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Opened 17 hours ago
#20409 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
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, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, torch._C, torch._C._dynamo.autograd_compiler, torch._C._dynamo.eval_frame, torch._C._dynamo.guards, torch._C._dynamo.utils, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.morph._morph (total: 72)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 371074000-3722e0000 [ 18.4M] rw-\/rwx SM=PRV
GAP OF 0x221d20000 BYTES
---> commpage (reserved) 594000000-827800000 [ 10.3G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 827800000-827c00000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000800001540","rawCodes":[2,34359743808],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000800001540"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":63284},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 371074000-3722e0000 [ 18.4M] rw-\/rwx SM=PRV
GAP OF 0x221d20000 BYTES
---> commpage (reserved) 594000000-827800000 [ 10.3G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 827800000-827c00000 [ 4096K] rw-\/rwx SM=PRV ",
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===== 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
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