id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17807 Crash in python_instances_of_class saving session chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84b706b40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 52 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in python_instances_of_class File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 2642 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 290 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 290 in include_state File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 260 in discovery File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 646 in save File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 922 in save File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, 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bgColor grey > lighting shadows false > lighting depthCue false > graphics silhouettes true > lighting simple > functionkey F1 cofr sel > functionkey F2 mousemode rightMode 'mark surface' > functionkey F3 mousemode rightMode 'move markers' > functionkey F4 mk 3 1 > functionkey F5 view > functionkey F6 view sel pad 0.92 clip false > functionkey F7 mousemode rightMode 'delete markers' > functionkey F8 mousemode rightMode zoom > functionkey F9 sequence chain sel > functionkey F10 transparency sel 65 > functionkey F11 transparency sel 0 > functionkey F12 tool show 'Fit in Map' > color name f01graublau #BADBED Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed > color name f02silber #F6FAFC Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc > color name f03muschel #FFFFE5 Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5 > color name f04beige #F3F3A9 Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9 > color name f05gelb #f2b701 Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701 > color name f06orange #e68310 Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310 > color name f07rotorange #FF6A25 Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25 > color name f08rot #dd3d2d Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d > color name f09lachs #f97b72 Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72 > color name f10flieder #D57AD5 Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5 > color name f11violett #cf1c90 Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90 > color name f12lila #4b148f Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f > color name f13dunkelblau #2E2EF7 Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7 > color name f14blau #00AAFF Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff > color name f15cyan #60e2d6 Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6 > color name f16blaugrün #30ffa6 Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6 > color name f17grün #00FF00 Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00 > color name f18dunkelgrün #228B22 Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 > color name f19hellgrau #DCDCDC Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc > color name f20grau #B2B2B2 Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2 > color name f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.0 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 width 5500 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 width 5500 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust surface dust #$2 size $1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho > alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ; > camera ortho; cartoon style width 2.4 thickness 0.4; lighting > ambientintensity 1.2 fillIntensity 0.4 > alias abbild sel zone sel 1 #$1 residues true extend true > alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel > intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues > true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel > intersect :MG; style sel ball; size sel ballscale 0.5 > alias network sel zone sel $1 #$2 residues true extend true > alias network34 sel zone sel 3.4 #$1 residues true extend true > alias network4 sel zone sel 4 #$1 residues true extend true > alias network10 sel zone sel 10 #$1 residues true extend true > alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect > #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true > alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel > intersect #$2:HOH > alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 & > protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel > f17; sel #$1:K; color sel f15 > alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect > #$1@o*:HOH:MG > alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect > #$1@o*:HOH:MG > alias upsplit color zone #$1 near #$3 sharpEdges true distance $2 > alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel > intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2 > residues true extend true; sel subtract badwaters > alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel > ballscale 0.5 > alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel > ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect > ##name=""K""; color sel blueviolet > alias pixel zoom pixelsize 0.04 > alias da sel #$1 @@display > alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix > Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2; > abbild+ $1 > alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet; > hbonds sel color f05 restrict both interModel false intraMol false intraRes > false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel > intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect > ##name=""hydrogen bonds""; del pbonds sel; sel temp; show sel; da $2; sel > intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect > ##name=""hydrogen bonds""; hide sel; da $2; sel intersect protein; sel > intersect ##name=""hydrogen bonds""; hide sel; da $1; sel intersect > ##name=""hydrogen bonds""; color sel f15 > alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale > 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect > @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K > log true > alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale > 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp > overlapCutoff -0.8 color #00FF00 name Mg log true UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/max/Documents/Projects/MKM/Figure/Supplementary_figure/SX17_congeners/SX17.cxs Opened PP_70S_AP_adjusted copy.mrc as #2, grid size 432,432,432, pixel 0.822, shown at level 0.0256, step 1, values float32 Opened PP_70S_AP_adjusted copy.mrc 5 as #3.6, grid size 432,432,432, pixel 0.822, shown at level 0.0179, step 1, values float32 Opened PP_70S_AP_adjusted copy.mrc 6 as #3.7, grid size 432,432,432, pixel 0.822, shown at level 0.0181, step 1, values float32 Opened PP_70S_AP_adjusted copy.mrc 2 1 as #6.2, grid size 432,432,432, pixel 0.822, shown at level 0.0185, step 1, values float32 opened ChimeraX session > open > /Users/max/Documents/Projects/MKM/Modelling/MKM_cifs/MKM_E_50S-coot-4.pdb Chain information for MKM_E_50S-coot-4.pdb #9 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 95 atoms, 97 bonds, 1 residue, 1 model selected > select ~sel & ##selected 89189 atoms, 96970 bonds, 282 pseudobonds, 6404 residues, 3 models selected > delete sel > select #9/8:6228@C1 1 atom, 1 residue, 1 model selected > select up 95 atoms, 97 bonds, 1 residue, 1 model selected > select up 600545 atoms, 651592 bonds, 44010 residues, 10 models selected > select down 95 atoms, 97 bonds, 1 residue, 1 model selected > color sel #00a9ffff > color sel byhetero > select clear > hide #!7 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > close #7 > save > /Users/max/Documents/Projects/MKM/Figure/Supplementary_figure/SX17_congeners/SX17.cxs ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > mousemode shift leftMode ""translate selected models"" > mousemode shift middleMode ""rotate selected models"" > mousemode rightMode zoom > mousemode control wheelMode ""contour level"" > mousemode setting ""contour level"" speed 0.1 > mousemode shift wheelMode ""rotate selected models"" > camera ortho > set bgColor grey > lighting shadows false > lighting depthCue false > graphics silhouettes true > lighting simple > functionkey F1 cofr sel > functionkey F2 mousemode rightMode 'mark surface' > functionkey F3 mousemode rightMode 'move markers' > functionkey F4 mk 3 1 > functionkey F5 view > functionkey F6 view sel pad 0.92 clip false > functionkey F7 mousemode rightMode 'delete markers' > functionkey F8 mousemode rightMode zoom > functionkey F9 sequence chain sel > functionkey F10 transparency sel 65 > functionkey F11 transparency sel 0 > functionkey F12 tool show 'Fit in Map' > color name f01graublau #BADBED Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed > color name f02silber #F6FAFC Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc > color name f03muschel #FFFFE5 Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5 > color name f04beige #F3F3A9 Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9 > color name f05gelb #f2b701 Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701 > color name f06orange #e68310 Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310 > color name f07rotorange #FF6A25 Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25 > color name f08rot #dd3d2d Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d > color name f09lachs #f97b72 Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72 > color name f10flieder #D57AD5 Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5 > color name f11violett #cf1c90 Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90 > color name f12lila #4b148f Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f > color name f13dunkelblau #2E2EF7 Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7 > color name f14blau #00AAFF Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff > color name f15cyan #60e2d6 Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6 > color name f16blaugrün #30ffa6 Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6 > color name f17grün #00FF00 Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00 > color name f18dunkelgrün #228B22 Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 > color name f19hellgrau #DCDCDC Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc > color name f20grau #B2B2B2 Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2 > color name f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.0 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 width 5500 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 width 5500 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust surface dust #$2 size $1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho > alias tryfigure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.01 ; set bgColor white ; > camera ortho; cartoon style width 2.4 thickness 0.4; lighting > ambientintensity 1.2 fillIntensity 0.4 > alias abbild sel zone sel 1 #$1 residues true extend true > alias abbild+ sel zone sel 1 #$1 residues true extend true; show sel; sel > intersect #$1; style sel stick; sel compound; sel zone sel 7 #$1 residues > true extend true; sel intersect :HOH:MG:K:ZN:SPD:SPM; show sel; sel > intersect :MG; style sel ball; size sel ballscale 0.5 > alias network sel zone sel $1 #$2 residues true extend true > alias network34 sel zone sel 3.4 #$1 residues true extend true > alias network4 sel zone sel 4 #$1 residues true extend true > alias network10 sel zone sel 10 #$1 residues true extend true > alias wasser sel zone #$1 3.4 #$2 residues true extend true; sel intersect > #$2:HOH; sel add #$1; sel zone sel 3.4 #$2 residues true extend true > alias 1st-wasser sel zone #$1 3.4 #$2 residues true extend true; sel > intersect #$2:HOH > alias farben color sel f14; sel #$1 & nucleic; color sel f20; sel #$1 & > protein; color sel f07; sel #$1:HOH; color sel red; sel #$1:MG; color sel > f17; sel #$1:K; color sel f15 > alias magnesiumcluster sel zone sel 2.7 #$1 extend true; sel intersect > #$1@o*:HOH:MG > alias magnesiumcluster4 sel zone sel 4 #$1 extend true; sel intersect > #$1@o*:HOH:MG > alias upsplit color zone #$1 near #$3 sharpEdges true distance $2 > alias weihwasser sel zone #$1 3.4 #$2 residues true extend true; sel > intersect #$2:HOH; sel add #$1; sel subtract badwaters; sel zone sel 3.4 #$2 > residues true extend true; sel subtract badwaters > alias fixall size pseudobondRadius 0.075; sel :MG; style sel ball; size sel > ballscale 0.5 > alias fix size pseudobondRadius 0.075; da $1; sel intersect :MG; style sel > ball; color sel f17; size sel ballscale 0.5; da $1; sel intersect > ##name=""K""; color sel blueviolet > alias pixel zoom pixelsize 0.04 > alias da sel #$1 @@display > alias neu hide #$1; da $2; sel intersect ligand; mm #$1 to #$2 matrix > Nucleic; network10 $1,$2; mm #!$1 & sel to #$2 & sel matrix Nucleic; da $2; > abbild+ $1 > alias neu2 da $1; sel intersect ligand; farben $1; da $1; color sel byhet; > hbonds sel color f05 restrict both interModel false intraMol false intraRes > false; sel intersect :HOH; style sel stick; combine #$1; da $1; sel > intersect :HOH; name frozen temp sel; hide sel; da $1; sel intersect > ##name=""hydrogen bonds""; del pbonds sel; sel temp; show sel; da $2; sel > intersect :HOH; hide sel; da $2; sel intersect nucleic; sel intersect > ##name=""hydrogen bonds""; hide sel; da $2; sel intersect protein; sel > intersect ##name=""hydrogen bonds""; hide sel; da $1; sel intersect > ##name=""hydrogen bonds""; color sel f15 > alias kalium da $1; sel intersect :K; style sel ball; size sel ballscale > 0.3; name frozen temp sel; sel zone sel 3.5 #$1 extend true; sel intersect > @o*,n*:K; contacts sel restrict temp overlapCutoff -3.0 color #8A2BE2 name K > log true > alias magnesium da $1; sel intersect :MG; style sel ball; size sel ballscale > 0.5; name frozen temp sel; magnesiumcluster $1; contacts sel restrict temp > overlapCutoff -0.8 color #00FF00 name Mg log true UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3,7 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 32 GB System Firmware Version: 2069.0.0.0.0 OS Loader Version: 582~2132 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 21 minutes, 34 seconds Graphics/Displays: Radeon Pro 580X: Chipset Model: Radeon Pro 580X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A1X-009 EFI Driver Version: 01.B1.042 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: YPPY075P29KS Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Sessions can't reproduce all ChimeraX