id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18273 Crash in NSAccessibilityEntryPointIsAccessibilityElement on Mac chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/hp/data/map_L/figure/figure_zjl_20250724/Upa_GC_density_20250725.cxs Opened Upa_ECD_sharpened_map.ccp4 as #3, grid size 400,400,400, pixel 0.93, shown at level 8.16, step 1, values float32 Log from Fri Jul 25 09:21:27 2025UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/hp/data/map_L/figure/Chimera X Data from L/UP ECD 25.7.11/UP > ECD 25.7.8.cxs"" Log from Thu Jul 10 16:42:08 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:/Users/hongn/Desktop/Chimera X Data/UP ECD 25.7.8.cxs"" Log from Tue Jul 8 10:28:52 2025 Startup Messages --- note | available bundle cache has not been initialized yet 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 C:/Users/hongn/Desktop/CaSR/map/Upa_ECD-model- > coot-2_real_space_refined_010.pdb Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #1 --- Chain | Description A | No description available B | No description available > select /B:545@CG 1 atom, 1 residue, 1 model selected > select clear > select /E:2@C6 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 28 atoms, 29 bonds, 2 residues, 1 model selected > select up 8689 atoms, 8906 bonds, 1096 residues, 1 model selected > select down 28 atoms, 29 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 28 atoms, 29 bonds, 2 residues, 1 model selected > select up 8661 atoms, 8876 bonds, 1094 residues, 1 model selected > select down 28 atoms, 29 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > select /B:901@O4 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3417 atoms, 3508 bonds, 431 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 28 atoms, 29 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:901@O6 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3427 atoms, 3516 bonds, 437 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3403 atoms, 3493 bonds, 430 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3413 atoms, 3501 bonds, 436 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /B:902@O6 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3389 atoms, 3478 bonds, 429 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /B:904@O4 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 3375 atoms, 3463 bonds, 428 residues, 1 model selected > select down 14 atoms, 14 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > delete pbonds > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select /A:909@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:907@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /B:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel ball Changed 5 atom styles > select /A:910@O2 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel ball Changed 5 atom styles > select /F:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 34 atoms, 34 bonds, 1 residue, 1 model selected > style sel stick Changed 34 atom styles > show sel atoms > hide sel atoms > undo [Repeated 1 time(s)] > style sel ball Changed 34 atom styles > undo > color sel byelement > color sel byhetero > color sel cornflower blue > undo > lighting simple > lighting soft > lighting full > undo [Repeated 4 time(s)] > ui tool show ""Color Actions"" > color sel byhetero > color sel purple > color sel bychain target acsp > color sel bypolymer target acsp > color sel byhetero target acsp > color sel byelement target acsp > color sel bynucleotide target acsp > color sel cyan target acsp > color sel cyan > color sel byhetero > color sel light sea green > color sel light sea green target f > color sel orange target f > color sel orange target af > color sel byhetero > color sel medium blue > color sel byhetero > color sel cornflower blue > color sel byhetero > select clear [Repeated 2 time(s)] > select /A:598 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 182 atoms, 185 bonds, 26 residues, 1 model selected > select up 3399 atoms, 3486 bonds, 435 residues, 1 model selected > select up 3412 atoms, 3498 bonds, 437 residues, 1 model selected > select up 4222 atoms, 4327 bonds, 541 residues, 1 model selected > select up 4230 atoms, 4331 bonds, 545 residues, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 4230 atoms, 4331 bonds, 545 residues, 1 model selected > select down 4222 atoms, 4327 bonds, 541 residues, 1 model selected > select down 3412 atoms, 3498 bonds, 437 residues, 1 model selected > select down 3399 atoms, 3486 bonds, 435 residues, 1 model selected > select up 3412 atoms, 3498 bonds, 437 residues, 1 model selected > select up 4222 atoms, 4327 bonds, 541 residues, 1 model selected > select up 4230 atoms, 4331 bonds, 545 residues, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 4230 atoms, 4331 bonds, 545 residues, 1 model selected > select /A:908@CA 1 atom, 1 residue, 1 model selected > select /A:908@CA 1 atom, 1 residue, 1 model selected > select /A:908@CA 1 atom, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select /A:591 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 