Z 0 target s > wait 20 > show #1/X surfaces > transparency #1/X 100 target s > wait 10 > transparency #1/X 75 target s > wait 20 > transparency #1/X 50 target s > wait 20 > transparency #1/X 25 target s > wait 20 > transparency #1/X 0 target s > wait 20 > show #1/2 surfaces > transparency #1/2 100 target s > wait 10 > transparency #1/2 75 target s > wait 20 > transparency #1/2 50 target s > wait 20 > transparency #1/2 25 target s > wait 20 > transparency #1/2 0 target s > wait 20 > show #1/Y surfaces > show #1/3 surfaces > transparency #1/Y 100 target s > transparency #1/3 100 target s > wait 10 > transparency #1/Y 75 target s > transparency #1/3 75 target s > wait 30 > transparency #1/Y 50 target s > transparency #1/3 50 target s > wait 30 > transparency #1/Y 25 target s > transparency #1/3 25 target s > wait 30 > transparency #1/Y 0 target s > transparency #1/3 0 target s > wait 20 > 2dlabels create preIC text ""30S Pre-Initiation Complex"" xpos 0.05 ypos 0.92 > size 28 color #222222 > wait 180 > 2dlabels delete all > 2dlabels create ge text ""GE81112 traps this complex"" xpos 0.05 ypos 0.92 > size 28 color #CC2200 > wait 180 > 2dlabels delete all > 2dlabels create credit text ""Connell Lab | Biobizkaia | ICMTB 2026"" xpos 0.05 ypos 0.05 size 18 color #555555 > wait 60 > movie encode > /Users/sconnell/Documents/Scans/ICMTB_2026/GE81112_assembly_movie.mp4 format > h264 quality high framerate 30 Movie saved to /Users/sconnell/.../ICMTB_2026/GE81112_assembly_movie.mp4 > movie reset No movie being recorded. executed GE81112_assembly_movie.cxc > close session > open Ge81112_comparison_figure.cxc > open 9H9H 9h9h title: Complex 1 30S-IF1-IF2-IF3-GE81112 [more info...] Chain information for 9h9h #1 --- Chain | Description | UniProt 2 | mRNA (5'-R(P*AP*AP*UP*G)-3') | 3 | t-RNA (77-MER) | A | 16S RNA (1534-MER) | B | Small ribosomal subunit protein uS2 | RS2_ECOLI 1-241 C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233 D | Small ribosomal subunit protein uS4 | RS4_ECOLI 1-206 E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167 F | Small ribosomal subunit protein bS6, fully modified isoform | RS6_ECOLI 1-135 G | Small ribosomal subunit protein uS7 | RS7_ECOLI 1-179 H | Small ribosomal subunit protein uS8 | RS8_ECOLI 1-130 I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130 J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103 K | Small ribosomal subunit protein uS11 | RS11_ECOLI 1-129 L | Small ribosomal subunit protein uS12 | RS12_ECOLI 1-124 M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118 N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101 O | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 P | Small ribosomal subunit protein bS16 | RS16_ECOLI 1-82 Q | Small ribosomal subunit protein uS17 | RS17_ECOLI 1-84 R | Small ribosomal subunit protein bS18 | RS18_ECOLI 1-75 S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92 T | Small ribosomal subunit protein bS20 | RS20_ECOLI 1-87 U | Small ribosomal subunit protein bS21 | RS21_ECOLI 1-71 X | Translation initiation factor IF-1 | IF1_ECOLI 1-72 Y | Translation initiation factor IF-2 | IF2_ECO24 1-890 Z | Translation initiation factor IF-3 | IF3_ECOLI 1-180 Non-standard residues in 9h9h #1 --- A1IC4 — (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl- propanoic acid K — potassium ion MG — magnesium ion ZN — zinc ion > 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 > delete solvent > delete ions > tile #1,2 columns 2 spacingFactor 1.2 2 models tiled > surface #1 > surface #2 > color #1 & ~(#1/X | #1/Y | #1/Z | #1/2 | #1/3) #b0b0b0 target s > color #1/X #FFD700 target s > color #1/Y #CC2200 target s > color #1/Z #1A5FA8 target s > color #1/2 #00CED1 target s > color #1/3 #FF8C00 target s > color #2 #b0b0b0 target s > select clear > camera ortho > lighting flat > graphics silhouettes true > set bgColor white > windowsize 1800 900 > view matrix camera > 0.029709,0.23038,-0.97265,-171.4,-0.86024,0.50144,0.092495,202.3,0.50903,0.83396,0.21308,212.63 > 2dlabels create leftLabel text ""30S pre-IC + GE81112 (unlocked)"" xpos 0.05 > ypos 0.95 size 24 color #CC2200 > 2dlabels create rightLabel text ""30S pre-IC state-III (locked)"" xpos 0.55 > ypos 0.95 size 24 color #1A5FA8 > 2dlabels create pdb1 text ""PDB: 9H9H"" xpos 0.05 ypos 0.04 size 16 color > #555555 > 2dlabels create pdb2 text ""PDB: 5LMV Hussain et al. 2016"" xpos 0.55 ypos > 0.04 size 16 color #555555 > save > /Users/sconnell/Documents/Scans/ICMTB_2026/GE81112_comparison_figure.png > width 3600 height 1800 supersample 3 executed Ge81112_comparison_figure.cxc > hide #!2 models > show #!2 models > hide #!1 models > hide #!3 models > hide #!2 models > show #!2 models > select add #2 59466 atoms, 63980 bonds, 1819 pseudobonds, 4736 residues, 3 models selected > select subtract #2 26 models selected > select add #2 59466 atoms, 63980 bonds, 1819 pseudobonds, 4736 residues, 3 models selected > hide sel atoms > show sel cartoons > lighting simple > hide #2.29 models > hide #2.28 models > hide #2.27 models > hide #2.26 models > hide #2.25 models > hide #2.24 models > hide #2.23 models > hide #2.22 models > hide #2.21 models > hide #2.20 models > hide #2.19 models > hide #2.18 models > hide #2.17 models > hide #2.16 models > hide #2.15 models > hide #2.14 models > hide #2.13 models > hide #2.12 models > hide #2.11 models > hide #2.10 models > hide #2.9 models > hide #2.8 models > hide #2.7 models > hide #2.6 models > hide #2.5 models > hide #2.4 models > hide #2.3 models > hide #2.2 models > hide #2.1 models > select subtract #2 26 models selected > select subtract #2.2 Nothing selected > select add #2 59466 atoms, 63980 bonds, 1819 pseudobonds, 4736 residues, 3 models selected > select subtract #2 26 models selected > show #!1 models > close session > open 9H9H 9h9h title: Complex 1 30S-IF1-IF2-IF3-GE81112 [more info...] Chain information for 9h9h #1 --- Chain | Description | UniProt 2 | mRNA (5'-R(P*AP*AP*UP*G)-3') | 3 | t-RNA (77-MER) | A | 16S RNA (1534-MER) | B | Small ribosomal subunit protein uS2 | RS2_ECOLI 1-241 C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233 D | Small ribosomal subunit protein uS4 | RS4_ECOLI 1-206 E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167 F | Small ribosomal subunit protein bS6, fully modified isoform | RS6_ECOLI 1-135 G | Small ribosomal subunit protein uS7 | RS7_ECOLI 1-179 H | Small ribosomal subunit protein uS8 | RS8_ECOLI 1-130 I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130 J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103 K | Small ribosomal subunit protein uS11 | RS11_ECOLI 1-129 L | Small ribosomal subunit protein uS12 | RS12_ECOLI 1-124 M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118 N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101 O | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 P | Small ribosomal subunit protein bS16 | RS16_ECOLI 1-82 Q | Small ribosomal subunit protein uS17 | RS17_ECOLI 1-84 R | Small ribosomal subunit protein bS18 | RS18_ECOLI 1-75 S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92 T | Small ribosomal subunit protein bS20 | RS20_ECOLI 1-87 U | Small ribosomal subunit protein bS21 | RS21_ECOLI 1-71 X | Translation initiation factor IF-1 | IF1_ECOLI 1-72 Y | Translation initiation factor IF-2 | IF2_ECO24 1-890 Z | Translation initiation factor IF-3 | IF3_ECOLI 1-180 Non-standard residues in 9h9h #1 --- A1IC4 — (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl- propanoic acid K — potassium ion MG — magnesium ion ZN — zinc ion > 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 > delete solvent > delete ions > lighting simple > hide atoms > show cartoons > mmaker #2/A to #1/A Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb 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 9h9h, chain A (#1) with 5lmv, chain A (#2), sequence alignment score = 4167.6 RMSD between 316 pruned atom pairs is 1.380 angstroms; (across all 1497 pairs: 8.181) > open /Users/sconnell/Library/CloudStorage/OneDrive- > Personal/Documents/CurrentWork/Ge811112-2022/GE81112/For_deposition/Complex1/job167_run_class001.mrc Opened job167_run_class001.mrc as #3, grid size 300,300,300, pixel 1.09, shown at level 0.0105, step 1, values float32 > volume #3 level 0.006682 > hide #!2 models > open /Users/sconnell/Library/CloudStorage/Dropbox/Seans_Folder/RsmB/RsmB- > Shared_models_24032026/mature- > job1041-9h9h-job1041-IF3AF_NOCTD-8a3lS1-ROUGH.pdb Chain information for mature-job1041-9h9h-job1041-IF3AF_NOCTD-8a3lS1-ROUGH.pdb #4 --- 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 V | No description available Y | No description available > hide #!1 models > mmaker #3/A to #1/A No molecules/chains to match specified > mmaker #4/A to #1/A Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb 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 9h9h, chain A (#1) with mature- job1041-9h9h-job1041-IF3AF_NOCTD-8a3lS1-ROUGH.pdb, chain A (#4), sequence alignment score = 6158.4 RMSD between 854 pruned atom pairs is 1.306 angstroms; (across all 1534 pairs: 4.965) > show #!1 models > select add #4 91507 atoms, 95587 bonds, 142 pseudobonds, 4330 residues, 2 models selected > hide sel atoms > show sel cartoons > show #!3 models > select #1:GE8 Nothing selected > select add #4 91507 atoms, 95587 bonds, 142 pseudobonds, 4330 residues, 2 models selected > select subtract #4 Nothing selected > view > ui tool show ""Side View"" Drag select of 97 residues, 3 job167_run_class001.mrc > volume #3 color #b2b2b289 > log metadata #1 Metadata for 9h9h #1 --- Title | Complex 1 30S-IF1-IF2-IF3-GE81112 Citation | Schedlbauer, A., Han, X., van Bakel, W., Kaminishi, T., Ochoa-Lizarralde, B., Iturrioz, I., Capuni, R., Parry, R., Zegarra, R., Gil-Carton, D., Lopez-Alonso, J.P., Barragan Sanz, K., Brandi, L., Gualerzi, C.O., Fucini, P., Connell, S.R. (2024). A binding site for the antibiotic GE81112 in the ribosomal mRNA channel. bioRxiv. PMID: 39386670. DOI: 10.1101/2024.09.26.614503 Non-standard residue | A1IC4 — (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl-propanoic acid Gene source | Escherichia coli CryoEM Map | EMDB 51964 — open map Experimental method | Electron microscopy Resolution | 3.8Å > select :A1IC4 44 atoms, 46 bonds, 1 residue, 1 model selected > select :A1IC4 44 atoms, 46 bonds, 1 residue, 1 model selected > show sel atoms > hide #!3 models > hide #!4 models > show #!4 models > combine #1 close false name 30S-start > hide #!1 models > hide #!4 models > show #!4 models > hide #!5 models > combine #4/V:1-69 close false name 30S-start > close #6 > combine #4/V:1-69 close false name IF3-CTD-start > hide #!4 models > hide #!6 models > show #!6 models > show #!5 models > hide #!6 models > hide #!5 models > show #!4 models > close #6 > select #4/V:1-69 910 atoms, 913 bonds, 59 residues, 1 model selected > combine sel close false name IF3-CTD-start > hide #!4 models > select add #4 91507 atoms, 95587 bonds, 142 pseudobonds, 4330 residues, 2 models selected > select subtract #4 Nothing selected > select #6&~#6/V:1-69 90597 atoms, 94673 bonds, 142 pseudobonds, 4271 residues, 2 models selected > delete sel > show #!5 models > hide #!5 models > changechains 9 #6/V No residues specified have any of the 'from' chain IDs > changechains #6/V 9 Chain IDs of 59 residues changed > show #!5 models > combine #5,#6 name ""30S-start-IF3"" Expected a keyword > combine #5,6 name 30S-start-IF3 > hide #!5 models > hide #!6 models > combine #2 name 5lmv-temp > mmaker #8/Z to #7/3 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb 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 30S-start-IF3, chain 3 (#7) with 5lmv-temp, chain Z (#8), sequence alignment score = 175.7 RMSD between 44 pruned atom pairs is 1.271 angstroms; (across all 77 pairs: 3.876) > hide #!7 models > select #8&~#8/a:479-566/Z 57119 atoms, 61433 bonds, 1734 pseudobonds, 4570 residues, 3 models selected > delete sel > show #!7 models > delete #7/3 > changechains #8/a Y Chain IDs of 88 residues changed > changechains #8/Z 3 Chain IDs of 78 residues changed > combine #7,8 retainIds true name 30S-start-IF3-IF2 'retainIds' requires residues number / insertion code combos be unique in each chain with the same ID (duplicate: /Y LEU 479) > combine #7,8 name 30S-start-IF3-IF2 Remapping chain ID 'Y' in 5lmv-temp #8 to 'a' > hide #!7 models > hide #!8 models > changechains #9/a Y Proposed chainID change conflicts with existing residue 30S-start-IF3-IF2 #9/Y THR 479 > renumber #9/a start 790 88 residues renumbered > changechains #9/a Y Chain IDs of 88 residues changed > pwd Current working directory is: /Users/sconnell/Documents/Scans/ICMTB_2026 > save 9h9h_5lmv-af-mashup-30S-PREIC model #9 Cannot determine format for '9h9h_5lmv-af-mashup-30S-PREIC' > save 9h9h_5lmv-af-mashup-30S-PREIC.pdb models #9 Residue names longer than 4 characters; truncating > open 9h9h_5lmv-af-mashup-30S-PREIC.pdb Chain information for 9h9h_5lmv-af-mashup-30S-PREIC.pdb #10 --- Chain | Description 2 | No description available 3 | No description available 9 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 X | No description available Y | No description available > select add #10 60268 atoms, 64755 bonds, 4825 residues, 1 model selected > hide sel atoms > show sel cartoons > hide #!9 models > select subtract #10 Nothing selected > hide #10 models > show #!7 models > show #!2 models > combine #7 > close #11 > combine #7 name 30S-end > hide #!7 models > hide #!2 models > select #11/Z 923 atoms, 934 bonds, 112 residues, 1 model selected > select #11/Z,9 1833 atoms, 1847 bonds, 171 residues, 1 model selected > delete sel > show #10 models > hide #!11 models > hide #10 models > show #!11 models > show #!8 models > hide #!11 models > hide #!8 models > show #!8 models > show #!11 models > hide #!8 models > show #!2 models > close #8 > combine #2 > hide #!2 models > select #8&~#8/a:479-566/x,Z 57119 atoms, 61433 bonds, 1734 pseudobonds, 4570 residues, 3 models selected > select #8&~#8/a:479-566/X,Z 55783 atoms, 60079 bonds, 1733 pseudobonds, 4406 residues, 3 models selected > delete sel > changechains #8/Z 3 Chain IDs of 78 residues changed > hide #!8 models > show #10 models > hide #10 models > show #!8 models > changechains #8/X Z Chain IDs of 164 residues changed > show #10 models > hide #10 models > changechains #8/a Y Chain IDs of 88 residues changed > renumber 8/Y start 790 Expected a keyword > renumber #8/Y start 790 88 residues renumbered > combine #11,8 Remapping chain ID 'Y' in copy of 5lmv #8 to 'a' > hide #!11 models > hide #!8 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > combine #12 name temp > select #13/A:1-926,1391-1534/D,E,F,H,K,L,O,P,Q,R,T,U 33043 atoms, 35942 bonds, 1088 pseudobonds, 2350 residues, 2 models selected > delete sel > hide #!12 models > show #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > select #13/A:927-1390/B,C,G,I,J,M,N,S 18700 atoms, 20013 bonds, 426 pseudobonds, 1575 residues, 2 models selected > mmaker #13/A:927-1390 to #2/A Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb 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 A (#2) with temp, chain A (#13), sequence alignment score = 2927 RMSD between 306 pruned atom pairs is 1.350 angstroms; (across all 463 pairs: 3.112) > hide #!2 models > select add #13 26728 atoms, 28318 bonds, 502 pseudobonds, 2468 residues, 3 models selected > select subtract #13 Nothing selected > hide #!12 models > select #13&~#13/A:927-1390/B,C,G,I,J,M,N,S 8028 atoms, 8305 bonds, 76 pseudobonds, 893 residues, 3 models selected > delete sel > show #!2 models > hide #!2 models > show #!12 models > select #12&~#12/A:927-1390/B,C,G,I,J,M,N,S 41071 atoms, 44247 bonds, 1164 pseudobonds, 3243 residues, 3 models selected > hide #!13 models > select #12/A:927-1390/B,C,G,I,J,M,N,S 18700 atoms, 20013 bonds, 426 pseudobonds, 1575 residues, 2 models selected > delete sel > show #!13 models > hide #!12 models > show #!12 models > combine #12,13 name 30S-end-IF3-IF2 Remapping chain ID 'A' in temp #13 to 'V' > hide #!13 models > hide #!12 models > changechains #14/a Y Chain IDs of 88 residues changed > save 9h9h_5lmv-af-mashup-30S-IC.pdb models #14 Residue names longer than 4 characters; truncating > open 9h9h_5lmv-af-mashup-30S-IC.pdb Chain information for 9h9h_5lmv-af-mashup-30S-IC.pdb #15 --- Chain | Description 2 | No description available 3 | No description available A V | 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 X | No description available Y | No description available Z | No description available > select add #15 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > show sel atoms > show sel cartoons > hide #!14 models > hide sel atoms > select subtract #15 Nothing selected > show #10 models > save