id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18131 Crash on Mac waking from sleep elmena@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open 8USB 8usb title: Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1 [more info...] Chain information for 8usb #1 --- Chain | Description | UniProt A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN 1-433 B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN 1-440 C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406 D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN 1-418 E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389 F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN 1-439 G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246 H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234 I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261 J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248 K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241 L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263 M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254 O | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234 U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953 V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534 W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456 X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422 Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389 Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324 a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376 b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377 c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310 d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN 1-350 e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN 1-70 f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908 g | NEDD8 ultimate buster 1 | NUB1_HUMAN 1-601 Non-standard residues in 8usb #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > ui mousemode right translate > set bgColor white > hide atoms > show atoms > show cartoons > hide atoms > lighting simple > ui mousemode right zoom > cd projects Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > pwd Current working directory is: /Users/emena/Desktop > cd ../projects Current working directory is: /Users/emena/projects > cd crispr-bean/a_19s_6bp Current working directory is: /Users/emena/projects/crispr-bean/a_19s_6bp > open gene_outputs/combined_residue_scores.defattr Summary of feedback from opening gene_outputs/combined_residue_scores.defattr --- note | Assigned attribute 'edit_score' to 2242 residues using match mode: any > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > show atoms > style stick Changed 70140 atom styles > select clear > color light gray > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r,a palette white:red range 0,5 Invalid ""target"" argument: Character ',' is not an allowed target, must be one of acrsbmpfl > color byattribute edit_score target a palette white:red range 0,5 70140 atoms, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target a palette white:red range 0,3 70140 atoms, atom edit_score range 0.007 to 17.1 > show surfaces > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r palette white:red range 0,2 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r palette white:red range 0,3 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target s palette white:red range 0,3 27 surfaces, atom edit_score range 0.007 to 17.1 > transparency 30 > transparency 20 > transparency 80 > hide surfaces > ui tool show ""Side View"" > hide atoms > show atoms > hide atoms > show surfaces > hide surfaces > show surfaces > lighting simple > lighting soft > hide atoms > hide cartoons > show cartoons > hide cartoons > show atoms > surface hidePatches > hide atoms > show cartoons > lighting simple > lighting full > lighting flat > show atoms > select ~sel & ##selected Nothing selected > show surfaces > hide surfaces > hide atoms > show atoms > hide atoms > lighting soft > lighting full > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > open gene_outputs/combined_residue_scores_libAB.defattr Summary of feedback from opening gene_outputs/combined_residue_scores_libAB.defattr --- note | Assigned attribute 'edit_score' to 2296 residues using match mode: any > color byattribute edit_score target s palette white:red range 0,3 27 surfaces, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target a palette white:red range 0,3 70140 atoms, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target c palette white:red range 0,3 8855 residues, atom edit_score range 0.007 to 17.1 > show atoms > set bgColor white > hide atoms > show cartoons > show atoms > hide atoms > lighting simple > lighting soft > lighting full > set bgColor white > lighting simple > show atoms > hide atoms > select :/edit_score>1 Expected an objects specifier or a keyword > select #1 & :edit_score>1 Expected a keyword > select :/edit_score>1 Expected an objects specifier or a keyword > select attr edit_score > 1 Expected an objects specifier or a keyword > select #1 & attr edit_score > 1 Expected a keyword > select #1 & attr edit_score > 1 Expected a keyword > select attr:edit_score>1 Expected an objects specifier or a keyword > list attributes Unknown command: list attributes > list Unknown command: modelcif list > showattr sel Unknown command: showattr sel > select attr:edit_score>1 Expected an objects specifier or a keyword > select :/edit_score>1 Expected an objects specifier or a keyword > select #.edit_score > 1 Expected an objects specifier or a keyword > show cartoons > show atoms > hide atoms > ui tool show ""Model Panel"" > setattr show #1 Missing or invalid ""attrValue"" argument: Expected a text string > setattr show #1 Missing or invalid ""attrValue"" argument: Expected a text string > info #1 attributes Expected a keyword > attributes list #1 Unknown command: attributes list #1 > attributes show #1 Unknown command: attributes show #1 > info models model id #1 type AtomicStructure name 8usb model id #1.1 type PseudobondGroup name ""metal coordination bonds"" model id #1.2 type PseudobondGroup name ""missing structure"" model id #1.3 type MolecularSurface name ""8usb_A SES surface"" model id #1.4 type MolecularSurface name ""8usb_B SES surface"" model id #1.5 type MolecularSurface name ""8usb_C SES surface"" model id #1.6 type MolecularSurface name ""8usb_D SES surface"" model id #1.7 type MolecularSurface name ""8usb_E SES surface"" model id #1.8 type MolecularSurface name ""8usb_F SES surface"" model id #1.9 type MolecularSurface name ""8usb_G SES surface"" model id #1.10 type MolecularSurface name ""8usb_H SES surface"" model id #1.11 type MolecularSurface name ""8usb_I SES surface"" model id #1.12 type MolecularSurface name ""8usb_J SES surface"" model id #1.13 type MolecularSurface name ""8usb_K SES surface"" model id #1.14 type MolecularSurface name ""8usb_L SES surface"" model id #1.15 type MolecularSurface name ""8usb_M SES surface"" model id #1.16 type MolecularSurface name ""8usb_O SES surface"" model id #1.17 type MolecularSurface name ""8usb_U SES surface"" model id #1.18 type MolecularSurface name ""8usb_V SES surface"" model id #1.19 type MolecularSurface name ""8usb_W SES surface"" model id #1.20 type MolecularSurface name ""8usb_X SES surface"" model id #1.21 type MolecularSurface name ""8usb_Y SES surface"" model id #1.22 type MolecularSurface name ""8usb_Z SES surface"" model id #1.23 type MolecularSurface name ""8usb_a SES surface"" model id #1.23.1 type ClipCap name ""cap near"" model id #1.24 type MolecularSurface name ""8usb_b SES surface"" model id #1.25 type MolecularSurface name ""8usb_c SES surface"" model id #1.26 type MolecularSurface name ""8usb_d SES surface"" model id #1.27 type MolecularSurface name ""8usb_e SES surface"" model id #1.28 type MolecularSurface name ""8usb_f SES surface"" model id #1.29 type MolecularSurface name ""8usb_g SES surface"" > info atomattr atomattr alt_loc atomattr alt_locs atomattr aniso_u atomattr aniso_u6 atomattr atomspec atomattr bfactor atomattr bonds atomattr color atomattr coord atomattr coord_index atomattr cpp_pointer atomattr custom_attrs atomattr default_radius atomattr deleted atomattr display atomattr display_radius atomattr draw_mode atomattr effective_coord atomattr element atomattr has_custom_attrs atomattr hide atomattr idatm_type atomattr is_ribose atomattr is_side_chain atomattr is_side_connector atomattr is_side_only atomattr name atomattr neighbors atomattr num_alt_locs atomattr num_bonds atomattr num_explicit_bonds atomattr occupancy atomattr pb_coord atomattr pb_scene_coord atomattr radius atomattr residue atomattr ribbon_coord atomattr scene_coord atomattr selected atomattr serial_number atomattr session atomattr structure atomattr structure_category atomattr visible > open gene_outputs/combined_residue_scores_libAB.defattr Summary of feedback from opening gene_outputs/combined_residue_scores_libAB.defattr --- note | Assigned attribute 'edit_score' to 2296 residues using match mode: any > info resattr resattr alt_loc resattr alt_locs resattr atoms resattr atomspec resattr center resattr chain resattr chain_id resattr chi1 resattr chi2 resattr chi3 resattr chi4 resattr cpp_pointer resattr custom_attrs resattr deleted resattr description resattr edit_score resattr has_custom_attrs resattr insertion_code resattr is_helix resattr is_strand resattr label_one_letter_code resattr label_specifier resattr mmcif_chain_id resattr name resattr neighbors resattr num_atoms resattr number resattr omega resattr one_letter_code resattr phi resattr polymer_type resattr principal_atom resattr psi resattr ribbon_adjust resattr ribbon_color resattr ribbon_display resattr ribbon_hide_backbone resattr ring_color resattr ring_display resattr selected resattr session resattr ss_id resattr ss_type resattr standard_aa_name resattr structure resattr sym_chi1 resattr sym_chi2 resattr sym_chi3 resattr sym_chi4 resattr thin_rings resattr worm_radius > select :/edit_score > 0.8 Expected an objects specifier or a keyword > color byattribute :/edit_score palette rainbow No known/registered numeric attribute :/edit_score > select #1 :/edit_score > 0.8 Expected a keyword > select :#1/edit_score > 0.8 Expected an objects specifier or a keyword > select:#1/edit_score > 0.8 Unknown command: select:#1/edit_score > 0.8 > undo > select (attribute edit_score > 0.8) Expected an objects specifier or a keyword > select #1 & (attribute edit_score > 0.8) Expected a keyword > select :/edit_score > 0.8 Expected an objects specifier or a keyword > select attribute:edit_score > 0.8 Expected an objects specifier or a keyword > select #1 & attribute:edit_score > 0.8 Expected a keyword > attribute list Unknown command: attribute list > select :/edit_score > 0.8 Expected an objects specifier or a keyword > select attribute:edit_score > 0.8 Expected an objects specifier or a keyword > select #1 & @ca & attribute edit_score > 0.8 Expected a keyword > select #1 & :. & attribute edit_score > 0.8 Expected a keyword > select (:/edit_score > 0.8) Expected an objects specifier or a keyword > select (#1:/edit_score > 0.8) Expected an objects specifier or a keyword > select attribute edit_score > 0.8 target r Expected an objects specifier or a keyword > select (#1 & attribute edit_score > 0.8 target r) Expected an objects specifier or a keyword > hide atoms > show atoms > color byhetero > hide atoms > save /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs > ui tool show Distances > show atoms > select add /D:239@OH 1 atom, 1 bond, 1 residue, 1 model selected Exactly two atoms must be selected! > select /c:52@OE1 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select add /D:239@OH 2 atoms, 1 bond, 2 residues, 1 model selected > select add /E:77@CD 3 atoms, 1 bond, 3 residues, 2 models selected Exactly two atoms must be selected! No distances to delete! > select /c:129@OG1 1 atom, 1 residue, 1 model selected > select add /C:72@OH 2 atoms, 2 residues, 2 models selected > distance /c:129@OG1 /C:72@OH Distance between /c THR 129 OG1 and /C TYR 72 OH: 34.277Å > show sel surfaces > select clear > show surfaces > hide surfaces > select #1: 593, 595 28 atoms, 24 bonds, 4 residues, 1 model selected > select #1/U: 593, 595 14 atoms, 12 bonds, 2 residues, 1 model selected > select #1/U: 590, 593 18 atoms, 17 bonds, 2 residues, 1 model selected > style sel sphere Changed 18 atom styles > style sel stick Changed 18 atom styles ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs Log from Thu Jul 3 00:04:57 2025UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8USB 8usb title: Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1 [more info...] Chain information for 8usb #1 --- Chain | Description | UniProt A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN 1-433 B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN 1-440 C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406 D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN 1-418 E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389 F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN 1-439 G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246 H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234 I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261 J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248 K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241 L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263 M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254 O | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234 U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953 V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534 W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456 X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422 Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389 Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324 a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376 b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377 c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310 d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN 1-350 e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN 1-70 f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908 g | NEDD8 ultimate buster 1 | NUB1_HUMAN 1-601 Non-standard residues in 8usb #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > ui mousemode right translate > set bgColor white > hide atoms > show atoms > show cartoons > hide atoms > lighting simple > ui mousemode right zoom > cd projects Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > pwd Current working directory is: /Users/emena/Desktop > cd ../projects Current working directory is: /Users/emena/projects > cd crispr-bean/a_19s_6bp Current working directory is: /Users/emena/projects/crispr-bean/a_19s_6bp > open gene_outputs/combined_residue_scores.defattr Summary of feedback from opening gene_outputs/combined_residue_scores.defattr --- note | Assigned attribute 'edit_score' to 2242 residues using match mode: any > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > show atoms > style stick Changed 70140 atom styles > select clear > color light gray > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r,a palette white:red range 0,5 Invalid ""target"" argument: Character ',' is not an allowed target, must be one of acrsbmpfl > color byattribute edit_score target a palette white:red range 0,5 70140 atoms, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target a palette white:red range 0,3 70140 atoms, atom edit_score range 0.007 to 17.1 > show surfaces > color byattribute edit_score target r palette white:red range 0,5 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r palette white:red range 0,2 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target r palette white:red range 0,3 8855 residues, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target s palette white:red range 0,3 27 surfaces, atom edit_score range 0.007 to 17.1 > transparency 30 > transparency 20 > transparency 80 > hide surfaces > ui tool show ""Side View"" > hide atoms > show atoms > hide atoms > show surfaces [Repeated 1 time(s)] > hide surfaces > show surfaces > lighting simple > lighting soft > hide atoms > hide cartoons > show cartoons > hide cartoons > show atoms [Repeated 1 time(s)] > surface hidePatches > hide atoms > show cartoons > lighting simple > lighting full > lighting flat > show atoms > select ~sel & ##selected Nothing selected > show surfaces > hide surfaces > hide atoms > show atoms > hide atoms > lighting soft > lighting full > lighting soft [Repeated 1 time(s)] > lighting full [Repeated 1 time(s)] > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > open gene_outputs/combined_residue_scores_libAB.defattr Summary of feedback from opening gene_outputs/combined_residue_scores_libAB.defattr --- note | Assigned attribute 'edit_score' to 2296 residues using match mode: any > color byattribute edit_score target s palette white:red range 0,3 27 surfaces, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target a palette white:red range 0,3 70140 atoms, atom edit_score range 0.007 to 17.1 > color byattribute edit_score target c palette white:red range 0,3 8855 residues, atom edit_score range 0.007 to 17.1 > show atoms > set bgColor white > hide atoms > show cartoons > show atoms > hide atoms > lighting simple > lighting soft > lighting full > set bgColor white > lighting simple > show atoms > hide atoms > select :/edit_score>1 Expected an objects specifier or a keyword > select #1 & :edit_score>1 Expected a keyword > select :/edit_score>1 Expected an objects specifier or a keyword > select attr edit_score > 1 Expected an objects specifier or a keyword > select #1 & attr edit_score > 1 Expected a keyword > select #1 & attr edit_score > 1 Expected a keyword > select attr:edit_score>1 Expected an objects specifier or a keyword > list attributes Unknown command: list attributes > list Unknown command: modelcif list > showattr sel Unknown command: showattr sel > select attr:edit_score>1 Expected an objects specifier or a keyword > select :/edit_score>1 Expected an objects specifier or a keyword > select #.edit_score > 1 Expected an objects specifier or a keyword > show cartoons > show atoms > hide atoms > ui tool show ""Model Panel"" > setattr show #1 Missing or invalid ""attrValue"" argument: Expected a text string > setattr show #1 Missing or invalid ""attrValue"" argument: Expected a text string > info #1 attributes Expected a keyword > attributes list #1 Unknown command: attributes list #1 > attributes show #1 Unknown command: attributes show #1 > info models model id #1 type AtomicStructure name 8usb model id #1.1 type PseudobondGroup name ""metal coordination bonds"" model id #1.2 type PseudobondGroup name ""missing structure"" model id #1.3 type MolecularSurface name ""8usb_A SES surface"" model id #1.4 type MolecularSurface name ""8usb_B SES surface"" model id #1.5 type MolecularSurface name ""8usb_C SES surface"" model id #1.6 type MolecularSurface name ""8usb_D SES surface"" model id #1.7 type MolecularSurface name ""8usb_E SES surface"" model id #1.8 type MolecularSurface name ""8usb_F SES surface"" model id #1.9 type MolecularSurface name ""8usb_G SES surface"" model id #1.10 type MolecularSurface name ""8usb_H SES surface"" model id #1.11 type MolecularSurface name ""8usb_I SES surface"" model id #1.12 type MolecularSurface name ""8usb_J SES surface"" model id #1.13 type MolecularSurface name ""8usb_K SES surface"" model id #1.14 type MolecularSurface name ""8usb_L SES surface"" model id #1.15 type MolecularSurface name ""8usb_M SES surface"" model id #1.16 type MolecularSurface name ""8usb_O SES surface"" model id #1.17 type MolecularSurface name ""8usb_U SES surface"" model id #1.18 type MolecularSurface name ""8usb_V SES surface"" model id #1.19 type MolecularSurface name ""8usb_W SES surface"" model id #1.20 type MolecularSurface name ""8usb_X SES surface"" model id #1.21 type MolecularSurface name ""8usb_Y SES surface"" model id #1.22 type MolecularSurface name ""8usb_Z SES surface"" model id #1.23 type MolecularSurface name ""8usb_a SES surface"" model id #1.23.1 type ClipCap name ""cap near"" model id #1.24 type MolecularSurface name ""8usb_b SES surface"" model id #1.25 type MolecularSurface name ""8usb_c SES surface"" model id #1.26 type MolecularSurface name ""8usb_d SES surface"" model id #1.27 type MolecularSurface name ""8usb_e SES surface"" model id #1.28 type MolecularSurface name ""8usb_f SES surface"" model id #1.29 type MolecularSurface name ""8usb_g SES surface"" > info atomattr atomattr alt_loc atomattr alt_locs atomattr aniso_u atomattr aniso_u6 atomattr atomspec atomattr bfactor atomattr bonds atomattr color atomattr coord atomattr coord_index atomattr cpp_pointer atomattr custom_attrs atomattr default_radius atomattr deleted atomattr display atomattr display_radius atomattr draw_mode atomattr effective_coord atomattr element atomattr has_custom_attrs atomattr hide atomattr idatm_type atomattr is_ribose atomattr is_side_chain atomattr is_side_connector atomattr is_side_only atomattr name atomattr neighbors atomattr num_alt_locs atomattr num_bonds atomattr num_explicit_bonds atomattr occupancy atomattr pb_coord atomattr pb_scene_coord atomattr radius atomattr residue atomattr ribbon_coord atomattr scene_coord atomattr selected atomattr serial_number atomattr session atomattr structure atomattr structure_category atomattr visible > open gene_outputs/combined_residue_scores_libAB.defattr Summary of feedback from opening gene_outputs/combined_residue_scores_libAB.defattr --- note | Assigned attribute 'edit_score' to 2296 residues using match mode: any > info resattr resattr alt_loc resattr alt_locs resattr atoms resattr atomspec resattr center resattr chain resattr chain_id resattr chi1 resattr chi2 resattr chi3 resattr chi4 resattr cpp_pointer resattr custom_attrs resattr deleted resattr description resattr edit_score resattr has_custom_attrs resattr insertion_code resattr is_helix resattr is_strand resattr label_one_letter_code resattr label_specifier resattr mmcif_chain_id resattr name resattr neighbors resattr num_atoms resattr number resattr omega resattr one_letter_code resattr phi resattr polymer_type resattr principal_atom resattr psi resattr ribbon_adjust resattr ribbon_color resattr ribbon_display resattr ribbon_hide_backbone resattr ring_color resattr ring_display resattr selected resattr session resattr ss_id resattr ss_type resattr standard_aa_name resattr structure resattr sym_chi1 resattr sym_chi2 resattr sym_chi3 resattr sym_chi4 resattr thin_rings resattr worm_radius > select :/edit_score > 0.8 Expected an objects specifier or a keyword > color byattribute :/edit_score palette rainbow No known/registered numeric attribute :/edit_score > select #1 :/edit_score > 0.8 Expected a keyword > select :#1/edit_score > 0.8 Expected an objects specifier or a keyword > select:#1/edit_score > 0.8 Unknown command: select:#1/edit_score > 0.8 > undo > select (attribute edit_score > 0.8) Expected an objects specifier or a keyword > select #1 & (attribute edit_score > 0.8) Expected a keyword > select :/edit_score > 0.8 Expected an objects specifier or a keyword > select attribute:edit_score > 0.8 Expected an objects specifier or a keyword > select #1 & attribute:edit_score > 0.8 Expected a keyword > attribute list Unknown command: attribute list > select :/edit_score > 0.8 Expected an objects specifier or a keyword > select attribute:edit_score > 0.8 Expected an objects specifier or a keyword > select #1 & @ca & attribute edit_score > 0.8 Expected a keyword > select #1 & :. & attribute edit_score > 0.8 Expected a keyword > select (:/edit_score > 0.8) Expected an objects specifier or a keyword > select (#1:/edit_score > 0.8) Expected an objects specifier or a keyword > select attribute edit_score > 0.8 target r Expected an objects specifier or a keyword > select (#1 & attribute edit_score > 0.8 target r) Expected an objects specifier or a keyword > hide atoms > show atoms > color byhetero > hide atoms > save /Users/emena/projects/crispr-bean/a_19s_6bp/8USB_libAB.cxs ——— End of log from Thu Jul 3 00:04:57 2025 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 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: Mac15,3 Model Number: Z1A90001BLL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 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: 19 hours, 8 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 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 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: 3.4.0 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: 1.10rc202506130232 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: 1.45.1 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: 2.4.0 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