id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7305 Basic Actions session save: 'QEventLoop' object has no attribute 'exec_' tent.tangpradabkul@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description I just recently installed Chimera X to my computer and when I tried to save the session, this error showed up and couldn't let me save the session. Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/tenttiya/Downloads/miniPTC-Feb8.cxs format session Not registering illegal selector name ""tRNA-interacting nucleotides"" Log from Tue Feb 8 17:23:45 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/sarahsmaga/Desktop/miniPTC-7k00.cxs format session registering illegal selector name ""tRNA-interacting nucleotides"" Log from Wed Jan 26 14:18:02 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs registering illegal selector name ""tRNA-interacting nucleotides"" Log from Thu Jan 20 17:59:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs Log from Thu Jan 20 10:12:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Updating list of available bundles failed: [Errno 61] Connection refused > open /Users/sarahsmaga/Downloads/Chimera/PDB/7K00.cif Summary of feedback from opening /Users/sarahsmaga/Downloads/Chimera/PDB/7K00.cif --- notes | Fetching CCD PAR from http://ligand- expo.rcsb.org/reports/P/PAR/PAR.cif Fetching CCD SPD from http://ligand-expo.rcsb.org/reports/S/SPD/SPD.cif Fetching CCD SPM from http://ligand-expo.rcsb.org/reports/S/SPM/SPM.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif Fetching CCD G7M from http://ligand-expo.rcsb.org/reports/G/G7M/G7M.cif Fetching CCD UR3 from http://ligand-expo.rcsb.org/reports/U/UR3/UR3.cif Fetching CCD MA6 from http://ligand-expo.rcsb.org/reports/M/MA6/MA6.cif Fetching CCD IAS from http://ligand-expo.rcsb.org/reports/I/IAS/IAS.cif Fetching CCD D2T from http://ligand-expo.rcsb.org/reports/D/D2T/D2T.cif Fetching CCD 1MG from http://ligand-expo.rcsb.org/reports/1/1MG/1MG.cif Fetching CCD 6MZ from http://ligand-expo.rcsb.org/reports/6/6MZ/6MZ.cif Fetching CCD 3TD from http://ligand-expo.rcsb.org/reports/3/3TD/3TD.cif Fetching CCD OMG from http://ligand-expo.rcsb.org/reports/O/OMG/OMG.cif Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif Fetching CCD OMC from http://ligand-expo.rcsb.org/reports/O/OMC/OMC.cif Fetching CCD 2MA from http://ligand-expo.rcsb.org/reports/2/2MA/2MA.cif Fetching CCD OMU from http://ligand-expo.rcsb.org/reports/O/OMU/OMU.cif Fetching CCD MEQ from http://ligand-expo.rcsb.org/reports/M/MEQ/MEQ.cif Fetching CCD 4D4 from http://ligand-expo.rcsb.org/reports/4/4D4/4D4.cif Fetching CCD MS6 from http://ligand-expo.rcsb.org/reports/M/MS6/MS6.cif 7K00.cif title: Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...] Chain information for 7K00.cif #1 --- Chain | Description 0 | 50S ribosomal protein L33 1 | 50S ribosomal protein L34 2 | 50S ribosomal protein L35 3 | 50S ribosomal protein L36 4 | 50S ribosomal protein L31 5 | E-site tRNA A | 16S rRNA B | 30S ribosomal protein S2 C | 30S ribosomal protein S3 D | 30S ribosomal protein S4 E | 30S ribosomal protein S5 F | 30S ribosomal protein S6 G | 30S ribosomal protein S7 H | 30S ribosomal protein S8 I | 30S ribosomal protein S9 J | 30S ribosomal protein S10 K | 30S ribosomal protein S11 L | 30S ribosomal protein S12 M | 30S ribosomal protein S13 N | 30S ribosomal protein S14 O | 30S ribosomal protein S15 P | 30S ribosomal protein S16 Q | 30S ribosomal protein S17 R | 30S ribosomal protein S18 S | 30S ribosomal protein S19 T | 30S ribosomal protein S20 U | 30S ribosomal protein S21 X | mRNA Y | A-site tRNA-val Z | P-site tRNA-fMet a | 23S rRNA b | 5S rRNA c | 50S ribosomal protein L2 d | 50S ribosomal protein L3 e | 50S ribosomal protein L4 f | 50S ribosomal protein L5 g | 50S ribosomal protein L6 h | 50S ribosomal protein L9 i | 50S ribosomal protein L13 j | 50S ribosomal protein L14 k | 50S ribosomal protein L15 l | 50S ribosomal protein L16 m | 50S ribosomal protein L17 n | 50S ribosomal protein L18 o | 50S ribosomal protein L19 p | 50S ribosomal protein L20 q | 50S ribosomal protein L21 r | 50S ribosomal protein L22 s | 50S ribosomal protein L23 t | 50S ribosomal protein L24 u | 50S ribosomal protein L25 v | 50S ribosomal protein L27 w | 50S ribosomal protein L28 x | 50S ribosomal protein L29 y | 50S ribosomal protein L30 z | 50S ribosomal protein L32 Non-standard residues in 7K00.cif #1 --- MG — magnesium ion MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin; monomycin A; neomycin E) SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) SPM — spermine ZN — zinc ion > sequence chain #1/a Alignment identifier is 1/a > select /a:2043 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2043-2098 1191 atoms, 1331 bonds, 2 pseudobonds, 56 residues, 2 models selected > select /a:2043 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2043-2625 10521 atoms, 11770 bonds, 501 pseudobonds, 491 residues, 3 models selected > name frozen miniPTC sel > select ~sel 138817 atoms, 142320 bonds, 5734 pseudobonds, 17228 residues, 4 models selected > hide (#!1 & sel) target a > select /a:2043 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2043-2064 475 atoms, 532 bonds, 22 residues, 1 model selected QGestureManager::deliverEvent: could not find the target for gesture > select /a:2043-2091,2228-2258, Expected an objects specifier or a keyword > select /a:2043-2091,2228-2258 1712 atoms, 1912 bonds, 48 pseudobonds, 80 residues, 2 models selected > select /a:2043-2091,2228-2258,2426-2625 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > name frozen miniPTC-cut sel > select ~sel 143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models selected > hide (#!1 & sel) target a > select /a:2470-2480 232 atoms, 258 bonds, 7 pseudobonds, 11 residues, 2 models selected > select /a:2470-2480, 2525-2535 473 atoms, 528 bonds, 11 pseudobonds, 22 residues, 2 models selected > color (#!1 & sel) red > color (#!1 & sel) hot pink > nucleotides sel atoms > style nucleic & sel stick Changed 473 atom styles > select 149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models selected > nucleotides sel atoms > style nucleic & sel stick Changed 97795 atom styles > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 97795 atom styles > nucleotides sel ladder > nucleotides sel ladder > nucleotides sel ladder > nucleotides sel ladder > style sel stick Changed 149338 atom styles > style sel stick Changed 149338 atom styles > hide sel atoms > style sel stick Changed 149338 atom styles > nucleotides sel ladder > nucleotides sel ladder > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 97795 atom styles > show sel atoms > show sel cartoons > show sel cartoons > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > select ~sel 143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models selected > hide (#!1 & sel) target a > cartoon hide (#!1 & sel) > show sel cartoons > select clear > save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs ——— End of log from Thu Jan 20 10:12:13 2022 ——— opened ChimeraX session > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > select ~sel 143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models selected > hide (#!1 & sel) target a > cartoon hide (#!1 & sel) > select /a:2252 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2252,2602 45 atoms, 49 bonds, 2 residues, 1 model selected > color sel cyan > select clear > lighting soft > save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs Drag select of 4311 atoms, 280 residues, 281 pseudobonds, 4739 bonds, 708 shapes > select clear > select /a:2590,2588.2618 Expected an objects specifier or a keyword > select /a:2590,2588,2618 68 atoms, 74 bonds, 3 residues, 1 model selected > select /a:2555,2553,2583 66 atoms, 71 bonds, 3 residues, 1 model selected > select /a:2555,2553,2583, 2585,2551,2552,2451 149 atoms, 161 bonds, 7 residues, 1 model selected > name frozen ""tRNA-interacting nucleotides"" sel registering illegal selector name ""tRNA-interacting nucleotides"" Drag select of 2013 atoms, 143 residues, 121 pseudobonds, 2208 bonds, 345 shapes > color (#!1 & sel) cornflower blue > select up 3090 atoms, 3443 bonds, 121 pseudobonds, 147 residues, 2 models selected > select up 3155 atoms, 3520 bonds, 121 pseudobonds, 147 residues, 2 models selected > select up 59130 atoms, 66225 bonds, 121 pseudobonds, 2753 residues, 2 models selected > select up 63520 atoms, 66364 bonds, 121 pseudobonds, 7004 residues, 2 models selected > select up 149338 atoms, 154090 bonds, 4727 pseudobonds, 17719 residues, 2 models selected > color (#!1 & sel) cornflower blue > select clear > select /a:2555,2553,2583, 2585,2551,2552,2451 149 atoms, 161 bonds, 7 residues, 1 model selected > name frozen tRNA-int sel > color sel hot pink > select clear > select /a:2471-2479,2527-2535 384 atoms, 428 bonds, 8 pseudobonds, 18 residues, 2 models selected > color (#!1 & sel) purple > select clear > ui tool show ""Basic Actions"" > show /X target c > show /X target c > show /X target c > show /X target c > hide /X target c > hide /X target c > show /Y target c > show /Y target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > show /Z target c > show /Z target c > color /Y #abd0c1 target abp > color /Y #abd0c1 target abp > color /Y #abd0c1 target c > color /Y #abd0c1 target c > color /Z #a5c7df target c > color /Z #a5c7df target c > select /Y:74-76 62 atoms, 68 bonds, 3 residues, 1 model selected > select /Y:74-76, Z:74-76 62 atoms, 68 bonds, 3 residues, 1 model selected > select /Y:74-76 / Z:74-76 124 atoms, 136 bonds, 6 residues, 1 model selected > name frozen CCAends sel > hide CCAends target abp > hide CCAends target abp > hide CCAends target abp > show sel atoms > hide /Y target c > hide /Y target c > hide /Y target c > show /Y target c > show /Y target c > show /Y target c > nucleotides sel atoms > style nucleic & sel stick Changed 124 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 124 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 124 atom styles > select /Y:74-76 62 atoms, 68 bonds, 3 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #abd0c1ff > select /Z:74-76 62 atoms, 68 bonds, 3 residues, 1 model selected > color sel #a5c7dfff > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c JS console(basic_actions.js:166:warning): Throttling navigation to prevent the browser from hanging. See https://crbug.com/882238. Command line switch --disable-ipc-flooding-protection can be used to bypass the protection > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Y target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c JS console(basic_actions.js:166:warning): Throttling navigation to prevent the browser from hanging. See https://crbug.com/882238. Command line switch --disable-ipc-flooding-protection can be used to bypass the protection > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > hide /Z target c > nucleotides sel atoms > style nucleic & sel stick Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > style sel stick Changed 62 atom styles > style sel stick Changed 62 atom styles > style sel ball Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > hide sel cartoons > show sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > style sel stick Changed 62 atom styles > style sel stick Changed 62 atom styles > style sel sphere Changed 62 atom styles > style sel ball Changed 62 atom styles > style sel stick Changed 62 atom styles > style sel stick Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 62 atom styles > select /Y:74-76 62 atoms, 68 bonds, 3 residues, 1 model selected > style sel stick Changed 62 atom styles > show sel cartoons > select tRNA-int 149 atoms, 161 bonds, 7 residues, 1 model selected > select up 59130 atoms, 66225 bonds, 2753 residues, 1 model selected > select up 63520 atoms, 66364 bonds, 7004 residues, 1 model selected > select down 59130 atoms, 66225 bonds, 2753 residues, 1 model selected > select down 149 atoms, 161 bonds, 7 residues, 1 model selected > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c > show /Y target c JS console(basic_actions.js:166:warning): Throttling navigation to prevent the browser from hanging. See https://crbug.com/882238. Command line switch --disable-ipc-flooding-protection can be used to bypass the protection > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > show /Z target c > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > show sel atoms > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > show sel atoms > nucleotides sel fill > style nucleic & sel stick Changed 1623 atom styles > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide 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target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp > hide /Z target abp JS console(basic_actions.js:166:warning): Throttling navigation to prevent the browser from hanging. See https://crbug.com/882238. Command line switch --disable-ipc-flooding-protection can be used to bypass the protection > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show sel atoms > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z target abp > show /Z 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#a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > nucleotides sel fill > style nucleic & sel stick Changed 1623 atom styles > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > color /Z #a5c7df target abp > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > show sel atoms > show sel atoms > hide sel atoms > hide sel atoms > hide sel cartoons > show sel cartoons > show sel atoms > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > color sel bynucleotide > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > color sel bychain > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select clear > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > show sel atoms > hide sel atoms > show sel atoms > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel tube/slab shape box > nucleotides sel atoms > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel slab > style nucleic & sel stick Changed 1579 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 1579 atom styles > save /Users/sarahsmaga/Desktop/miniPTC-ribosome.cxs ——— End of log from Thu Jan 20 17:59:07 2022 ——— opened ChimeraX session > save ""/Users/sarahsmaga/Desktop/mini PTC.pdb"" displayedOnly true relModel #1 > select clear Drag select of 13 atoms, 4 residues, 2 pseudobonds, 8 shapes, 20 bonds Drag select of 2 residues > select clear Drag select of 1 residues, 1 shapes > select clear > select :a 2552,2551 Expected a keyword > select :a 2552,2551 Expected a keyword > select :a/2552,2551 25586 atoms, 28274 bonds, 143 pseudobonds, 1163 residues, 2 models selected > select /a:2552,2551 41 atoms, 44 bonds, 2 residues, 1 model selected > select /a:2252,2251 47 atoms, 52 bonds, 2 residues, 1 model selected > select :a 25586 atoms, 28274 bonds, 143 pseudobonds, 1163 residues, 2 models selected > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected Drag select of 611 atoms, 44 residues, 38 pseudobonds, 110 shapes, 674 bonds > select clear > select tRNA-int 149 atoms, 161 bonds, 7 residues, 1 model selected > select tRNA-int 149 atoms, 161 bonds, 7 residues, 1 model selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > select :Y,Z Nothing selected > select /Y,Z 3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected > hide sel atoms > hide sel cartoons > hide sel cartoons Drag select of 1460 atoms, 112 residues, 78 pseudobonds, 1620 bonds, 255 shapes > color (#!1 & sel) cornflower blue > select clear > select /Y,Z 3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected > show sel cartoons > show sel atoms > hide sel cartoons > hide sel atoms > select /Y,Z:70-76 293 atoms, 325 bonds, 14 residues, 1 model selected > show sel atoms > style sel stick Changed 293 atom styles > style sel stick Changed 293 atom styles > style sel stick Changed 293 atom styles > style sel stick Changed 293 atom styles > style sel ball Changed 293 atom styles > style sel stick Changed 293 atom styles > select clear > select /Y,Z:70-76 293 atoms, 325 bonds, 14 residues, 1 model selected > select /Y:70-76 144 atoms, 159 bonds, 7 residues, 1 model selected > select /Z:70-76 149 atoms, 166 bonds, 7 residues, 1 model selected > color sel orange > color sel purple > select /Y:70-76 144 atoms, 159 bonds, 7 residues, 1 model selected > color sel light sea green > select clear Drag select of 108 atoms, 7 residues, 117 bonds, 21 shapes > select up 192 atoms, 213 bonds, 9 residues, 1 model selected > select up 59130 atoms, 66225 bonds, 2753 residues, 1 model selected > select down 192 atoms, 213 bonds, 9 residues, 1 model selected > select up 59130 atoms, 66225 bonds, 2753 residues, 1 model selected > select down 192 atoms, 213 bonds, 9 residues, 1 model selected Drag select of 288 atoms, 22 residues, 13 pseudobonds, 316 bonds, 52 shapes > color (#!1 & sel) cornflower blue > color (#!1 & sel) red > select clear > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select sel :< 5 634 atoms, 693 bonds, 13 pseudobonds, 32 residues, 2 models selected > select clear > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select sel :< 3 428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected > select sel :< 3 959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected > select clear > select /Y, Z 3234 atoms, 3577 bonds, 139 pseudobonds, 182 residues, 3 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > hide sel atoms > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > hide CCAends target abp > show CCAends target abp > select sel :< 3 428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected > color (#!1 & sel) light sea green > color (#!1 & sel) hot pink > color (#!1 & sel) magenta > select sel :< 3 959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected > select clear > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select /Y, Z:70-76 293 atoms, 325 bonds, 14 residues, 1 model selected > hide sel atoms > show sel atoms > select /Y, Expected an objects specifier or a keyword > select /Y 1592 atoms, 1764 bonds, 67 pseudobonds, 87 residues, 3 models selected > ui tool show ""Color Actions"" > color sel pale green > color sel aquamarine > select /Z 1642 atoms, 1813 bonds, 72 pseudobonds, 95 residues, 2 models selected > color sel plum > select clear > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select up 3202 atoms, 3577 bonds, 150 residues, 1 model selected > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select sel :< 3 428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected > select sel :< 3 959 atoms, 1025 bonds, 30 pseudobonds, 72 residues, 3 models selected > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select CCAends 124 atoms, 136 bonds, 6 residues, 1 model selected > select sel :< 3 428 atoms, 468 bonds, 12 pseudobonds, 21 residues, 2 models selected > select subtract CCAends 304 atoms, 332 bonds, 12 pseudobonds, 15 residues, 2 models selected > select subtract /Y 281 atoms, 307 bonds, 12 pseudobonds, 13 residues, 2 models selected > select subtract /Z 259 atoms, 282 bonds, 12 pseudobonds, 12 residues, 2 models selected > ui tool show ""Color Actions"" > color sel khaki > color sel goldenrod > color sel gold > select clear > show miniPTC target abp > hide miniPTC target abp > save /Users/sarahsmaga/Desktop/miniPTC-7k00.cxs ——— End of log from Wed Jan 26 14:18:02 2022 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain /a Alignment identifier is 1/a > select /a:2450 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2450 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2191-2317 2724 atoms, 3047 bonds, 79 pseudobonds, 127 residues, 2 models selected > select /a:2317 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2191-2317 2724 atoms, 3047 bonds, 79 pseudobonds, 127 residues, 2 models selected > select clear > select /a:2555 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2555 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2502-2503 46 atoms, 51 bonds, 2 residues, 1 model selected > select /a:2502-2517 339 atoms, 377 bonds, 16 residues, 1 model selected > select /a:2502-2517,2567-2593 922 atoms, 1029 bonds, 28 pseudobonds, 43 residues, 2 models selected > select /a:2502-2517,2567-2610 1286 atoms, 1436 bonds, 50 pseudobonds, 60 residues, 2 models selected > select clear > select a:2058-2079,2241-2258,2427-2463,2487-2522,2543-2609 Expected an objects specifier or a keyword > select /a:2058-2079,2241-2258,2427-2463,2487-2522,2543-2609 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > name frozen Yonath_A2P2 sel registering illegal selector name ""Yonath_A2P2"" > name frozen Yonath_A2P2 sel registering illegal selector name ""Yonath_A2P2"" > name frozen Yonath_A2P2 sel registering illegal selector name ""Yonath_A2P2"" > name frozen A2P2 sel > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > color (#!1 & sel) cornflower blue > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) purple > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > color (#!1 & sel) gray > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) cornflower blue > select clear > set bgColor white > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting simple > lighting simple > lighting flat > lighting soft > lighting simple > lighting soft > save /Users/sarahsmaga/Desktop/image21.png supersample 3 > save /Users/sarahsmaga/Downloads/miniPTC.cxs > set bgColor transparent > save /Users/sarahsmaga/Desktop/image22.png supersample 3 > set bg, transparent Expected a keyword > set bgColor Missing ""bgColor"" keyword's argument > set bgColor transparent > save /Users/sarahsmaga/Desktop/image23.png supersample 3 > set bgColor nonesparent Invalid ""bgColor"" argument: Invalid color name or specifier > set bgColor none Invalid ""bgColor"" argument: Invalid color name or specifier > set background color none Expected a keyword > set background none Expected a keyword > set bgColor none Invalid ""bgColor"" argument: Invalid color name or specifier > set bgtransparency Expected a keyword > set bgColor transparent > ui windowfill toggle > ui windowfill toggle > show #!1 target m > select #1 149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models selected > hide sel cartoons > show sel cartoons > select clear > select #1 149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models selected > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > select ~sel 143347 atoms, 147394 bonds, 5954 pseudobonds, 17439 residues, 4 models selected > hide sel cartoons > select clear > set bgColor white > select /a:2058-2075,2434-2463,2487-2522,2543-2609 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > name frozen A1P1 sel > name frozen A1P1 sel > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) gray > select miniPTC-cut 5991 atoms, 6696 bonds, 281 pseudobonds, 280 residues, 2 models selected > color (#!1 & sel) light gray > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) cornflower blue > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) light gray > select A1P1 3226 atoms, 3602 bonds, 147 pseudobonds, 151 residues, 2 models selected > color (#!1 & sel) cornflower blue > select clear > save /Users/sarahsmaga/Downloads/miniPTC-Feb8.cxs > select /a:2058-2075,2434-2463,2487-2517,2567-2609 2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected > name frozen A1P1 sel > name frozen A1P1 sel > name frozen A1P1 sel > select A2P2 3849 atoms, 4298 bonds, 169 pseudobonds, 180 residues, 2 models selected > color (#!1 & sel) light gray > select A1P1 2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected > color (#!1 & sel) cornflower blue > select /a:2058-2075,2434-2463,2487-2517,2567-2609 2612 atoms, 2917 bonds, 118 pseudobonds, 122 residues, 2 models selected > save /Users/sarahsmaga/Downloads/miniPTC-Feb8.cxs ——— End of log from Tue Feb 8 17:23:45 2022 ——— opened ChimeraX session > color miniPTC #d6d6d6 target c > select /a:2466 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2466-2468 62 atoms, 68 bonds, 3 residues, 1 model selected > select /a:2469 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2469 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2468-2469 44 atoms, 49 bonds, 2 residues, 1 model selected > select /a:2468-2472 112 atoms, 126 bonds, 5 residues, 1 model selected > select /a:2468 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2468 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2458 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2458 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2441 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2441 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2441 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2441,2458 43 atoms, 46 bonds, 2 residues, 1 model selected > select /a:2070,2441,2458 65 atoms, 70 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /a:2070,2441,2458 65 atoms, 70 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /a:2070,2083,2441,2458 88 atoms, 95 bonds, 2 pseudobonds, 4 residues, 2 models selected > select /a:2070,2083,2237,2441,2458 111 atoms, 120 bonds, 2 pseudobonds, 5 residues, 2 models selected > select /a:2070,2083,2237,2253-2254,2441,2458 154 atoms, 167 bonds, 2 pseudobonds, 7 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458 174 atoms, 188 bonds, 2 pseudobonds, 8 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2625 197 atoms, 213 bonds, 5 pseudobonds, 9 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:746,955,1911,1917,2457,2504,2580,2604-2605 180 atoms, 190 bonds, 9 residues, 1 model selected > select /a:746,955,1911,1917,2457,2504,2580,2604-2605 180 atoms, 190 bonds, 9 residues, 1 model selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625 283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625 283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625 283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625 283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2508,2625 283 atoms, 308 bonds, 5 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2509,2625 306 atoms, 334 bonds, 5 pseudobonds, 14 residues, 2 models selected > select /a:2516 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2516 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2516 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2516 22 atoms, 24 bonds, 1 residue, 1 model selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2625 240 atoms, 260 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2625 262 atoms, 284 bonds, 5 pseudobonds, 12 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625 282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected > name frozen PTC_1-1 sel [Repeated 1 time(s)] > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625 282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505-2506,2516,2568,2625 282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected > select /a:2504 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2504-2506 63 atoms, 69 bonds, 3 residues, 1 model selected > select /a:2508 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2506-2508 63 atoms, 69 bonds, 3 residues, 1 model selected > select /a:2505 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2505 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2505,2516-2517 65 atoms, 71 bonds, 3 residues, 1 model selected > select /a:2505 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2505-2506 43 atoms, 47 bonds, 2 residues, 1 model selected > select /a:2505-2506 43 atoms, 47 bonds, 2 residues, 1 model selected > select /a:2507-2508 43 atoms, 47 bonds, 2 residues, 1 model selected > select /a:2507-2510 86 atoms, 95 bonds, 4 residues, 1 model selected > select /a:2505,2507-2510 109 atoms, 120 bonds, 5 residues, 1 model selected > select /a:2510-2511 40 atoms, 43 bonds, 2 residues, 1 model selected > select /a:2507-2511 106 atoms, 117 bonds, 5 residues, 1 model selected > select /a:2508-2509 46 atoms, 51 bonds, 2 residues, 1 model selected > select /a:2508-2511 86 atoms, 95 bonds, 4 residues, 1 model selected > select /a:2506 20 atoms, 21 bonds, 1 residue, 1 model selected > select /a:2506-2508 63 atoms, 69 bonds, 3 residues, 1 model selected > select /a:2506-2507 40 atoms, 43 bonds, 2 residues, 1 model selected > select /a:2506-2508 63 atoms, 69 bonds, 3 residues, 1 model selected > select /a:2506-2507 40 atoms, 43 bonds, 2 residues, 1 model selected > select /a:2506-2508 63 atoms, 69 bonds, 3 residues, 1 model selected > select /a:2505 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2505 23 atoms, 25 bonds, 1 residue, 1 model selected > select /a:2505,2516 45 atoms, 49 bonds, 2 residues, 1 model selected > select /a:2505,2516,2625 68 atoms, 74 bonds, 3 residues, 1 model selected > select /a:2441,2505,2516,2625 88 atoms, 95 bonds, 4 residues, 1 model selected > select /a:2253-2254,2441,2505,2516,2625 131 atoms, 142 bonds, 6 residues, 1 model selected > select /a:2253-2254,2441,2458,2505,2516,2625 154 atoms, 167 bonds, 7 residues, 1 model selected > select /a:2237,2253-2254,2441,2458,2505,2516,2625 177 atoms, 192 bonds, 8 residues, 1 model selected > select /a:2083,2237,2253-2254,2441,2458,2505,2516,2625 200 atoms, 217 bonds, 9 residues, 1 model selected > select /a:2043,2083,2237,2253-2254,2441,2458,2505,2516,2625 220 atoms, 238 bonds, 3 pseudobonds, 10 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505,2516,2625 242 atoms, 262 bonds, 5 pseudobonds, 11 residues, 2 models selected > select /a:2043,2070,2083,2237,2253-2254,2441,2458,2505,2516,2568,2625 262 atoms, 283 bonds, 7 pseudobonds, 12 residues, 2 models selected > name frozen 1-1_mut sel Not registering illegal selector name ""1-1_mut"" > name frozen 1-1_mut sel Not registering illegal selector name ""1-1_mut"" > name frozen 1-1_mut sel Not registering illegal selector name ""1-1_mut"" > name frozen 1-1 sel Not registering illegal selector name ""1-1"" > name frozen 1-1 sel Not registering illegal selector name ""1-1"" > name frozen mut sel [Repeated 1 time(s)] > select mut 262 atoms, 283 bonds, 7 pseudobonds, 12 residues, 2 models selected > select PTC_1-1 282 atoms, 305 bonds, 7 pseudobonds, 13 residues, 2 models selected > save /Users/tenttiya/Desktop/1-1.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' Populating font family aliases took 294 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save /Users/tenttiya/Desktop/PTC_1-1.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 1 day 16:24 Graphics/Displays: Apple G13X: Chipset Model: Apple G13X Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 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: 1.2 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: 1.1.1 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Sessions duplicate Tom Goddard Eric Pettersen all ChimeraX