ChimeraX-build-mashups-001.cxs > morph #10,15 Computed 51 frame morph #16 > coordset #16 1,51 > morph #10,15 Computed 51 frame morph #17 > coordset #17 1,51 > close #17 > close #16 > show #!15 models > show #10 models > hide #!15 models > show #!14 models > hide #!14 models > show #!13 models > hide #10 models > show #!12 models > combine #12,13 name 30S-end-IF3-IF2 Remapping chain ID 'A' in temp #13 to 'V' > hide #!12 models > hide #!13 models > show #10 models > hide #10 models > changechains #16/V A Chain IDs of 464 residues changed > save 9h9h_5lmv-af-mashup-30S-IC.pdb models #14 Residue names longer than 4 characters; truncating > save 9h9h_5lmv-af-mashup-30S-IC.pdb models #16 Residue names longer than 4 characters; truncating > close #15 > open 9h9h_5lmv-af-mashup-30S-IC.pdb Chain information for 9h9h_5lmv-af-mashup-30S-IC.pdb #15 --- Chain | Description 2 | No description available 3 | 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 X | No description available Y | No description available Z | No description available a | No description available > select add #15 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > hide sel atoms > show sel cartoons > select subtract #15 Nothing selected > hide #!16 models > show #10 models > morph #10,15 Computed 51 frame morph #17 > coordset #17 1,51 > close #17 > show #!15 models > show #10 models > morph #10/Z,#15/Z Missing or invalid ""structures"" argument: only initial part ""#10/Z"" of atom specifier valid > morph #10/Z,15/Z Require at least 2 structures for morph > select #10,15/Z 2259 atoms, 2288 bonds, 1 pseudobond, 276 residues, 3 models selected > morph sel Computed 51 frame morph #17 > coordset #17 1,51 > close #17 > show #10 models > show #!15 models > select add #10 61604 atoms, 66109 bonds, 1 pseudobond, 4989 residues, 3 models selected > select add #15 120039 atoms, 129015 bonds, 2 pseudobonds, 9643 residues, 3 models selected > select subtract #15 60268 atoms, 64755 bonds, 4825 residues, 1 model selected > select subtract #10 Nothing selected > select #10 60268 atoms, 64755 bonds, 4825 residues, 1 model selected > select #15 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > select subtract #15 Nothing selected > hide #16.3 models > hide #16.2 models > hide #16.1 models > select #10/a 32974 atoms, 36918 bonds, 1535 residues, 1 model selected > hide #!15 models > select add #10 60268 atoms, 64755 bonds, 4825 residues, 1 model selected > select subtract #10 Nothing selected > select #10/a 32974 atoms, 36918 bonds, 1535 residues, 1 model selected > select #15/a 692 atoms, 701 bonds, 88 residues, 1 model selected > hide #10 models > show #!15 models > changechains #15/a Y Chain IDs of 88 residues changed > select #15/9 Nothing selected > hide #!15 models > show #10 models > select #15/9 Nothing selected > select #10/9 910 atoms, 913 bonds, 59 residues, 1 model selected > changechains #10/9 Z Proposed chainID change conflicts with existing residue 9h9h_5lmv-af- mashup-30S-PREIC.pdb #10/Z ASP 69 > delete #10/Z:69 > changechains #10/9 Z Chain IDs of 59 residues changed > save 9h9h_5lmv-af-mashup-30S-IC-001.pdb models #15 > open 9h9h_5lmv-af-mashup-30S-IC-001.pdb Chain information for 9h9h_5lmv-af-mashup-30S-IC-001.pdb #17 --- Chain | Description 2 | No description available 3 | 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 X | No description available Y | No description available Z | No description available > save 9h9h_5lmv-af-mashup-30S-PreIC-001.pdb models #10 > open 9h9h_5lmv-af-mashup-30S-PreIC-001.pdb Chain information for 9h9h_5lmv-af-mashup-30S-PreIC-001.pdb #18 --- Chain | Description 2 | No description available 3 | 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 X | No description available Y | No description available Z | No description available > hide #10 models > select add #10 60260 atoms, 64747 bonds, 4824 residues, 1 model selected > select subtract #10 Nothing selected > select add #17 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > select add #18 120031 atoms, 129007 bonds, 2 pseudobonds, 9642 residues, 3 models selected > hide sel atoms > show sel cartoons > select subtract #18 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > select subtract #17 Nothing selected > select #17 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > select #18 60260 atoms, 64747 bonds, 4824 residues, 1 model selected > select subtract #18 Nothing selected > show #17.1 target m > view #17.1 clip false No displayed objects specified. > select add #17.1 2 pseudobonds, 1 model selected > close #17-18 > open /Users/sconnell/Documents/Scans/ICMTB_2026/9h9h_5lmv-af- > mashup-30S-IC-001.pdb /Users/sconnell/Documents/Scans/ICMTB_2026/9h9h_5lmv- > af-mashup-30S-PreIC-001.pdb Chain information for 9h9h_5lmv-af-mashup-30S-IC-001.pdb #17 --- Chain | Description 2 | No description available 3 | 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 X | No description available Y | No description available Z | No description available Chain information for 9h9h_5lmv-af-mashup-30S-PreIC-001.pdb #18 --- Chain | Description 2 | No description available 3 | 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 X | No description available Y | No description available Z | No description available > select #17 59771 atoms, 64260 bonds, 2 pseudobonds, 4818 residues, 2 models selected > select #18 60260 atoms, 64748 bonds, 4824 residues, 1 model selected Desktop color scheme is dark ===== Log before crash end ===== Log: > runscript /Users/sconnell/local/chimerax-trimmings/chimerax_trimmings.py > camera ortho > cofr centerOfView > mousemode alt rightMode ""contour level"" > mousemode rightMode clip > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot 7,0.25 > alias usage cofron synopsis ""Center the rotation point on the view and show > the pivot"" > alias cofroff cofr centerofview showpivot false > alias usage cofroff synopsis ""Recenter the rotation point on the view and > hide the pivot marker"" > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias usage symclip synopsis ""Set symmetric clip planes around the center of > rotation"" $1 half-distance > alias selmodel sel ##num_residues > alias usage selmodel synopsis ""Select atomic models"" > alias selmap sel ~##num_residues > alias usage selmap synopsis ""Select non-atomic models such as maps"" > alias selside sel sidechain & $1 | ~backbone & nucleic & $1 > alias usage selside synopsis ""Select protein sidechains and nucleic-acid > bases"" $1 atom-spec > alias dispside sel sidechain & $1 | ~backbone & nucleic & $1; disp sel > alias usage dispside synopsis ""Display protein sidechains and nucleic-acid > bases"" $1 atom-spec > alias cootmode_white set bgColor white; surface cap false; surface style > solid; nucleotides #* atoms; lighting flat; graphics silhouettes false; > style stick; ~rib; color ##num_residues orange; color byhet ; disp > ##num_residues & ##display; ~disp @H*; style ions sphere; style solvent > ball; size ballscale 0.2; size stickradius 0.07; transparency 85; cofr > centerofview; clip near -10 far 10 position cofr; color ~##num_residues > medium blue > alias usage cootmode_white synopsis ""Apply the white-background Coot-style > display preset"" > alias cootmode set bgColor black; surface cap false; surface style solid; > nucleotides #* atoms; lighting flat; graphics silhouettes false; style > stick; ~rib; color ##num_residues gold; color byhet ; disp ##num_residues & > ##display; ~disp @H*; style ions sphere; style solvent ball; size ballscale > 0.2; size stickradius 0.07; transparency 70; cofr centerofview; clip near > -10 far 10 position cofr; color ~##num_residues cornflower blue > alias usage cootmode synopsis ""Apply the dark-background Coot-style display > preset"" > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > nucleotides #* atoms; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp ##num_residues & ##display; ~disp > @H*; style solvent ball; style ions sphere; size ballscale 0.2; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ~##num_residues #3d60ffff; transparency 50 > alias usage cootmode_mesh synopsis ""Apply the mesh Coot-style display > preset"" > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias usage ca_and_sidechains synopsis ""Show CA or phosphate trace plus > sidechains or bases"" $1 model-spec > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias usage ca_trace synopsis ""Show a CA or phosphate trace"" $1 model-spec > alias expand_sym ~disp $1; rib $1; sym $1 assembly 1 copies false newModel > true > alias usage expand_sym synopsis ""Expand an asymmetric unit to biological > assembly 1 as ribbon copies"" $1 model-spec > alias map_sphere_15 volume unzone ~##num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel > minimalBounds true range 15; close #10000 > alias usage map_sphere_15 synopsis ""Zone maps to a 15 A sphere around the > center of rotation"" > alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask > #10000 spacing 1 border -0.5 > alias usage cubic_map synopsis ""Create a spherical mask map on a cubic grid"" > $1 ""sphere radius"" > alias map_unsphere volume unzone ~##num_residues > alias usage map_unsphere synopsis ""Remove map zoning from all maps"" > alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine > $1.* close true > alias usage fit_by_chain synopsis ""Split a model by chain, fit each chain > into a map, and recombine"" $1 model-spec $2 map-spec > alias rainbow_new rainbow palette RdYlBu-5 > alias usage rainbow_new synopsis ""Color models by rainbow using the RdYlBu-5 > palette"" > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias usage default_mol_display synopsis ""Restore the default cartoon > molecular display"" > alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; > sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 > minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; > close sel; show $2 > alias usage local_fitmap synopsis ""Fit a model or map into a local zone > around the center of rotation"" $1 ""model or map to fit"" $2 ""target map"" $3 > ""zone radius"" > alias hidemodels hide ##num_residues models > alias usage hidemodels synopsis ""Hide all atomic models"" > alias showmodels show ##num_residues models > alias usage showmodels synopsis ""Show all atomic models"" > alias caps_off surface cap false > alias usage caps_off synopsis ""Turn clipped surface caps off"" > alias caps_on surface cap true > alias usage caps_on synopsis ""Turn clipped surface caps on"" > alias open_vseries ""open browse vseries true"" > alias usage open_vseries synopsis ""Open a file browser with volume series > enabled"" > alias selbetween ks ri > alias usage selbetween synopsis ""Select residues between the current > selection endpoints"" > alias helix setattr $1 res is_helix true > alias usage helix synopsis ""Mark residues as helix"" $1 residue-spec > alias strand setattr $1 res is_strand true > alias usage strand synopsis ""Mark residues as strand"" $1 residue-spec > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias usage coil synopsis ""Clear helix and strand assignment for residues"" > $1 residue-spec > alias rock_movie cofr showpivot false; movie record; rock y 50; wait 600; > movie encode ~/Desktop/rock_movie.mp4; stop > alias usage rock_movie synopsis ""Record a rocking movie and save it to the > default Desktop file"" > alias centersel cofr sel; clip near 10 position cofr; clip far -10 position > cofr; cofr centerOfView showpivot true; view sel > alias usage centersel synopsis ""Center the view on the selection and apply > local clipping"" > alias volume_project set bgColor black; volume $1 step 1 sd_level 0,0 > sd_level 50,1 color white color white style image projection_mode auto > maximum_intensity_projection true bt_correction true linear_interpolation > true; lighting depth_cue false > alias usage volume_project synopsis ""Display a map as a maximum-intensity > projection"" $1 map-spec > alias split_diff_map volume scale $1 rms 1 modelId $2; close $1; volume $2 > capFaces false meshLighting false squareMesh false level -3 color > #da1200000000 level 3 color #0000bda00000; lighting depthCue true; volume $2 > style mesh > alias usage split_diff_map synopsis ""Replace a map with a scaled positive > and negative mesh difference map"" $1 ""input map"" $2 ""output model-id"" > alias local_diff_map view name tmp; close #1001,1002,1003,1004,1005; fitmap > $1 inMap $2; vol zone $2 near $1 range 5 newMap true modelId 1000 > minimalBounds true; fitmap $1 inMap $3; vol zone $3 near $1 range 5 newMap > true modelId 