id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10271 mcopy command missing kdr2001@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description mcopy seems to be completely broken, gives error Unknown command: mcopy Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/miscellaneous/Figure1/apo-Na-NaAsp_GltPh_2.cxs"" > format session Log from Wed Oct 4 22:55:57 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" format session Log from Wed Oct 4 22:15:15 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" Log from Mon Sep 25 21:50:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" format session Log from Tue May 23 19:08:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" Log from Fri May 19 07:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" Log from Tue May 16 20:23:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1e.cxs"" format session Log from Mon May 15 14:59:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kdr2001/Downloads/6x15.pdb format pdb 6x15.pdb title: Inward-facing state of the glutamate transporter homologue gltph In complex with L-aspartate and sodium ions [more info...] Chain information for 6x15.pdb #1 --- Chain | Description A B C | glutamate transporter homologue gltph Non-standard residues in 6x15.pdb #1 --- 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate ASP — aspartic acid FME — N-formylmethionine HG — mercury (II) ion NA — sodium ion > hide #1/b-c > hide #1/b-c cartoons > hide cartoons > hide atoms > show #1/a:405 > show #1/a:90-94 > show #1/a:90-94 cartoons > show #1/a:500-504 > show #1/a:310-314 > show #1/a:310-314 cartoons > show #1/b cartoons > ui mousemode right zoom > show #1/a:344-363 cartoons > show #1/a:344-363 > hide #1/b cartoons > view orient > help help:user > cartoon style #1/a width 0.4 > hide #1/a:344-363 atoms > show #1/a:350@o > hide #1/a:313,314 atoms > hide #1/a:91,92,94 atoms > hide #1/a:90,91,94 atoms > color #1/a:344-363 red > color #1/a:344-363 dark orange > color #1/a dark orange > color #1/a:2-314,405 dark orange > color #1/a:344-363 red > color byhetero > show #1/a:405 cartoons > show #1/a:349,350,352 atoms > hide #1/a:349,350,352 cartoons > color #1/a:344-363 dark orange > color byhetero > show #1/a:349,350,352 cartoons > suppressbackbonedisplay false Unknown command: suppressbackbonedisplay false > suppressBackboneDisplay false Unknown command: suppressBackboneDisplay false > cartoon style #1/a width 0.4 suppressBackboneDisplay false Expected a keyword > cartoon #1/a:349,350,352 suppressBackboneDisplay false > cartoon #1/a:310 suppressBackboneDisplay false > color byhetero > cartoon style #1/a width 0.8\ Invalid ""width"" argument: Expected a number > cartoon style #1/a width 0.8 > ui tool show H-Bonds > hbonds reveal true 1083 hydrogen bonds found > undo > ~hbonds [Repeated 1 time(s)] > hide atoms > show #1/a:92,93,310,312,405 > show #1/a:500-504 > show #1/a:349,350,352 > cartoon #1/a:349,350,352 suppressBackboneDisplay false > show #1/a:310 atoms > select down Nothing selected > cartoon #1/a:310 suppressBackboneDisplay false > cartoon #1/a:311 > show #1/a:311 > color #1/a dark orange > color byhetero > cartoon style #1/a width 0.8 > ui mousemode right select > select /A:502@NA 1 atom, 1 residue, 1 model selected > select /A:311@SD 1 atom, 1 residue, 1 model selected > select clear > select /A:311@SD 1 atom, 1 residue, 1 model selected > select /A:502@NA 1 atom, 1 residue, 1 model selected > select /A:311@SD 1 atom, 1 residue, 1 model selected > select /A:502@NA 1 atom, 1 residue, 1 model selected > ui mousemode right distance > distance /A:502@NA /A:311@SD Distance between /A NA 502 NA and MET 311 SD: 2.940Å > ui mousemode right distance > ui mousemode right select > select clear > ui mousemode right label > label #1/A:502 [Repeated 1 time(s)] > help help:user > distance /A:502@NA /A:311@SD color skyblue radius 0.075 dashes 6 Distance already exists; modify distance properties with 'distance style' > distance style #2 color skyblue radius 0.075 dashes 6 > distance style color skyblue > distance style dashes 6 > distance style radius 0.075 > hide #2.1 models > hbonds color skyblue 1083 hydrogen bonds found > undo > hbonds hide Expected a keyword > hbonds delete > ui mousemode right label > label #1/A:502 > hide #2.1 models > label delete residues > label #1/A:92 > label delete residues > ui mousemode right select > ui mousemode right zoom > ui mousemode right select > color sel skyblue > select add /A:310@O 1 atom, 1 pseudobond, 1 residue, 2 models selected > select clear > color sel skyblue > ui mousemode right zoom > ui mousemode right select > color sel skyblue > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" includeMaps true > ui mousemode right zoom > ui mousemode right pivot > lighting soft > graphics silhouettes true > set bgColor white > lighting multiShadow 512 > ui mousemode right select > select clear > ui tool show ""Side View"" > view name 1 > view 1 > save /Users/kdr2001/Desktop/image131.png supersample 3 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1e.cxs"" includeMaps true ——— End of log from Mon May 15 14:59:45 2023 ——— opened ChimeraX session > view 1 > hide #1:310,349,350,352 atoms > undo > cartoon #1:310,349,350,352 backbonesuppressdisplay true Expected a keyword > cartoon #1:310,349,350,352 backboneSuppressDisplay true Expected a keyword > cartoon #1:310,349,350,352 suppressbackboneDisplay true Expected a keyword > cartoon #1:310,349,350,352 suppressBackboneDisplay true > view 1 > hide #1:310,349,350,352 atoms > view 1 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" includeMaps true > show #1:310 atoms > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" ——— End of log from Tue May 16 20:23:40 2023 ——— opened ChimeraX session > open /Users/kdr2001/Downloads/6x12.pdb 6x12.pdb title: Inward-facing apo-open state of the glutamate transporter homologue gltph [more info...] Chain information for 6x12.pdb #3 --- Chain | Description A | glutamate transporter homologue gltph Non-standard residues in 6x12.pdb #3 --- 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate > mmaker #3/a:75-90,225-415 > matchmaker #3/a:75-90,225-415 Missing required ""to"" argument > mmaker #3/a:75-90,225-415 to #1/a 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 6x15.pdb, chain A (#1) with 6x12.pdb, chain A (#3), sequence alignment score = 1013 RMSD between 152 pruned atom pairs is 0.680 angstroms; (across all 207 pairs: 2.124) > hide #3 cartoons > show #3/a:405,344-363,310-314,90-94 > show #3/a:405,344-363,310-314,90-94 cartoons > hide #3/a:405,344-363,310-314,90-94 atoms > shiow #3/a:405,92,93,310,312,311 Unknown command: shiow #3/a:405,92,93,310,312,311 > shiow #3/a:405,92,93,310,312,311 atoms Unknown command: shiow #3/a:405,92,93,310,312,311 atoms > show #3/a:405,92,93,310,312,311 atoms > hide #!2 models > hide #1.1 models > color #3 #feb255ff > color #3 #ffcb8dff > color #3 #ffe5c6ff > color byhetero > view orient > hide #3/b-c atoms > hide #3/a atoms > hide #1/b-c atoms > hide #1/b-c cartoons > view orient > hide #3/a:4,7,501,196,199 > view 1 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" includeMaps true ——— End of log from Fri May 19 07:41:16 2023 ——— opened ChimeraX session > view 1 [Repeated 1 time(s)] > lighting multiShadow 512 > save /Users/kdr2001/Desktop/image132.png supersample 3 > help help:user > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 3 width 900 height 900 > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample ""9\\\"" width 900 > height 900 Invalid ""supersample"" argument: Expected an integer > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900 > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 18 width 900 height > 900 > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900 > view 1 > save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900 > ui mousemode right distance > distance #1/A:311@SD #1/A:502@NA Distance already exists; modify distance properties with 'distance style' > show #2.1 models > style > cartoon style #3 width 0.8 > view 1 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/S1/S1d.cxs"" includeMaps true ——— End of log from Tue May 23 19:08:01 2023 ——— opened ChimeraX session > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > open ""/Users/kdr2001/Downloads/7ahk (2).pdb"" 7ahk (2).pdb title: Crystal structure of the outward-facing state of the substrate-free Na+-ONLY bound glutamate transporter homolog gltph [more info...] Chain information for 7ahk (2).pdb #4 --- Chain | Description | UniProt A | glutamate transporter homolog | GLT_PYRHO 1-417 Non-standard residues in 7ahk (2).pdb #4 --- BOG — octyl β-D-glucopyranoside (β-octylglucoside; octyl β-D-glucoside; octyl D-glucoside; octyl glucoside) GOL — glycerol (glycerin; propane-1,2,3-triol) LFA — eicosane (lipid fragment) NA — sodium ion OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol) PO4 — phosphate ion > mmaker #4/a:75-90,225-425 > matchmaker #4/a:75-90,225-425 Missing required ""to"" argument > mmaker #4/a:75-90,225-425 to #1 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 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence alignment score = 1006.3 RMSD between 186 pruned atom pairs is 0.732 angstroms; (across all 211 pairs: 2.593) > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #4 > hide #4 cartoons > show #4/a:90-94,405,310-314,344-363 > show #4/a:90-94,405,310-314,344-363 cartoons [Repeated 1 time(s)] > view 1 > show #4/a:92,93,405,310-312, Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #4/a:92,93,405,310-312 atoms > mmaker #4/a:75-90,225-344,363-425 to #1 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 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence alignment score = 924.6 RMSD between 184 pruned atom pairs is 0.715 angstroms; (across all 193 pairs: 2.006) > show #4@na atoms > hide #!4 models > show #!4 models > hide #2.1 models > hide #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #4.1 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > style > cartoon style #4 1 Expected a keyword > cartoon style #4 width 1 > cartoon style #1-4 width 1 > cartoon style #1-4 width 0.5 > view 1 > cartoon style #1-4 width 0.75 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > mmaker #4/a:75-90,225-344,363-425@ca to #1 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 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence alignment score = 924.6 RMSD between 184 pruned atom pairs is 0.715 angstroms; (across all 193 pairs: 2.006) > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > color #1-4 aluminum Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1 darkgrey > color #3 darkgrey > color #4 darkgrey > color byhetero > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" includeMaps true > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > hide #!4 models > save Missing or invalid ""fileName"" argument: Expected a file name > show #!1 models > color #1:504 mocha Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1:504 byatom mocha Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1:504 brown > color #!1 byhetero > color #1:504 salmon > color #!1 byhetero > color #1:504 teal > color #!1 byhetero > lighting multiShadow 512 > save /Users/kdr2001/Desktop/image10.png supersample 3 > save /Users/kdr2001/Desktop/NaAsp.png supersample 3 width 900 height 900 > hide #!1 models > show #!3 models > save /Users/kdr2001/Desktop/apo.png supersample 3 width 900 height 900 > hide #!3 models > show #!4 models > save /Users/kdr2001/Desktop/Na.png supersample 3 width 900 height 900 > view 1 > save /Users/kdr2001/Desktop/Na.png supersample 3 width 900 height 900 > hide #!4 models > show #!3 models > save /Users/kdr2001/Desktop/apo.png supersample 3 width 900 height 900 > show #!1 models > hide #!3 models > save /Users/kdr2001/Desktop/NaAsp.png supersample 3 width 900 height 900 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" ——— End of log from Mon Sep 25 21:50:45 2023 ——— opened ChimeraX session > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > open 4p19 4p19 title: Closed, apo inward-facing state of the glutamate transporter homologue GltPh [more info...] Chain information for 4p19 #5 --- Chain | Description | UniProt A B C | 425aa long hypothetical proton glutamate symport protein | O59010_PYRHO 1-417 Non-standard residues in 4p19 #5 --- HG — mercury (II) ion > color #5 darkgrey > mmaker #5/a:78-106,225-425 > matchmaker #5/a:78-106,225-425 Missing required ""to"" argument > mmaker #5/a:78-106,225-425 to #1 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 6x15.pdb, chain A (#1) with 4p19, chain A (#5), sequence alignment score = 1090 RMSD between 189 pruned atom pairs is 0.906 angstroms; (across all 224 pairs: 1.755) > hide #!5 models > hide #5 cartoons > show #!5 models > hide #5 atoms > show #5/a:90-94,405,310-314,344-363 > show #5/a:90-94,405,310-314,344-363 cartoons > show #5:92-93,405,311-314 atoms > color #!1,5 byhetero > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4 models > hide #!1 models > view 1 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" includeMaps true ——— End of log from Wed Oct 4 22:15:15 2023 ——— opened ChimeraX session > view 1 > windowsize 900 900 > ui tool show ""Side View"" > hie #5/b-c cartoon Unknown command: hie #5/b-c cartoon > hide #5/b-c cartoons > hide #5/b-c atoms > view 1 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > style #5 > cartoon style #5 1 Expected a keyword > cartoon style #5 width 1 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"" > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Structures_Maps/Node7-apo/J1136.pdb"" > ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Structures_Maps/Node7-apo/J1139.pdb"" Chain information for J1136.pdb #6 --- Chain | Description B | No description available Chain information for J1139.pdb #7 --- Chain | Description B | No description available > color #6 #00ff8cff > color #7 #00ff8cff > mmaker #6,7 to #5/a:78-106,225-425 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 4p19, chain A (#5) with J1136.pdb, chain B (#6), sequence alignment score = 780.1 RMSD between 188 pruned atom pairs is 0.951 angstroms; (across all 216 pairs: 1.642) Matchmaker 4p19, chain A (#5) with J1139.pdb, chain B (#7), sequence alignment score = 761.5 RMSD between 195 pruned atom pairs is 0.851 angstroms; (across all 216 pairs: 1.407) > hide #6-7 cartoons > hide #6-7 atoms > show #6-7:377,76-80,288-292,322-341 cartoons > cartoon style #6-7 width 1 > show #6-7:78-79,377,289-291 atoms [Repeated 1 time(s)] > hide H > color #!5-7 byhetero > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > open ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Structures_Maps/Node7-apo/J1140.pdb"" Chain information for J1140.pdb #8 --- Chain | Description B | No description available > mmaker #8 to #5/a:78-106,225-425 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 4p19, chain A (#5) with J1140.pdb, chain B (#8), sequence alignment score = 765.1 RMSD between 166 pruned atom pairs is 0.922 angstroms; (across all 216 pairs: 2.607) > hide #8 cartoons > hide #8 atoms > mmaker #8 to #5/a:78-106,225-425 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 4p19, chain A (#5) with J1140.pdb, chain B (#8), sequence alignment score = 765.1 RMSD between 166 pruned atom pairs is 0.922 angstroms; (across all 216 pairs: 2.607) > show #8:377,76-80,288-292,322-341 cartoons > color #8 #00ff8cff > cartoon style #8 width 1 > show #8:78-79,377,289-291 atoms > hide H > color #!5-8 byhetero > hide #!7 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > save /Users/kdr2001/Desktop/image20.png supersample 3 > hide #!8 models > show #!6 models > save /Users/kdr2001/Desktop/image21.png supersample 3 > hide #!6 models > show #!7 models > save /Users/kdr2001/Desktop/4p19_1139.png supersample 3 > hide #!5 models > show #!4 models > save /Users/kdr2001/Desktop/7ahk_1139.png supersample 3 > hide #!7 models > show #!6 models > save /Users/kdr2001/Desktop/7ahk_1136.png supersample 3 > hide #!6 models > hide #!4 models > show #!3 models > show #!6 models > save /Users/kdr2001/Desktop/6x12_1136.png supersample 3 > hide #!6 models > show #!7 models > save /Users/kdr2001/Desktop/6x12_1139.png supersample 3 > show #!1 models > hide #!1 models > show #!8 models > show #!6 models > hide #!8 models > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh_2.cxs"" > hide #!3 models > show #!5 models > hide #!7 models > save /Users/kdr2001/Desktop/4p19_1136.png supersample 3 > hide #!6 models > save /Users/kdr2001/Desktop/4p19.png supersample 3 > hide #!5 models > show #!4 models > save /Users/kdr2001/Desktop/7ahk.png supersample 3 > hide #!4 models > show #!3 models > save /Users/kdr2001/Desktop/6x12.png supersample 3 > show #!5 models > hide #!3 models > SHOW :310 ATOMS Unknown command: SHOW :310 ATOMS > show #5:310 atoms > view 1 > save /Users/kdr2001/Desktop/4p19.png supersample 3 > show #!6 models > save /Users/kdr2001/Desktop/4p19_1136.png supersample 3 > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > show #!6 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!6 models > show #6-7:288 > hide H > hide #!6 models > show #!6 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!5 models > view 1 > hide #!5 models > hide #!4 models > show #!5 models > show #!6 models > hide #1-5:314 > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > hide #!5 models > view 1 > save ""/Users/kdr2001/Dropbox/Krishna Cryo-EM > data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh_2.cxs"" ——— End of log from Wed Oct 4 22:55:57 2023 ——— opened ChimeraX session > show #!7 models > show #!8 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > show #!4 models > close #5 > close #3 > show #!2 models > hide #!2 models > close #2 > open ""/Users/kdr2001/Library/CloudStorage/OneDrive-med.cornell.edu/Olga > Boudker - Olga Boudker's files/Krishna-Olga-ASR/Farideh's map > model/NewClasses/ofs.pdb"" ofs.pdb title: Gltph In complex with L-aspartate and sodium ions In outward-facing state [more info...] Chain information for ofs.pdb #2 --- Chain | Description C | No description available > mmaker #2 to #4:225-309,364-425 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 7ahk (2).pdb, chain A (#4) with ofs.pdb, chain C (#2), sequence alignment score = 700.3 RMSD between 125 pruned atom pairs is 0.649 angstroms; (across all 138 pairs: 1.320) > mcopy Unknown command: mcopy > mcopy #4 toAtoms #2 Unknown command: mcopy #4 toAtoms #2 > toolshed show OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11C000EMLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 11 days, 12 hours, 20 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: D3218HN: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.1.11 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Structure Editing not a bug Tom Goddard all ChimeraX