182 atoms, 185 bonds, 26 residues, 1 model selected > select up 3399 atoms, 3486 bonds, 435 residues, 1 model selected > select up 3412 atoms, 3498 bonds, 437 residues, 1 model selected > select up 4222 atoms, 4327 bonds, 541 residues, 1 model selected > select up 4230 atoms, 4331 bonds, 545 residues, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 4230 atoms, 4331 bonds, 545 residues, 1 model selected > color sel #6fffbcff > color sel #70ffbcff > color sel #72ffb4ff > color sel #73ffb4ff > color sel #75ffb5ff > color sel #78ffb7ff > color sel #7cffb9ff > color sel #86ffbcff > color sel #8cffc0ff > color sel #94ffc4ff > color sel #98ffc6ff > color sel #9bffc8ff > color sel #9cffc9ff > color sel #a0ffcbff > color sel #a0ffc3ff > color sel #9effbeff > color sel #9cffa8ff > color sel #9eff9cff > color sel #a3ff99ff > color sel #b1ff99ff > color sel #c1ff98ff > color sel #caff98ff > color sel #cdff98ff > color sel #d5ff97ff > color sel #dfff94ff > color sel #e2ff93ff > color sel #dcff7dff > color sel #daff73ff > color sel #d9ff70ff > color sel #d0ff69ff > color sel #c1ff5dff > color sel #b7ff58ff > color sel #b1ff57ff > color sel #acff53ff > color sel #abff52ff > color sel #9eff4fff > color sel #9bff4fff > color sel #95ff4fff > color sel #8dff4fff > color sel #8cff4eff > color sel #8aff4bff > color sel #84ff4bff > color sel #81ff4bff > color sel #75ff4bff > color sel #72ff4bff > color sel #6cff4bff > color sel #63ff4bff > color sel #5dff4bff > color sel #57ff4bff > color sel #4eff4bff > color sel #4bff57ff > color sel #4bff66ff > color sel #4bff6fff > color sel #4bff7eff > color sel #4bff84ff > color sel #4bff8dff > color sel #4bff93ff > color sel #4bff96ff > color sel #4bff9cff > color sel #4bffabff > color sel #4bffaeff > color sel #4cffaeff > color sel #4fffb0ff > color sel #50ffb0ff > color sel #50ffa2ff > color sel #50ff87ff > color sel #4eff54ff > color sel #5eff4cff > color sel #64ff4cff > color sel #6dff4cff > color sel #76ff4cff > color sel #82ff4cff > color sel #84ff4fff > color sel #97ff52ff > color sel #a7ff54ff > color sel #acff54ff > color sel #b8ff5aff > color sel #bbff61ff > color sel #c2ff61ff > color sel #c3ff62ff > color sel #bbff62ff > color sel #b6ff62ff > color sel #aeff62ff > color sel #a9ff62ff > color sel #99ff62ff > color sel #9aff63ff > color sel #9cff67ff > color sel #9fff6bff > color sel #9fff6cff > color sel #a1ff6eff > color sel #a1ff6fff > color sel #a2ff70ff > color sel #a5ff75ff > color sel #a7ff78ff > color sel #a8ff79ff > color sel #a9ff7bff > color sel #abff7dff > color sel #abff7eff > color sel #acff80ff > color sel #aeff83ff > color sel #b0ff85ff > color sel #b0ff86ff > color sel #b1ff87ff > color sel #b4ff8bff > color sel #afff8cff > color sel #b1ff8fff > color sel #a9ff8fff > color sel #adff8fff > color sel #b1ff8fff > color sel #b6ff8fff > color sel #baff8fff > color sel #bcff8fff > color sel #c1ff8fff > color sel #c0ff8fff > color sel #bcff8fff > color sel #b6ff8fff > color sel #b2ff8fff > color sel #b6ff8fff > color sel #c4ff8cff > color sel #d1ff8bff > color sel #d3ff8bff > color sel #cdff8bff > color sel #c7ff8bff > color sel #bfff8bff > color sel #bdff8bff > color sel #b4ff8bff > color sel #aeff8bff > color sel #aaff8bff > select clear > select /B:570 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 129 atoms, 131 bonds, 18 residues, 1 model selected > select up 3361 atoms, 3448 bonds, 427 residues, 1 model selected > select up 3382 atoms, 3468 bonds, 430 residues, 1 model selected > select up 4203 atoms, 4308 bonds, 534 residues, 1 model selected > select up 4209 atoms, 4312 bonds, 536 residues, 1 model selected > color sel #3cffefff > select clear > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > lighting simple > lighting soft > lighting full > lighting shadows false > lighting flat [Repeated 1 time(s)] > undo > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > lighting flat > lighting shadows true intensity 0.5 > lighting flat > undo [Repeated 6 time(s)] > lighting simple > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > select clear > select /B:570 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 129 atoms, 131 bonds, 18 residues, 1 model selected > select up 3361 atoms, 3448 bonds, 427 residues, 1 model selected > select up 3382 atoms, 3468 bonds, 430 residues, 1 model selected > select up 4203 atoms, 4308 bonds, 534 residues, 1 model selected > color #1 #3cffefff > color #1 #aaff8bff > select clear > select /B:585 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 129 atoms, 131 bonds, 18 residues, 1 model selected > select up 3361 atoms, 3448 bonds, 427 residues, 1 model selected > select up 3382 atoms, 3468 bonds, 430 residues, 1 model selected > select up 4203 atoms, 4308 bonds, 534 residues, 1 model selected > select up 4209 atoms, 4312 bonds, 536 residues, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 4209 atoms, 4312 bonds, 536 residues, 1 model selected > color sel byelement > color sel #d7e9f8ff > color sel #f9f9f9ff > color sel #f0f0f0ff > color sel #aaff8bff > color sel #828790ff > color sel #f0f0f0ff > color sel #3cffefff > select clear > select /A:909@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select /A:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow Drag select of 2 residues > select clear > select /A:907@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /B:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:910@O1 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel byelement > select clear > select /B:909@O2 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 4209 atoms, 4312 bonds, 536 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel byelement > select clear > select /G:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel forest green > color sel purple > color sel byhetero > select clear > select /F:1@S02 1 atom, 1 residue, 1 model selected Drag select of 1 atoms, 2 residues > select clear > select /F:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > select up 8507 atoms, 8711 bonds, 1083 residues, 1 model selected > select down 34 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel purple > color sel byhetero > select clear > set bgColor white > set bgColor #ffffff00 > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > color sel #885599ff > color sel #859ed7ff > select clear > transparency 30 > select clear > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > transparency sel 50 > select clear > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > lighting simple > lighting soft > lighting simple > select clear > select /B 4209 atoms, 4312 bonds, 536 residues, 1 model selected > color sel #7722ddff > color sel #72d3d4ff > color sel #000099ff > color sel #009e75ff > color sel #009e74ff > select clear > select /A:570 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 182 atoms, 185 bonds, 26 residues, 1 model selected > select up 3399 atoms, 3486 bonds, 435 residues, 1 model selected > select up 3412 atoms, 3498 bonds, 437 residues, 1 model selected > select up 4222 atoms, 4327 bonds, 541 residues, 1 model selected > select clear > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > color sel #cc00eeff > color sel #c0e7daff > select clear > color #998899ff > color #989cc8ff > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > color sel #ee5599ff > color sel #e59693ff > select clear > select /A:908@CA 1 atom, 1 residue, 1 model selected > transparency sel 50 > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > transparency sel 100 > select clear > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > cartoon style sel xsection oval modeHelix default > cartoon style sel xsection rectangle modeHelix default > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > cartoon style sel modeHelix tube sides 20 > undo > select clear > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > cartoon style sel modeHelix tube sides 20 > select clear > lighting simple > lighting soft > lighting full > lighting shadows false > lighting simple > lighting soft [Repeated 2 time(s)] > lighting shadows true intensity 0.5 > lighting soft > select /A:909@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:909@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:233 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select /A:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /A:907@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /B:908@CA 1 atom, 1 residue, 1 model selected > color sel yellow > select clear > select /F:1@S02 1 atom, 1 residue, 1 model selected > select clear > select /F:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel orange red > color sel byhetero > color sel forest green > color sel byhetero > select clear > select /G:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel forest green > color sel byhetero > select clear > select /B:909@O4 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel ball Changed 5 atom styles > style sel ball Changed 5 atom styles > color sel byelement > select clear > select /A:910@O2 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel byelement > select clear [Repeated 1 time(s)] > select /A:592 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A 4230 atoms, 4331 bonds, 545 residues, 1 model selected > lighting flat > select clear > undo [Repeated 1 time(s)] > select clear > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 No Surface models open > graphics silhouettes false > lighting shadows false > lighting full > lighting soft > lighting full > lighting shadows false > undo [Repeated 6 time(s)] > lighting simple > lighting soft > lighting full > lighting shadows false > graphics silhouettes true > lighting flat > graphics silhouettes false > lighting simple > lighting soft > lighting full > lighting shadows false > graphics silhouettes true > lighting shadows true > lighting soft > lighting full > lighting shadows false > save ""C:/Users/hongn/Desktop/Up ECD 25.7.8.cxs"" > style ringFill thick Changed 1083 residue ring styles > style ringFill thin Changed 1083 residue ring styles > style