1001 minimalBounds true; volume scale #1000 sd 0.1 modelId > 1002; volume scale #1001 sd 0.1 modelId 1003; fitmap #1003 inMap #1002; > volume resample #1003 onGrid #1002 modelId 1004; volume subtract #1002 #1004 > modelId 1005 minRms true; volume #1005 step 1; split_diff_map #1005 #1006; > close #1000,1001,1002,1003,1004,1005; view tmp > alias usage local_diff_map synopsis ""Build a local difference map between > two fitted maps around a model"" $1 model-spec $2 ""first map"" $3 ""second map"" > alias local_diff_map_sphere ~sel; close > #10000,#1001,#1002,#1003,#1004,#1005; marker #10000 position cofr; sel > #10000; vol zone $1 near sel range $3 newMap true modelId 1000 minimalBounds > true; vol zone $2 near sel range $3 newMap true modelId 1001 minimalBounds > true; volume scale #1000 sd 0.1 modelId 1002; volume scale #1001 sd 0.1 > modelId 1003; fitmap #1003 inMap #1002; volume resample #1003 onGrid #1002 > modelId 1004; volume subtract #1002 #1004 modelId 1005 minRms true; volume > #1005 step 1; split_diff_map #1005 #1006; close > #10000,#1000,#1001,#1002,#1003,#1004,#1005 > alias usage local_diff_map_sphere synopsis ""Build a local difference map > between two maps around the center of rotation"" $1 ""first map"" $2 ""second > map"" $3 radius > alias binary_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum > 1 modelId 2000; volume #2000 level 0.5 > alias usage binary_mask synopsis ""Create a binary mask map at a chosen > contour level"" $1 map-spec $2 ""contour level"" > alias soft_mask volume threshold $1 minimum $2 set 0 maximum $2 setMaximum 1 > modelId 2000; volume falloff #2000 iterations 20 modelId 2001; volume #2001 > level 0.5; close #2000 > alias usage soft_mask synopsis ""Create a soft-edged mask map at a chosen > contour level"" $1 map-spec $2 ""contour level"" > alias delh delete @H* > alias usage delh synopsis ""Delete all hydrogen atoms"" > alias delh_sel delete sel & @H* > alias usage delh_sel synopsis ""Delete hydrogen atoms from the current > selection"" > alias carve surface zone ~##num_residues nearAtoms sel distance $1 > alias usage carve synopsis ""Carve displayed map surfaces to the current > selection"" $1 distance > alias uncarve surface unzone ~##num_residues > alias usage uncarve synopsis ""Remove surface carving from displayed map > surfaces"" > functionkey F1 prevmodel > functionkey F2 nextmodel > functionkey F3 centersel > functionkey F4 view all > functionkey F5 togglemaps > functionkey F6 togglemodels > functionkey F7 cyclelighting > functionkey F8 cyclemodeldisplay > functionkey F9 prevmap > functionkey F10 nextmap > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr > radius 1"" > buttonpanel Shortcuts add togglemaps command togglemaps > buttonpanel Shortcuts add togglemodels command togglemodels > buttonpanel Shortcuts add reset_mouse_and_help command ""mousemode alt right > contour ; mousemode right clip ; mousemode alt left 'translate selected > models' ; mousemode shift left 'rotate selected models' ; mousemode alt > control left 'pick blobs'; help https://github.com/olibclarke/chimerax- > trimmings/blob/main/default_mousemodes.md"" > buttonpanel Shortcuts add previous_model command prevmodel > buttonpanel Shortcuts add next_model command nextmodel > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > open /Users/sconnell/local/calc_level_ChimeraX/calc_level.py executed calc_level.py UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: Z1G5000E9Y/A Chip: Apple M3 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 24 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 17 days, 23 hours, 14 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMalign: 0.1.3 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.5.4 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-rRNA-Inspector: 0.93 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 finufft: 2.5.0 fonttools: 4.61.1 frozenlist: 1.8.0 fsspec: 2025.10.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 mpmath: 1.3.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 sympy: 1.14.0 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 torch: 2.9.1 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned