id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5722 Show Distances tool: wrapped C/C++ object of type QTabWidget has been deleted kimsk@… Eric Pettersen "The following bug report has been submitted: Platform: macOS-10.14.5-x86_64-i386-64bit ChimeraX Version: 1.4.dev202111111002 (2021-11-11 10:02:38 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs Log from Wed Dec 1 23:32:50 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs Log from Mon Nov 15 15:23:49 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs format session Log from Mon Nov 15 15:07:58 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs format session Log from Mon Nov 15 14:47:15 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs format session Log from Mon Nov 15 14:16:35 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs format session Log from Fri Nov 12 15:09:46 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs format session Log from Fri Nov 12 14:34:37 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs format session Log from Thu Nov 11 16:26:07 2021UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs format session Log from Thu Nov 11 15:51:45 2021UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs format session Log from Thu Nov 11 12:44:42 2021UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs Log from Wed Oct 27 22:15:56 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs Log from Wed Dec 23 20:51:39 2020UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. open /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs Log from Wed Dec 23 20:29:05 2020UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs format session Log from Wed Dec 23 19:41:28 2020UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs Log from Mon Dec 21 23:31:32 2020UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs Log from Thu Dec 17 16:57:46 2020UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. open /Users/katekim/Downloads/electrostatics.cxs Log from Mon Nov 9 14:23:02 2020UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. open /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs Log from Mon Nov 2 15:10:34 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. open /home/sasha/Desktop/pks/figure_1.cxs Log from Mon Nov 2 14:59:47 2020UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open CACP_KS_AT_conformer-coot-3.pdb Chain information for CACP_KS_AT_conformer-coot-3.pdb #1 --- Chain | Description A | No description available B | No description available open NACP_KS_AT_conformer_4.pdb Chain information for NACP_KS_AT_conformer_4.pdb #2 --- Chain | Description A | No description available B | No description available lighting gentle select #1/A:1-98 753 atoms, 765 bonds, 1 model selected ui tool show ""Color Actions"" color sel tomato set bgColor white select #1:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected hide sel cartoons select #1/B:1-99 58 atoms, 57 bonds, 1 model selected hide sel cartoons select #2/B:1-99 768 atoms, 781 bonds, 1 model selected color sel tomato graphics silhouettes true hide pbonds select #2/A:99-521 3126 atoms, 3185 bonds, 2 pseudobonds, 2 models selected select clear select #2/B:99 8 atoms, 7 bonds, 1 model selected color sel cyan color sel deep sky blue color sel deep sky blue color sel dark turquoise color sel medium spring green color sel dodger blue color sel turquoise color sel light sea green color sel cornflower blue color sel cornflower blue color sel dark cyan color sel medium aquamarine color sel teal color sel steel blue color sel cadet blue color sel sky blue color sel light sky blue color sel sky blue select clear select #2/B:99 8 atoms, 7 bonds, 1 model selected select clear select #2:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected show sel surfaces hide sel surfaces select clear select #2/A:97 9 atoms, 8 bonds, 1 model selected select up 50 atoms, 49 bonds, 2 models selected hide sel cartoons select #2:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected show sel surfaces select #2/A:867@OH 1 atom, 1 model selected select up 12 atoms, 12 bonds, 2 models selected select up 29 atoms, 29 bonds, 2 models selected select up 6964 atoms, 7102 bonds, 2 models selected select down 29 atoms, 29 bonds, 2 models selected select clear select #2/A 6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected color sel gold target s color sel yellow target s color sel yellow target s color sel chartreuse target s color sel green target s color sel pale green target s color sel light green target s color sel burly wood target s color sel aquamarine target s color sel light coral target s color sel sky blue target s color sel light sky blue target s color sel light blue target s color sel light steel blue target s color sel pale turquoise target s color sel pale turquoise target s color sel light steel blue target s color sel powder blue target s color sel sky blue target s color sel white smoke target s color sel wheat target s color sel azure target s color sel beige target s color sel wheat target s color sel khaki target s color sel pale goldenrod target s select #2/B 7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected color sel floral white target s color sel lemon chiffon target s color sel lemon chiffon target s color sel seashell target s color sel lavender blush target s color sel light yellow target s color sel snow target s color sel misty rose target s select clear transparency #2 70 target s select #2/A 6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected color sel lemon chiffon target cs transparency #2/A 70 target s select #2/B 7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected color sel lemon chiffon target cs color sel papaya whip target cs color sel lavender blush target cs transparency #2/B 70 target s select #2/B:1098 Nothing selected select #2/B:1-98 760 atoms, 773 bonds, 1 model selected color sel tomato target cs select #2/B 7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected select #2/B:99-1074 6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected color sel medium purple target cs color sel dark orchid target cs color sel medium purple target cs color sel medium purple target cs color sel medium purple target cs color sel wheat target cs color sel khaki target cs color sel pale goldenrod target cs color sel violet target cs color sel violet target cs color sel lavender target cs color sel plum target cs color sel cornsilk target cs color sel powder blue target cs select clear select #2:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected 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 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 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 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 undo undo undo select #2:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected show sel surfaces select clear lighting flat lighting flat lighting full lighting soft lighting simple lighting shadows true lighting gentle ui tool show ""Side View"" select #2/A:99-1074 6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected color sel medium slate blue target cs color sel medium orchid target cs color sel medium violet red target cs color sel light sky blue target cs color sel aquamarine target cs color sel light coral target cs color sel rosy brown target cs color sel light coral target cs select #2/B:99-1074 6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected color sel peach puff target cs color sel navajo white target cs color sel navajo white target cs color sel peach puff target cs color sel navajo white target cs color sel moccasin target cs color sel navajo white target cs color sel peach puff target cs color sel navajo white target cs color sel bisque target cs color sel lemon chiffon target cs color sel cornsilk target cs color sel seashell target cs color sel lavender blush target cs color sel papaya whip target cs color sel blanched almond target cs color sel misty rose target cs color sel bisque target cs color sel pale turquoise target cs select #2/B:1-98 #1/A:1-98 1513 atoms, 1538 bonds, 2 models selected color sel light goldenrod yellow target cs color sel yellow target cs color sel orange target cs color sel gold target cs color sel orange target cs color sel dark orange target cs color sel fire brick target cs color sel tomato target cs color sel light salmon target cs color sel blue target cs color sel dark magenta target cs select clear save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample 24 quality 100 transparentBackground true Expected a keyword save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample 24 transparentBackground true save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample 24 quality 100 transparentBackground true Expected a keyword save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample 24 quality 100 transparentBackground true Expected a keyword Unknown data format: 'png' save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample 24 transparentBackground true lighting flat lighting soft lighting simple lighting shadows true lighting flat graphics silhouettes false lighting gentle graphics silhouettes true select :76-86 182 atoms, 178 bonds, 2 models selected show sel atoms size stickRadius 0.4 Changed 29848 bond radii select #2/B:1-98 #1/A:1-98 1513 atoms, 1538 bonds, 2 models selected color sel gold target acs color sel yellow target acs color sel gold target acs color sel byhetero select #2:99-521 6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected color sel fire brick target acs select #2:522-1074 7576 atoms, 7732 bonds, 8 pseudobonds, 2 models selected color sel royal blue target acs color sel indigo target acs color sel navy target acs color sel dark blue target acs color sel blue target acs color sel dodger blue target acs select clear select :HOH 573 atoms, 2 models selected hide sel atoms select clear select #2:420,500 40 atoms, 36 bonds, 1 model selected select #2:420,482,484,424,388,384,426,87-92,395,430,500,496 285 atoms, 257 bonds, 1 model selected show sel atoms color sel byhetero color sel byhetero color sel fire brick target acs select #2:420,482,484,424,388,384,426,395,430,500,496 223 atoms, 200 bonds, 1 model selected color sel byhetero select #2:99-521 6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected color sel fire brick target s select #2/B:1-98 760 atoms, 773 bonds, 1 model selected color sel gold target s color sel gold target acs color sel byhetero select clear select :HOH 573 atoms, 2 models selected hide sel atoms select #1/A:1-72 541 atoms, 548 bonds, 1 model selected show sel atoms hide sel atoms save /home/sasha/Desktop/pks/figure_1.cxs opened ChimeraX session open /home/sasha/Desktop/pks/sasha_figs/NACP1_ppant.pdb Chain information for NACP1_ppant.pdb #3 --- Chain | Description A | No description available B | No description available select #3/A:99-1074 6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected hide sel cartoons hide sel atoms select #3:99-1074 14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected hide sel cartoons hide sel atoms select #3/A:76-86 83 atoms, 85 bonds, 1 model selected show sel atoms select #1/A:1-98 753 atoms, 765 bonds, 1 model selected hide sel atoms hide sel cartoons size stickRadius 0.4 Changed 44789 bond radii select #3/A:1-98 753 atoms, 765 bonds, 1 model selected color sel gold target acs color sel byhetero select clear select #3/A:1101@C43 1 atom, 1 model selected select up 21 atoms, 20 bonds, 1 model selected select up 7688 atoms, 7839 bonds, 1 model selected select down 21 atoms, 20 bonds, 1 model selected color sel gold target acs color sel byhetero select clear lighting gentle save /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs opened ChimeraX session coloumbic #2:99-521 range -10,10 Unknown command: coloumbic #2:99-521 range -10,10 coulombic #2:99-521 range -10,10 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: NACP_KS_AT_conformer_4.pdb #2/A PHE 1074 OXT and NACP_KS_AT_conformer_4.pdb #2/B PHE 1074 OXT open ""/home/sasha/Desktop/pks/FINAL FINAL maps&pdb.zip"" Unrecognized file suffix '.zip' open ""/home/sasha/Desktop/pks/FINAL FINAL maps&pdb/NACP_KS_AT_conformer_4.pdb"" Chain information for NACP_KS_AT_conformer_4.pdb #4 --- Chain | Description A | No description available B | No description available select #4:1-98 831 atoms, 822 bonds, 125 residues, 1 model selected delete sel select #4:553-1074 7464 atoms, 7622 bonds, 4 pseudobonds, 968 residues, 2 models selected delete sel select #2 14932 atoms, 14928 bonds, 12 pseudobonds, 2220 residues, 2 models selected surface hidePatches (#!2 & sel) select #4 6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected coulombic #4 range -10,10 hide #4.3 models show #4.3 models hide #4.2 models show #4.2 models hide #4.1 models hide #4.2 models show #4.2 models select #4 6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected cartoon hide (#!4 & sel) select clear transparency #4 60 select clear ui tool show ""Side View"" save /home/sasha/Desktop/pks/sasha_figs/figure1/electrostatics.cxs opened ChimeraX session hide #1.1 models show #1.1 models hide #1.1 models show #1.1 models hide #2.1 models show #2.1 models hide #2.1 models show #2.1 models hide #2.2 models show #2.2 models hide #2.2 models show #2.2 models hide #2.3 models show #2.3 models hide #2.3 models show #2.3 models hide #2.3 models show #2.3 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!4.2 models show #!4.2 models hide #!4.2 models show #!4.2 models hide #!4.3 models show #!4.3 models hide #!4.3 models show #!4.3 models hide #!4.3 models show #!4.3 models hide #!4.3 models show #!4.3 models hide #!4.3 models show #!4.3 models select #1, 2, 3, 4:93-521 26418 atoms, 25780 bonds, 16 pseudobonds, 4498 residues, 8 models selected color (#!1-4 & sel) red select clear select #1, 2, 3, 4:93-529 26866 atoms, 26228 bonds, 16 pseudobonds, 4562 residues, 8 models selected color (#!1-4 & sel) red select clear ui tool show ""Side View"" hide #4.2 models hide #4.3 models select ::name=""PNS"" 21 atoms, 20 bonds, 1 residue, 1 model selected ui tool show ""Color Actions"" color sel navy color sel byhetero color sel blue color sel dark slate blue color sel dark slate gray color sel byhetero select clear save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs hide #!1 models show #!1 models hide #1.1 models show #1.1 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #2.1 models show #2.1 models hide #2.2 models show #2.2 models hide #2.3 models show #2.3 models close #2.2 close #2.1 close #1.1 close #2.3 hide #!3 models show #!3 models hide #!3 models show #!3 models hide #!3 models show #!3 models hide #!3 models show #!3 models hide #1 models show #1 models hide #1 models show #1 models hide #2 models hide #!3 models show #!3 models hide #!3 models show #2 models hide #2 models hide #1 models show #1 models hide #1 models show #1 models close #1 hide #!4 models show #!4 models show #4.1 models hide #4.1 models show #4.2 models hide #4.2 models show #4.3 models hide #4.3 models close #4.2 close #4.3 close #4.1 show #2 models show #!3 models hide #!3 models show #!3 models hide #3.1 models show #3.1 models hide #3.1 models close #3.1 hide #4 models show #4 models save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs opened ChimeraX session close #4 color #2/A:1-552 #f79292 color #2/A:553-1074 #9eddff lighting soft lighting full lighting simple lighting soft save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs turn turn turn turn turn y turn y turn y turn y turn x turn x turn x lighting soft select #2/A:1-552 3232 atoms, 3291 bonds, 433 residues, 1 model selected hide sel atoms select clear select #2/B: 420, 482,424,484,384,388,426,395,430,500,496 111 atoms, 100 bonds, 11 residues, 1 model selected color sel byhetero select clear save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs select #2/B:93-552 3232 atoms, 3291 bonds, 433 residues, 1 model selected show sel surfaces color (#!2 & sel) black transparency #32.1 80 transparency #2.1 80 select up 3399 atoms, 3463 bonds, 453 residues, 2 models selected select up 7674 atoms, 7826 bonds, 1009 residues, 2 models selected select up 14932 atoms, 14928 bonds, 2220 residues, 2 models selected select up 14932 atoms, 14928 bonds, 2220 residues, 2 models selected select #2/B:93-552 3232 atoms, 3291 bonds, 433 residues, 1 model selected color #2/B:93-552 #ff1616 color #2/B:2.1 white Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword color #2.1 white transparency #2.1 80 select clear lighting soft lighting soft save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs graphics silhouettes false graphics silhouettes true lighting soft select #2/B: 420, 482,424,484,384,388,426,395,430,500,496 111 atoms, 100 bonds, 11 residues, 1 model selected select #2.1: 420, 482,424,484,384,388,426,395,430,500,496 Nothing selected select #2/B: 420, 482,424,484,384,388,426,395,430,500,496 111 atoms, 100 bonds, 11 residues, 1 model selected color (#!2 & sel) byhetero select clear save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs hide #!2 models ui tool show ""Show Sequence Viewer"" sequence chain #3/A Alignment identifier is 3/A ui tool show ""Show Sequence Viewer"" sequence chain #2/A #3/B Alignment identifier is 1 show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models ui tool show ""Show Sequence Viewer"" sequence chain #2/B Alignment identifier is 2/B save /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb models #3 relModel #3 ui tool show ""Show Sequence Viewer"" sequence chain #3/A Alignment identifier is 3/A swapaa #3/A:84 tyrosine Using Dunbrack library NACP1_ppant.pdb #3/A ALA 84: phi -116.3, psi 124.7 trans Dunbrack rotamer library does not support TYROSINE open /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb Chain information for NACP1_ppant_edited.pdb #1 --- Chain | Description A | No description available B | No description available delete #1: 93-1074 hide #3 models sel#1 Unknown command: sel#1 select #1 731 atoms, 744 bonds, 93 residues, 1 model selected color sel yellow select clear select #1 731 atoms, 744 bonds, 93 residues, 1 model selected ui tool show ""Color Actions"" color sel gold color sel gold select clear select ::name=""PNS"" 42 atoms, 40 bonds, 2 residues, 2 models selected color (#1 & sel) light gray ui tool show ""Color Actions"" color sel dark slate gray color sel byhetero hide #1 models show #1 models save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs size #1 atomRadius 2 Changed 731 atom radii size #1 atomRadius 1 Changed 731 atom radii size #1 stickRadius 1 Changed 744 bond radii size #1 stickRadius 0.4 Changed 744 bond radii select clear select #1: 76-92 146 atoms, 151 bonds, 17 residues, 1 model selected show sel cartoons show sel atoms color sel byhetero select clear select #2/B: 76-92 146 atoms, 151 bonds, 17 residues, 1 model selected show sel atoms show sel atoms select clear save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs select clear turn center cofr turn turn turn save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs opened ChimeraX session save Fig1_D.png pixelSize 0.05 supersample 24 transparentBackground false hide #1 models show #1 models hide #1 models show #1 models hide #1 models show #1 models show #3 models hide #3 models show #3 models hide #3 models show #3 models hide #3 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #!2 models show #!2 models show #3 models hide #3 models hide #1 models hide #!2 models show #3 models hide #3 models show #1 models hide #1 models show #3 models hide #3 models show #3 models hide #3 models show #1 models hide #1 models show #1 models hide #1 models show #3 models close #3 show #1 models show #!2 models hide #1 models show #1 models hide #1 models show #1 models save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs opened ChimeraX session open /Users/katekim/Box/Pks13_ChimeraX_stuff/composite_4ACPs.pdb Chain information for composite_4ACPs.pdb #3 --- Chain | Description A | No description available B | No description available C D | No description available ui tool show Matchmaker matchmaker #!3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb, chain A (#3), sequence alignment score = 4887.4 RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs: 19.178) matchmaker #!3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb, chain A (#3), sequence alignment score = 4887.4 RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs: 19.178) close #3.1 hide #!2 models hide #1 models delete #3/A,D delete #3:93-1074 show #!2 models show #1 models save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs opened ChimeraX session ui tool show ""Model Panel"" select #3 1413 atoms, 1438 bonds, 184 residues, 1 model selected ui tool show ""Color Actions"" color sel light goldenrod yellow color sel lemon chiffon color sel lemon chiffon color sel lemon chiffon select clear turn center cofr turn turn turn save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs ——— End of log from Wed Dec 23 20:51:39 2020 ——— opened ChimeraX session hide #1 models show #1 models hide #!2 models show #!2 models hide #!2 models show #!2 models hide #3 models show #3 models select #2/B:588-694 821 atoms, 831 bonds, 107 residues, 1 model selected ui tool show ""Color Actions"" color sel navy select #2/A:588-694 821 atoms, 831 bonds, 107 residues, 1 model selected color sel royal blue select clear save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs includeMaps true ui tool show ""Volume Viewer"" lighting soft lighting soft lighting soft lighting soft lighting full lighting soft lighting simple lighting soft save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs includeMaps true ——— End of log from Wed Oct 27 22:15:56 2021 ——— opened ChimeraX session hide #1 models show #1 models hide #!2 models show #!2 models hide #3 models show #3 models hide #3 models show #3 models hide #3 models show #3 models hide surfaces ui tool show ""Side View"" save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ——— End of log from Thu Nov 11 12:44:42 2021 ——— opened ChimeraX session open /Users/katekim/Desktop/N-ACP2_wDCR-coot-7.pdb Chain information for N-ACP2_wDCR-coot-7.pdb #4 --- Chain | Description A | No description available B | No description available hide #1 models hide #!2 models hide #3 models hide #!4 atoms hide pbonds lighting simple lighting soft lighting full lighting soft select #4/A:76-92 146 atoms, 151 bonds, 17 residues, 1 model selected show sel atoms view matrix models #4,0.95994,-0.18223,0.21284,2.2549,0.2145,0.96667,-0.13976,-7.2093,-0.18028,0.17982,0.96704,5.3272 ui mousemode right zoom select #4/A:93-552 3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected select ::name=""ARG"" 2706 atoms, 2472 bonds, 246 residues, 4 models selected show sel & #!4 atoms select ::name=""LYS"" 1332 atoms, 1192 bonds, 148 residues, 2 models selected show sel & #!4 atoms ui tool show ""Side View"" save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:1-92 710 atoms, 723 bonds, 92 residues, 1 model selected color sel #FFF200 color sel byhetero select #4/A:93-552 3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected color sel ##ff1616 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword color sel #ff1616 color (#!4 & sel) byhetero select #4/A:553-694 821 atoms, 831 bonds, 107 residues, 1 model selected ui tool show ""Color Actions"" color sel navy select #4/A:695-1074 2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected select up 7693 atoms, 7844 bonds, 1 pseudobond, 1010 residues, 2 models selected select down 2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected color sel #23a7ff hide sel atoms select #4/A:553-694 821 atoms, 831 bonds, 107 residues, 1 model selected hide sel atoms select #4/B:553-694 821 atoms, 831 bonds, 107 residues, 1 model selected ui tool show ""Color Actions"" color sel royal blue select #4/B:695-1074 2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected color sel #9eddff select #4/B:1-552 3305 atoms, 3366 bonds, 1 pseudobond, 441 residues, 2 models selected color sel #f79292 select clear select #4/B:1-1074 7037 atoms, 7177 bonds, 3 pseudobonds, 925 residues, 2 models selected hide sel atoms select clear select #4/B:1-75 Nothing selected select #4/A:1-75 564 atoms, 571 bonds, 75 residues, 1 model selected hide sel atoms select clear save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true style #!4 stick Changed 14749 atom styles style #!4 ball Changed 14749 atom styles style #!4 stick Changed 14749 atom styles size #4/A:78 atomRadius 1 Changed 9 atom radii size #4/A:78 atomRadius 2 Changed 9 atom radii size #4/A:78 stickRadius 2 Changed 8 bond radii size #4/A:78 stickRadius 1 Changed 8 bond radii size #4/A:78 stickRadius 0.5 Changed 8 bond radii size #4/A:76-92 stickRadius 0.5 Changed 151 bond radii size #4/A:76-92 stickRadius 0.4 Changed 151 bond radii size #4/A:93-552 stickRadius 0.4 Changed 3291 bond radii transparency #4 80 target cr transparency #4 70 target cr transparency #4 90 target cr transparency #4 80 target cr ui tool show Contacts ui tool show H-Bonds hbonds showDist true twoColors true saltOnly true intraRes false select true 269 hydrogen bonds found 97 strict hydrogen bonds found hbonds showDist true distSlop 0.5 twoColors true saltOnly true intraRes false select true 299 hydrogen bonds found 97 strict hydrogen bonds found select clear ui tool show Distances Traceback (most recent call last): File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 554, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1263, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/__init__.py"", line 45, in start_tool return get_tool(session, tool_name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 19, in get_tool _tool.show_tab(tool_name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 56, in show_tab self.tab_widget.setCurrentIndex(index) RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1671, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show bi.start_tool(session, name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances in bundle ChimeraX-StructMeasure: wrapped C/C++ object of type QTabWidget has been deleted chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances in bundle ChimeraX-StructMeasure: wrapped C/C++ object of type QTabWidget has been deleted File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ——— End of log from Thu Nov 11 15:51:45 2021 ——— opened ChimeraX session ui tool show Distances hide hbonds select #4/A:92@NH2 1 atom, 1 residue, 1 model selected select add #4/A:282@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:92@NH2 #4/A:282@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 92 NH2 and ARG 282 NH2: 3.607Å select #4/A:89@OD1 1 atom, 1 residue, 1 model selected select add #4/A:388@NZ 2 atoms, 2 residues, 1 model selected distance #4/A:89@OD1 #4/A:388@NZ Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 89 OD1 and LYS 388 NZ: 5.933Å select #4/A:88@OE2 1 atom, 1 residue, 1 model selected select add #4/A:384@NH1 2 atoms, 2 residues, 1 model selected distance #4/A:88@OE2 #4/A:384@NH1 Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE2 and ARG 384 NH1: 3.308Å select #4/A:88@OE1 1 atom, 1 residue, 1 model selected select add #4/A:384@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:88@OE1 #4/A:384@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE1 and ARG 384 NH2: 3.642Å ~distance #4/A:89@OD1 #4/A:388@NZ ui tool show ""Side View"" select clear select #4/A:87@OD2 1 atom, 1 residue, 1 model selected select add #4/A:395@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:87@OD2 #4/A:395@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 87 OD2 and ARG 395 NH2: 7.086Å ~distance #4/A:87@OD2 #4/A:395@NH2 select #4/A:85@OD2 1 atom, 1 residue, 1 model selected select add #4/A:395@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:85@OD2 #4/A:395@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD2 and ARG 395 NH2: 5.736Å ~distance #4/A:85@OD2 #4/A:395@NH2 select #4/A:82@OE2 1 atom, 1 residue, 1 model selected select add #4/A:424@NZ 2 atoms, 2 residues, 1 model selected distance #4/A:82@OE2 #4/A:424@NZ Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 82 OE2 and LYS 424 NZ: 5.776Å ~distance #4/A:82@OE2 #4/A:424@NZ select #4/A:85@OD1 1 atom, 1 residue, 1 model selected select add #4/A:384@NH1 2 atoms, 2 residues, 1 model selected distance #4/A:85@OD1 #4/A:384@NH1 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD1 and ARG 384 NH1: 8.590Å ~distance #4/A:85@OD1 #4/A:384@NH1 select #4/A:85@OD2 1 atom, 1 residue, 1 model selected select add #4/A:395@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:85@OD2 #4/A:395@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD2 and ARG 395 NH2: 5.736Å ~distance #4/A:85@OD2 #4/A:395@NH2 select #4/A:82@OE2 1 atom, 1 residue, 1 model selected select add #4/A:424@NZ 2 atoms, 2 residues, 1 model selected distance #4/A:82@OE2 #4/A:424@NZ Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 82 OE2 and LYS 424 NZ: 5.776Å ~distance #4/A:82@OE2 #4/A:424@NZ select #4/A:78@OE2 1 atom, 1 residue, 1 model selected select add #4/A:482@NZ 2 atoms, 2 residues, 1 model selected distance #4/A:78@OE2 #4/A:482@NZ Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 78 OE2 and LYS 482 NZ: 6.075Å ~distance #4/A:78@OE2 #4/A:482@NZ select clear surface #4-6 transparency #4-6 90 ui tool show ""Surface Color"" No map chosen for coloring hide #!4 surfaces show #!4 surfaces coulombic #!4 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for N-ACP2_wDCR-coot-7.pdb_A SES surface #4.2: minimum, -26.54, mean -4.52, maximum 12.20 Coulombic values for N-ACP2_wDCR-coot-7.pdb_B SES surface #4.3: minimum, -19.09, mean -4.05, maximum 13.50 To also show corresponding color key, enter the above coulombic command and add key true transparency #4-6 80 hide #!4 surfaces select #4/A:93-552 3232 atoms, 3291 bonds, 34 pseudobonds, 433 residues, 3 models selected hide sel atoms select #4/A:420,482,424,484,384,388,426,395,430,500,496 111 atoms, 100 bonds, 11 residues, 1 model selected show sel atoms select #4/A:500,496,426,430,484 51 atoms, 46 bonds, 5 residues, 1 model selected hide sel atoms select #4/A:282 11 atoms, 10 bonds, 1 residue, 1 model selected show sel atoms select clear save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ——— End of log from Thu Nov 11 16:26:07 2021 ——— opened ChimeraX session ui tool show Distances select #4/A:476@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab select #4/A:59@N 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab size #4/A:1-552 stickRadius 0.4 Changed 4015 bond radii select clear select #4/A:59@N 1 atom, 1 residue, 1 model selected select add #4/A:476@O 2 atoms, 2 residues, 2 models selected distance #4/A:59@N #4/A:476@O Distance between N-ACP2_wDCR-coot-7.pdb #4/A THR 59 N and PRO 476 O: 3.791Å ~distance #4/A:88@OE2 #4/A:384@NH1 ~distance #4/A:88@OE1 #4/A:384@NH2 ~distance #4/A:92@NH2 #4/A:282@NH2 distance style radius 0.4 distance style radius 0.3 select #6.1 1 model selected ~select #6.1 Nothing selected distance style radius 0.25 save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true label listfonts 270 fonts available: .Al Bayan PUA .Al Nile PUA .Al Tarikh PUA .Apple Color Emoji UI .Apple SD Gothic NeoI .Apple Symbols Fallback .Aqua Kana .Arabic UI Display .Arabic UI Text .Arial Hebrew Desk Interface .Baghdad PUA .Beirut PUA .Damascus PUA .DecoType Naskh PUA .Diwan Kufi PUA .Farah PUA .Geeza Pro Interface .Geeza Pro PUA .Helvetica Neue DeskInterface .Hiragino Kaku Gothic Interface .Hiragino Sans GB Interface .Keyboard .KufiStandardGK PUA .LastResort .Lucida Grande UI .Muna PUA .Nadeem PUA .Noto Nastaliq Urdu UI .Noto Sans Universal .PingFang HK .PingFang SC .PingFang TC .SF Compact Display .SF Compact Rounded .SF Compact Text .SF NS Display .SF NS Display Condensed .SF NS Rounded .SF NS Symbols .SF NS Text .SF NS Text Condensed .Sana PUA .Savoye LET CC. Adobe Arabic Adobe Caslon Pro Adobe Fan Heiti Std Adobe Fangsong Std Adobe Garamond Pro Adobe Gothic Std Adobe Hebrew Adobe Heiti Std Adobe Kaiti Std Adobe Ming Std Adobe Myungjo Std Adobe Song Std Al Bayan Al Nile Al Tarikh American Typewriter Andale Mono Apple Braille Apple Chancery Apple Color Emoji Apple SD Gothic Neo Apple Symbols AppleGothic AppleMyungjo Arial Arial Black Arial Hebrew Arial Hebrew Scholar Arial Narrow Arial Rounded MT Bold Arial Unicode MS Athelas Avenir Avenir Next Avenir Next Condensed Ayuthaya Baghdad Bangla MN Bangla Sangam MN Baskerville Beirut Big Caslon Birch Std Blackoak Std Bodoni 72 Bodoni 72 Oldstyle Bodoni 72 Smallcaps Bodoni Ornaments Bradley Hand Brush Script MT Brush Script Std Chalkboard Chalkboard SE Chalkduster Chaparral Pro Charlemagne Std Charter Cochin Comic Sans MS Cooper Std Copperplate Corsiva Hebrew Courier Courier New DIN Alternate DIN Condensed Damascus DecoType Naskh Devanagari MT Devanagari Sangam MN Didot Diwan Kufi Diwan Thuluth Euphemia UCAS Farah Farisi Futura GB18030 Bitmap Geeza Pro Geneva Georgia Giddyup Std Gill Sans Gujarati MT Gujarati Sangam MN Gurmukhi MN Gurmukhi MT Gurmukhi Sangam MN Heiti SC Heiti TC Helvetica Helvetica Neue Herculanum Hiragino Kaku Gothic Pro Hiragino Kaku Gothic ProN Hiragino Kaku Gothic Std Hiragino Kaku Gothic StdN Hiragino Maru Gothic Pro Hiragino Maru Gothic ProN Hiragino Mincho Pro Hiragino Mincho ProN Hiragino Sans Hiragino Sans GB Hobo Std Hoefler Text ITF Devanagari ITF Devanagari Marathi Impact InaiMathi Iowan Old Style Kailasa Kannada MN Kannada Sangam MN Kefa Khmer MN Khmer Sangam MN Kohinoor Bangla Kohinoor Devanagari Kohinoor Telugu Kokonor Kozuka Gothic Pr6N Kozuka Gothic Pro Kozuka Mincho Pr6N Kozuka Mincho Pro Krungthep KufiStandardGK Lao MN Lao Sangam MN Letter Gothic Std Lithos Pro Lucida Grande Luminari Malayalam MN Malayalam Sangam MN Marion Marker Felt Menlo Mesquite Std Microsoft Sans Serif Minion Pro Mishafi Mishafi Gold Monaco Mshtakan Muna Myanmar MN Myanmar Sangam MN Myriad Pro Nadeem New Peninim MT Noteworthy Noto Nastaliq Urdu Nueva Std OCR A Std Optima Orator Std Oriya MN Oriya Sangam MN PT Mono PT Sans PT Sans Caption PT Sans Narrow PT Serif PT Serif Caption Palatino Papyrus Phosphate PingFang HK PingFang SC PingFang TC Plantagenet Cherokee Poplar Std Prestige Elite Std Raanana Rockwell Rosewood Std STIXGeneral STIXIntegralsD STIXIntegralsSm STIXIntegralsUp STIXIntegralsUpD STIXIntegralsUpSm STIXNonUnicode STIXSizeFiveSym STIXSizeFourSym STIXSizeOneSym STIXSizeThreeSym STIXSizeTwoSym STIXVariants STSong Sana Sathu Savoye LET Seravek Shree Devanagari 714 SignPainter Silom Sinhala MN Sinhala Sangam MN Skia Snell Roundhand Songti SC Songti TC Stencil Std Sukhumvit Set Superclarendon Symbol Tahoma Tamil MN Tamil Sangam MN Tekton Pro Telugu MN Telugu Sangam MN Thonburi Times Times New Roman Trajan Pro Trattatello Trebuchet MS Verdana Waseem Webdings Wingdings Wingdings 2 Wingdings 3 Zapf Dingbats Zapfino help help:user/tools/modelpanel.html distance style color #3aeafa distance style color gold distance style radius 0.1 distance style color #25faea [Repeated 1 time(s)] distance style radius 0.2 hide #6.1 models show #6.1 models label #6.1 height Missing ""height"" keyword's argument label #6.1 size 24 label #6.1 size 48 hide #6.1 models show #6.1 models label #6.1 size 90 label #6.1 height 1 label #6.1 height 3 select #6.1 1 model selected hide #!6 models show #!6 models label #6 height 3 label #6 height 2 label #6 height 1 label #6 height 1.5 select #6 1 pseudobond, 2 models selected ~select #6 Nothing selected select #6.1 1 model selected No visible atoms, bonds, or surfaces selected color #6.1 |default Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword color #6.1 | default Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword color #6.1 default Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword color #6.1 black color #6 black color #6.1 black No visible atoms, bonds, or surfaces selected distance style color #6df5e7 [Repeated 1 time(s)] distance style color #6cf5e7 distance style color #353ef5 distance style color #363ff5 distance style color #2b87f5 distance style color #2dc1f5 [Repeated 1 time(s)] distance style color #25f5f3 distance style color #25f5f2 distance style color #67f5ee distance style color #05f5e9 save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ——— End of log from Fri Nov 12 14:34:37 2021 ——— opened ChimeraX session select #4/A:92@NE 1 atom, 1 residue, 1 model selected select #4/A:389@O 1 atom, 1 residue, 1 model selected show (#!4 & sel-residues & sidechain) target ab color (#!4 & sel) byhetero select #4/A:389@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select #4/A:389@O 1 atom, 1 residue, 1 model selected select #4/A:389@O 1 atom, 1 residue, 1 model selected Drag select of 2 residues select clear select #4/A:389@O 1 atom, 1 residue, 1 model selected select clear select #4/A:389@O 1 atom, 1 residue, 1 model selected select add #4/A:92@NE 2 atoms, 2 residues, 2 models selected ui tool show Distances [Repeated 1 time(s)] save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ——— End of log from Fri Nov 12 15:09:46 2021 ——— opened ChimeraX session ui tool show Distances distance #4/A:92@NE #4/A:389@O Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 92 NE and ASP 389 O: 3.245Å select #4/A:92@NH2 1 atom, 1 residue, 1 model selected select #4/A:98@OD1 1 atom, 1 residue, 1 model selected show (#!4 & sel-residues & sidechain) target ab select add #4/A:92@NH2 2 atoms, 2 residues, 2 models selected distance #4/A:98@OD1 #4/A:92@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 98 OD1 and ARG 92 NH2: 2.421Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:92@NH2 1 atom, 1 residue, 1 model selected select #4/A:358@O 1 atom, 1 residue, 1 model selected hide (sel-residues & (protein|nucleic)) target a cartoon hide sel-residues show (sel-residues & backbone) target ab show (sel-residues & sidechain) target ab select add #4/A:92@NH2 2 atoms, 2 residues, 1 model selected distance #4/A:358@O #4/A:92@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ALA 358 O and ARG 92 NH2: 2.951Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:88@OE1 1 atom, 1 residue, 1 model selected ui tool show ""Side View"" select #4/A:88@OE1,384@NH2 1 atom, 1 residue, 1 model selected select #4/A:384@NH2 1 atom, 1 residue, 1 model selected select add #4/A:88@OE1 2 atoms, 2 residues, 2 models selected distance #4/A:384@NH2 #4/A:88@OE1 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 384 NH2 and GLU 88 OE1: 3.642Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:388@NZ 1 atom, 1 residue, 1 model selected select add #4/A:88@OE1 2 atoms, 2 residues, 2 models selected distance #4/A:388@NZ #4/A:88@OE1 Distance between N-ACP2_wDCR-coot-7.pdb #4/A LYS 388 NZ and GLU 88 OE1: 2.780Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:384@NH1 1 atom, 1 residue, 1 model selected select add #4/A:88@OE2 2 atoms, 2 residues, 2 models selected distance #4/A:384@NH1 #4/A:88@OE2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 384 NH1 and GLU 88 OE2: 3.308Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select clear select #4/A:88@OE2 1 atom, 1 residue, 1 model selected select clear select #4/A:88@OE2 1 atom, 1 residue, 1 model selected select add #4/A:384@NH2 2 atoms, 2 residues, 2 models selected distance #4/A:88@OE2 #4/A:384@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE2 and ARG 384 NH2: 3.683Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:90@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select #4/A:392@N 1 atom, 1 residue, 1 model selected hide (sel-residues & (protein|nucleic)) target a cartoon hide sel-residues show (sel-residues & backbone) target ab show (sel-residues & sidechain) target ab select #4/A:392 8 atoms, 7 bonds, 1 residue, 1 model selected color (#!4 & sel) byhetero select #4/A:392@N 1 atom, 1 residue, 1 model selected select add #4/A:90@O 2 atoms, 2 residues, 1 model selected distance #4/A:392@N #4/A:90@O Distance between N-ACP2_wDCR-coot-7.pdb #4/A ILE 392 N and TRP 90 O: 3.567Å select #4/A:91@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select #4/A:93@N 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab color (#!4 & sel) byhetero select #4/A:93 7 atoms, 6 bonds, 1 residue, 1 model selected color (#!4 & sel) byhetero select #4/A:93@N 1 atom, 1 residue, 1 model selected select #4/A:91@O 1 atom, 1 residue, 1 model selected select add #4/A:93@N 2 atoms, 2 residues, 2 models selected distance #4/A:91@O #4/A:93@N Distance between N-ACP2_wDCR-coot-7.pdb #4/A SER 91 O and THR 93 N: 3.505Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true hide #!5 models show #!5 models hide #5.1 models show #5.1 models close #5 hide #!6 models show #!6 models color #6 cyan distance style radius 0.25 distance style dashes 8 distance style dashes 7 distance style dashes 6 [Repeated 2 time(s)] distance style dashes 7 distance style dashes 8 distance style radius 0.2 save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:92@NH1 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select #4/A:92@NH1 1 atom, 1 residue, 1 model selected select #4/A:98@OD1 1 atom, 1 residue, 1 model selected select add #4/A:92@NH1 2 atoms, 2 residues, 2 models selected distance #4/A:98@OD1 #4/A:92@NH1 Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 98 OD1 and ARG 92 NH1: 3.488Å save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:92@O 1 atom, 1 residue, 1 model selected select #4/A:93@N 1 atom, 1 residue, 1 model selected save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true ui tool show ""Side View"" save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true distance style color #3aeafa select #4/A:7@NH2 1 atom, 1 residue, 1 model selected show (#!4 & sel-residues & sidechain) target ab select #4/A:975@O 1 atom, 1 residue, 1 model selected select #4/A:975@O 1 atom, 1 residue, 1 model selected save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true select #4/A:975@O 1 atom, 1 residue, 1 model selected select #4/A:975@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab delete atoms (#!4 & sel) delete bonds (#!4 & sel) select #4/B:975@O 1 atom, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab color (#!4 & sel) byhetero select #4/B:975 8 atoms, 7 bonds, 1 residue, 1 model selected color (#!4 & sel) byhetero size #4:1-1074 stickRadius 0.4 Changed 15002 bond radii select clear select #4/B:975@O 1 atom, 1 residue, 1 model selected select add #4/A:7@NH2 2 atoms, 2 residues, 2 models selected distance #4/B:975@O #4/A:7@NH2 Distance between N-ACP2_wDCR-coot-7.pdb #4/B ASP 975 O and /A ARG 7 NH2: 3.834Å select clear select #4/B:975@O 1 atom, 1 residue, 1 model selected select add #4/A:7@NH1 2 atoms, 2 residues, 2 models selected distance #4/B:975@O #4/A:7@NH1 Distance between N-ACP2_wDCR-coot-7.pdb #4/B ASP 975 O and /A ARG 7 NH1: 3.482Å distance style color #3aeafa save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true show #3 models hide #3 models hide #!4 models show #3 models hide #3 models show #!2 models hide #!2 models show #1 models hide #1 models close #1 show #3 models hide #3 models close #3 show #!2 models hide #!2 models show #!4 models hide #!4 models open ""/Users/katekim/Dropbox/PKS13/MAPS and MODELS_UPDATED/NACP1_noHETATM_real_space_refined.pdb"" Chain information for NACP1_noHETATM_real_space_refined.pdb #1 --- Chain | Description A | No description available B | No description available show #!4 models hide #!1 models hide #!4 models show #!1 models show #!2 models hide #!2 models open /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb Summary of feedback from opening /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb --- warning | Cannot find LINK/SSBOND residue SER (38 ) Chain information for NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available hide #!1 models hide #!3 models show #!3 models show #!1 models hide #!1 models close #1 close #3 show #!2 models hide #!2 models open /Users/katekim/Box/Kate_Oren_figs/N_ACP1_conformer/RealSpaceRefine_5/N-ACP1_wPNSnDCR_real_space_refined- coot-2_real_space_refined.pdb Chain information for N-ACP1_wPNSnDCR_real_space_refined- coot-2_real_space_refined.pdb #1 --- Chain | Description A | No description available B | No description available close #1 open /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb Summary of feedback from opening /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 3 THR A 18 1 16 Start residue of secondary structure not found: HELIX 2 2 ALA A 22 ALA A 24 1 3 Start residue of secondary structure not found: HELIX 3 3 MET A 31 GLU A 33 1 3 Start residue of secondary structure not found: HELIX 4 4 SER A 38 THR A 52 1 15 Start residue of secondary structure not found: HELIX 5 5 ALA A 58 ARG A 63 1 6 1 messages similar to the above omitted Chain information for NACP1-KSAT_wHET_real_space_refined- coot-0_brokenup4PISA_edited.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs includeMaps true [Repeated 1 time(s)] show #!4 models hide #!1 models select #4/A:39,42,45,46,49,55,56,57,58,59,61,62,63,78,80,81,83-85,88-92 199 atoms, 195 bonds, 24 residues, 1 model selected select #4/A:39,42,45,46,49,55,56,57,58,59,61,62,63,78,80,81,83-85,88-92,93,94,96-98,282,358,384,387-396,421,430,460,461,463,496-499,521-524,527,528,645,646,1047-1053 517 atoms, 502 bonds, 10 pseudobonds, 66 residues, 2 models selected select clear select #4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483 411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true ——— End of log from Mon Nov 15 14:16:35 2021 ——— opened ChimeraX session select clear hide #!4 atoms cartoon #4,6 ui tool show ""Side View"" hide #!6 models select #4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483 411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected show sel atoms cartoon style (#!4 & sel) modeHelix tube sides 20 select clear size #4:1-1074 stickRadius 0.2 Changed 15002 bond radii select #4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483 411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected style sel sphere Changed 411 atom styles select clear save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true style #!4 stick Changed 14748 atom styles style #!4 ball Changed 14748 atom styles style #!4 stick Changed 14748 atom styles select #4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483 411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected surface (#!4 & sel) hide sel surfaces coulombic sel Coulombic values for N-ACP2_wDCR-coot-7.pdb_A SES surface #4.2: minimum, -26.53, mean -4.46, maximum 12.24 To also show corresponding color key, enter the above coulombic command and add key true hide sel surfaces interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier select clear cartoon style #4 xsection oval modeHelix default cartoon style #4 xsection rectangle modeHelix default cartoon style (#4 & coil) xsection oval cartoon style #4 xsection barbell modeHelix default cartoon style #4 modeHelix tube sides 20 cartoon style (#4 & coil) xsection oval cartoon style #4 xsection barbell modeHelix default select #4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483 411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected color (#!4 & sel) byhetero select clear hide #!4 models show #!4 models show #!1 models hide #!1 models hide #!4 models show #!4 models show #!2 models hide #!2 models show #!2 models close #2 save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true ——— End of log from Mon Nov 15 14:47:15 2021 ——— opened ChimeraX session ui tool show ""Side View"" ui tool show Distances [Repeated 1 time(s)] save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true ——— End of log from Mon Nov 15 15:07:58 2021 ——— opened ChimeraX session show #!6 models ui tool show Distances distance style dashes 6 distance style radius 0.12 hide #6.1 models ~distance #4/A:91@O #4/A:93@N save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true ——— End of log from Mon Nov 15 15:23:49 2021 ——— opened ChimeraX session show #!1 models hide #!1 models hide #!4 models show #!4 models ui tool show ""Side View"" hide #!4 atoms hide #!6 models show #!1 models hide #!1 models transparency #4 0 target cr lighting simple lighting soft lighting full lighting soft save /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs includeMaps true ——— End of log from Wed Dec 1 23:32:50 2021 ——— opened ChimeraX session save NACP2_KSAT_Interacting_residues_closeup_numbers.png pixelSize 0.05 supersample 24 transparentBackground false select #4/C:30,33,58,59,62,63 Nothing selected select #4/A:30,33,58,59,62,63,369,409,412,413,416,476-479,482,483 142 atoms, 137 bonds, 1 pseudobond, 17 residues, 2 models selected show sel atoms color (#!4 & sel) byhetero select clear cartoon style (#4 & coil) xsection oval cartoon style #4 xsection barbell modeHelix default cartoon style #4 modeHelix tube sides 20 select #4/A:59 7 atoms, 6 bonds, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select clear select #4/A:476 7 atoms, 7 bonds, 1 residue, 1 model selected hide (#!4 & sel-residues & (protein|nucleic)) target a cartoon hide (#!4 & sel-residues) show (#!4 & sel-residues & backbone) target ab show (#!4 & sel-residues & sidechain) target ab select clear cartoon style (#4 & coil) xsection oval cartoon style #4 xsection barbell modeHelix default cartoon style #4 xsection rectangle modeHelix default cartoon style #4 xsection oval modeHelix default select #4/A:476@O 1 atom, 1 residue, 1 model selected select clear select #4/A:476@O 1 atom, 1 residue, 1 model selected select #4/A:476@O 1 atom, 1 residue, 1 model selected select add #4/A:59@N 2 atoms, 2 residues, 2 models selected ui tool show Distances Traceback (most recent call last): File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 554, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1264, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/__init__.py"", line 45, in start_tool return get_tool(session, tool_name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 19, in get_tool _tool.show_tab(tool_name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/struct_measure/tool.py"", line 56, in show_tab self.tab_widget.setCurrentIndex(index) RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1672, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2875, in run result = ci.function(session, **kw_args) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show bi.start_tool(session, name) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances in bundle ChimeraX-StructMeasure: wrapped C/C++ object of type QTabWidget has been deleted chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances in bundle ChimeraX-StructMeasure: wrapped C/C++ object of type QTabWidget has been deleted File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD- FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.9.22 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,2 Processor Name: Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 194.0.0.0.0 SMC Version (system): 2.44f1 Software: System Software Overview: System Version: macOS 10.14.5 (18F132) Kernel Version: Darwin 18.6.0 Time since boot: 8 days 8:05 Graphics/Displays: Intel Iris Plus Graphics 650: Chipset Model: Intel Iris Plus Graphics 650 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5927 Revision ID: 0x0006 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.1.5 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.1.7 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202111111002 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.3.2 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.14 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.5.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.22 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0" defect closed moderate Structure Analysis duplicate all ChimeraX