ringFill off Changed 1083 residue ring styles > select clear > select /A:591 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 182 atoms, 185 bonds, 26 residues, 1 model selected > select down 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /A:585 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > distance #1/A:585@CA #1/B:585@CA Distance between /A CYS 585 CA and /B CYS 585 CA: 24.395Å > color #2.1 black models > color #2.1 white models > color #2.1 black models > select clear > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 target m > hide #2.1 models > log metadata #1 No models had metadata > log chains #1 Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #1 --- Chain | Description A | No description available B | No description available > show #2.1 models > hide #2.1 models > color #2 black models > color #2 #9f9f9fff models > color #2 #d9d9d9ff models > color #2 #dededeff models > color #2 #969696ff models > color #2 #909090ff models > select /A:591 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:591 6 atoms, 5 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:598 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 176 atoms, 179 bonds, 25 residues, 1 model selected > select down 6 atoms, 5 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:597 6 atoms, 5 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:596 7 atoms, 6 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:595 10 atoms, 10 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /A:594 8 atoms, 7 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > save ""C:/Users/hongn/Desktop/UP ECD 25.7.8.jpg"" width 1981 height 1051 > supersample 3 > save ""C:/Users/hongn/Desktop/UP ECD 25.7.8.cxs"" ——— End of log from Tue Jul 8 10:28:52 2025 ——— opened ChimeraX session > select /A:592 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > hide #!2 models > select /G:1@O05 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > style sel ball Changed 34 atom styles > ui tool show ""Color Actions"" > color sel light sea green > color sel byhetero > select clear > select /F:1@CL01 1 atom, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > select up 8464 atoms, 8666 bonds, 1077 residues, 1 model selected > select down 34 atoms, 34 bonds, 1 residue, 1 model selected > style sel ball Changed 34 atom styles > ui tool show ""Color Actions"" > color sel light sea green > color sel byhetero > select clear > lighting simple > lighting soft > lighting shadows true intensity 0.5 > save C:\Users\hongn/Desktop\image3.png supersample 3 > save ""C:/Users/hongn/Desktop/Chimera X Data/UP ECD 25.7.8.cxs"" ——— End of log from Thu Jul 10 16:42:08 2025 ——— > view name session-start opened ChimeraX session > open > /Users/hp/data/map_L/phenix_upa/Autosharpen_19/Upa_ECD_sharpened_map.ccp4 Opened Upa_ECD_sharpened_map.ccp4 as #3, grid size 400,400,400, pixel 0.93, shown at level 2.9, step 2, values float32 > volume #3 step 1 > volume #3 level 8.161 > open /Users/hp/data/map_L/model_coot/Upa_ECD-model- > coot-2_real_space_refined_010.pdb Chain information for Upa_ECD-model-coot-2_real_space_refined_010.pdb #4 --- Chain | Description A | No description available B | No description available > hide #!3 models > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide #!4 models > show #!4 models > hide #!1 models > show #!1 models > hide #!1 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 1 residue, 1 model selected > select ~sel & ##selected 8655 atoms, 8872 bonds, 5 pseudobonds, 1095 residues, 2 models selected > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > volume zone #3 nearAtoms sel & #4 range 3.0 no atoms specified for zone > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select add #4 34 atoms, 34 bonds, 1 residue, 1 model selected > volume zone #3 nearAtoms sel & #4 range 3.0 > show #!3 models > volume zone #3 nearAtoms sel & #4 range 2.5 > transparency #3 50 > show #!1 models > hide #!4 models > volume zone #3 nearAtoms sel & #4 range 2.2 > volume zone #3 nearAtoms sel & #4 range 2.0 > save /Users/hp/Desktop/image3.png supersample 3 > save > /Users/hp/data/map_L/figure/figure_zjl_20250724/Upa_GC_density_20250725.cxs ——— End of log from Fri Jul 25 09:21:27 2025 ——— > view name session-start opened ChimeraX session > open ""/Users/hp/data/map_L/figure/Chimera X Data from L/Neo CRD > 25.7.11/Neo_ECD_model-coot-6(1).pdb"" Chain information for Neo_ECD_model-coot-6(1).pdb #5 --- Chain | Description A | No description available B | No description available > hide #!1 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,7 Model Number: Z1FT0008MCH/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 14天16小时23分钟 Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 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-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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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-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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX