id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7758 Crash during application exit chimerax-bug-report@… Tom Goddard "{{{ 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 Last time you used ChimeraX it crashed. 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{ ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000020 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ { ""treatmentId"" : ""5b729754-3882-4560-826f-9c0bc27d77c6"", ""experimentId"" : ""6192fb082171a2330e561df0"", ""deploymentId"" : 400000035 } ] } } Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/palcon/Desktop/220909.cxs Log from Fri Sep 9 17:19:50 2022UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/palcon/Desktop/220909.cxs Log from Fri Sep 9 15:20:29 2022UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/palcon/Desktop/220909.cxs Log from Fri Sep 9 15:10:40 2022UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/palcon/Desktop/30T_29ds_30T.pdb Chain information for 30T_29ds_30T.pdb #1 --- Chain | Description ? | No description available > open /Users/palcon/Desktop/30T_overhang.pdb Chain information for 30T_overhang.pdb #2 --- Chain | Description ? | No description available > set bgColor white > hide #2 models > show #1 cartoons > show #1 surfaces > hide #!1 cartoons > select #1/?:129@C2' 1 atom, 1 residue, 1 model selected > select up 32 atoms, 34 bonds, 1 residue, 2 models selected > select up 4302 atoms, 4667 bonds, 135 residues, 2 models selected > color (#!1 & sel) orange > select clear > show #!1 cartoons > hide #!1 surfaces > select #1/?:62 32 atoms, 34 bonds, 1 residue, 1 model selected > select up 4302 atoms, 4667 bonds, 135 residues, 2 models selected > select down 32 atoms, 34 bonds, 1 residue, 2 models selected > select add #1/?:63 64 atoms, 67 bonds, 2 residues, 2 models selected > select add #1/?:64 94 atoms, 98 bonds, 3 residues, 2 models selected > select add #1/?:65 126 atoms, 131 bonds, 4 residues, 2 models selected > select add #1/?:60 224 atoms, 164 bonds, 7 residues, 2 models selected > select add #1/?:59 256 atoms, 197 bonds, 8 residues, 2 models selected > select add #1/?:58 288 atoms, 231 bonds, 9 residues, 2 models selected > select add #1/?:57 321 atoms, 266 bonds, 10 residues, 2 models selected > select add #1/?:56 354 atoms, 301 bonds, 11 residues, 2 models selected > select add #1/?:55 386 atoms, 335 bonds, 12 residues, 2 models selected > select add #1/?:54 416 atoms, 366 bonds, 13 residues, 2 models selected > select add #1/?:53 448 atoms, 399 bonds, 14 residues, 2 models selected > select add #1/?:52 478 atoms, 430 bonds, 15 residues, 2 models selected > select add #1/?:51 511 atoms, 465 bonds, 16 residues, 2 models selected > select add #1/?:49 573 atoms, 496 bonds, 18 residues, 2 models selected > select add #1/?:50 605 atoms, 529 bonds, 19 residues, 2 models selected > select add #1/?:48 638 atoms, 564 bonds, 20 residues, 2 models selected > select add #1/?:46 668 atoms, 595 bonds, 21 residues, 2 models selected > select add #1/?:44 733 atoms, 630 bonds, 23 residues, 2 models selected > select add #1/?:43 765 atoms, 664 bonds, 24 residues, 2 models selected > select add #1/?:42 797 atoms, 697 bonds, 25 residues, 2 models selected > select add #1/?:41 827 atoms, 728 bonds, 26 residues, 2 models selected > select add #1/?:40 859 atoms, 761 bonds, 27 residues, 2 models selected > select add #1/?:39 889 atoms, 792 bonds, 28 residues, 2 models selected > select add #1/?:38 921 atoms, 825 bonds, 29 residues, 2 models selected > select add #1/?:37 954 atoms, 860 bonds, 30 residues, 2 models selected > select add #1/?:36 986 atoms, 893 bonds, 31 residues, 2 models selected > select add #1/?:35 1018 atoms, 927 bonds, 32 residues, 2 models selected > select add #1/?:34 1051 atoms, 962 bonds, 33 residues, 2 models selected > select add #1/?:33 1081 atoms, 993 bonds, 34 residues, 2 models selected > select add #1/?:32 1113 atoms, 1026 bonds, 35 residues, 2 models selected > select add #1/?:31 1145 atoms, 1060 bonds, 36 residues, 2 models selected > color (#!1 & sel) yellow > select clear > show #!1 surfaces > lighting soft > lighting flat > lighting simple > lighting soft > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting full > graphics silhouettes false > lighting soft > show #2 models > hide #2 models > open /Users/palcon/Downloads/91881959ABD.pdb Chain information for 91881959ABD.pdb #3 --- Chain | Description ? | No description available > close #3 > open /Users/palcon/Downloads/16058187ABD.pdb Chain information for 16058187ABD.pdb #3 --- Chain | Description ? | No description available > hide #!1 models > select #3/?:466 32 atoms, 34 bonds, 1 residue, 1 model selected > select add #3/?:467 64 atoms, 67 bonds, 2 residues, 1 model selected > select add #3/?:468 94 atoms, 98 bonds, 3 residues, 1 model selected > select add #3/?:469 127 atoms, 133 bonds, 4 residues, 1 model selected > select add #3/?:470 159 atoms, 167 bonds, 5 residues, 1 model selected > select add #3/?:471 191 atoms, 200 bonds, 6 residues, 1 model selected > select add #3/?:473 255 atoms, 233 bonds, 8 residues, 1 model selected > select add #3/?:474 287 atoms, 267 bonds, 9 residues, 1 model selected > select add #3/?:475 317 atoms, 298 bonds, 10 residues, 1 model selected > select add #3/?:477 350 atoms, 333 bonds, 11 residues, 1 model selected > select add #3/?:476 382 atoms, 367 bonds, 12 residues, 1 model selected > select add #3/?:478 414 atoms, 401 bonds, 13 residues, 1 model selected > select add #3/?:479 446 atoms, 434 bonds, 14 residues, 1 model selected > select add #3/?:480 476 atoms, 465 bonds, 15 residues, 1 model selected > select add #3/?:481 508 atoms, 499 bonds, 16 residues, 1 model selected > select add #3/?:482 540 atoms, 533 bonds, 17 residues, 1 model selected > select add #3/?:483 572 atoms, 566 bonds, 18 residues, 1 model selected > select add #3/?:484 602 atoms, 597 bonds, 19 residues, 1 model selected > select add #3/?:485 632 atoms, 628 bonds, 20 residues, 1 model selected > select add #3/?:487 665 atoms, 663 bonds, 21 residues, 1 model selected > select add #3/?:486 697 atoms, 696 bonds, 22 residues, 1 model selected > select add #3/?:488 729 atoms, 730 bonds, 23 residues, 1 model selected > select add #3/?:489 762 atoms, 765 bonds, 24 residues, 1 model selected > select add #3/?:490 792 atoms, 796 bonds, 25 residues, 1 model selected > select add #3/?:491 824 atoms, 830 bonds, 26 residues, 1 model selected > select add #3/?:492 857 atoms, 865 bonds, 27 residues, 1 model selected > select add #3/?:493 887 atoms, 896 bonds, 28 residues, 1 model selected > select add #3/?:494 919 atoms, 929 bonds, 29 residues, 1 model selected > select add #3/?:495 952 atoms, 964 bonds, 30 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #3/?:165 32 atoms, 33 bonds, 1 residue, 1 model selected > select up 19121 atoms, 20618 bonds, 600 residues, 1 model selected > show sel surfaces > hide sel cartoons > show sel surfaces > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 16058187ABD.pdb #3/? DT 316 OP1 16058187ABD.pdb #3/? DT 316 OP2 16058187ABD.pdb #3/? DT 316 P Treating 5' terminal nucleic acids with phosphates as non-standard Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue DT (net charge -2) with am1-bcc method Running ANTECHAMBER command: /private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.in.mol2 -fi mol2 -o /var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.out.mol2 -fo mol2 -c bcc -nc -3 -j 5 -s 2 -dr n (DT) `` (DT) `Welcome to antechamber 20.0: molecular input file processor.` (DT) `` (DT) `Info: Finished reading file (/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/tmp859wzru7/ante.in.mol2); atoms read (39), bonds read (40).` (DT) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (DT) `Running: /private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (DT) `` (DT) `` (DT) `Running: /private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (DT) `Info: Total number of electrons: 200; net charge: -3` (DT) `` (DT) `Running: /private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (DT) `/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (DT) `Cannot properly run ""/private/var/folders/rw/fsvz2rbj7nvc3jvstr4g8_8c0000gq/T/AppTranslocation/C5AE9BC0-0479-4C32-8D2C-AA6CD24C9531/d/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue DT Check reply log for details > hide sel surfaces > show sel cartoons > hide sel atoms > show sel atoms > select clear > select #3/?:496 32 atoms, 33 bonds, 1 residue, 1 model selected > select add #3/?:497 62 atoms, 64 bonds, 2 residues, 2 models selected > select add #3/?:498 94 atoms, 97 bonds, 3 residues, 2 models selected > select add #3/?:499 126 atoms, 131 bonds, 4 residues, 2 models selected > select add #3/?:500 159 atoms, 166 bonds, 5 residues, 2 models selected > select add #3/?:501 191 atoms, 200 bonds, 6 residues, 2 models selected > select add #3/?:502 224 atoms, 235 bonds, 7 residues, 2 models selected > select add #3/?:505 288 atoms, 269 bonds, 9 residues, 2 models selected > select add #3/?:504 318 atoms, 300 bonds, 10 residues, 2 models selected > select add #3/?:506 350 atoms, 333 bonds, 11 residues, 2 models selected > select add #3/?:507 380 atoms, 364 bonds, 12 residues, 2 models selected > select add #3/?:510 477 atoms, 397 bonds, 15 residues, 2 models selected > select add #3/?:511 509 atoms, 431 bonds, 16 residues, 2 models selected > select add #3/?:513 541 atoms, 465 bonds, 17 residues, 2 models selected > select subtract #3/?:513 509 atoms, 431 bonds, 16 residues, 2 models selected > select add #3/?:512 541 atoms, 465 bonds, 17 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #3/?:465 30 atoms, 31 bonds, 1 residue, 1 model selected > select add #3/?:464 62 atoms, 65 bonds, 2 residues, 2 models selected > select add #3/?:463 95 atoms, 100 bonds, 3 residues, 2 models selected > select add #3/?:461 160 atoms, 135 bonds, 5 residues, 2 models selected > select add #3/?:460 192 atoms, 169 bonds, 6 residues, 2 models selected > select add #3/?:459 224 atoms, 202 bonds, 7 residues, 2 models selected > select add #3/?:458 254 atoms, 233 bonds, 8 residues, 2 models selected > select add #3/?:457 286 atoms, 266 bonds, 9 residues, 2 models selected > select add #3/?:456 319 atoms, 301 bonds, 10 residues, 2 models selected > select add #3/?:455 351 atoms, 334 bonds, 11 residues, 2 models selected > select add #3/?:454 381 atoms, 365 bonds, 12 residues, 2 models selected > select add #3/?:453 414 atoms, 400 bonds, 13 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/? Alignment identifier is 3/ > select #3/*:513 32 atoms, 34 bonds, 1 residue, 1 model selected > select #3/*:513-572 1920 atoms, 2099 bonds, 60 residues, 1 model selected > select #3/*:1 30 atoms, 31 bonds, 1 residue, 1 model selected > select #3/*:1-450 14327 atoms, 15389 bonds, 450 residues, 1 model selected > select #3/*:630 33 atoms, 35 bonds, 1 residue, 1 model selected > select #3/*:1-630 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected > select clear > select #3/*:1-2 62 atoms, 65 bonds, 2 residues, 1 model selected > select #3/*:1-450 14327 atoms, 15389 bonds, 450 residues, 1 model selected > select clear > select #3/*:1-2 62 atoms, 65 bonds, 2 residues, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > ui tool show ""Color Actions"" > color sel gold [Repeated 1 time(s)] > select clear > select #3/*:316-317 62 atoms, 65 bonds, 2 residues, 1 model selected > select #3/*:316-630 8060 atoms, 8751 bonds, 1 pseudobond, 253 residues, 2 models selected > color sel yellow > show sel surfaces Drag select of 16058187ABD.pdb_ SES surface, 56091 of 1862060 triangles, 38 residues, 72 shapes > select up 18104 atoms, 19519 bonds, 568 residues, 2 models selected > select up 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 3 models selected > select up 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 3 models selected > show sel surfaces > hide sel cartoons > select clear > lighting soft > lighting full > lighting soft > lighting full > hide #!3 surfaces > show #!3 cartoons > nucleotides #!3 tube/slab shape box > lighting soft > graphics silhouettes true > graphics silhouettes false > select #3/*:316 30 atoms, 31 bonds, 1 residue, 1 model selected > select #3/*:316-630 8060 atoms, 8751 bonds, 1 pseudobond, 253 residues, 2 models selected > color sel gold > select #3/*:315 33 atoms, 35 bonds, 1 residue, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > color sel orange > select clear > select #3/*:315 33 atoms, 35 bonds, 1 residue, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > color sel khaki > select clear > show #!3 surfaces > hide #!3 cartoons > lighting soft > lighting full > ~hbonds > interfaces #!3 & ~solvent 0 buried areas: > color #!3 bypolymer > undo > nucleotides #!3 ladder > hide #!3 surfaces > show #!3 cartoons > nucleotides #!3 fill > style nucleic & #!3 stick Changed 18104 atom styles > hide #!3 atoms [Repeated 1 time(s)] > show #!3 atoms > hide #!3 atoms > nucleotides #!3 fill > style nucleic & #!3 stick Changed 18104 atom styles > nucleotides #!3 fill > style nucleic & #!3 stick Changed 18104 atom styles > nucleotides #!3 ladder > cartoon style width 4 thickness 1 > cartoon style width 3 thickness 1.5 > cartoon style width 5 thickness 1.5 > cartoon style width 5 thickness 1 > show #!3 atoms > cartoon style width 5 thickness 1 > cartoon style width 4 thickness 1 > cartoon style width 4 thickness 0.5 > select #3/*:315 33 atoms, 35 bonds, 1 residue, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > ui tool show ""Color Actions"" > color sel wheat > color sel navajo white > select clear > select #3/*:209-315 3406 atoms, 3672 bonds, 107 residues, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > color sel gold > select clear > select #3/*:1 30 atoms, 31 bonds, 1 residue, 1 model selected > select #3/*:1-312 9947 atoms, 10663 bonds, 312 residues, 1 model selected > select #3/*:315 33 atoms, 35 bonds, 1 residue, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > color sel sandy brown > color sel light salmon > select clear > select #3/*:161-315 4933 atoms, 5317 bonds, 155 residues, 1 model selected > select #3/*:1-315 10044 atoms, 10768 bonds, 315 residues, 1 model selected > color sel orange > select clear > hide #!3 atoms > open /Users/palcon/6vad.pdb 6vad.pdb title: Fanconi anemia id complex [more info...] Chain information for 6vad.pdb #4 --- Chain | Description | UniProt A | fanconi anemia, complementation group I | B7ZMF2_HUMAN B | protein FACD2 | FACD2_HUMAN > select add #3 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected > select subtract #3 1 model selected > hide #!3 models > select add #3 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected > select subtract #3 1 model selected > select #4/B:463 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 321 atoms, 326 bonds, 19 residues, 1 model selected > select up 4015 atoms, 4046 bonds, 251 residues, 1 model selected > select up 4120 atoms, 4150 bonds, 258 residues, 1 model selected > select up 8607 atoms, 8677 bonds, 537 residues, 1 model selected > select up 8643 atoms, 8712 bonds, 539 residues, 1 model selected > select up 9875 atoms, 9954 bonds, 614 residues, 1 model selected > select up 18734 atoms, 18908 bonds, 1153 residues, 1 model selected > select up 37613 atoms, 37931 bonds, 2321 residues, 1 model selected > select down 18734 atoms, 18908 bonds, 1153 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > color sel light sea green > color sel dark turquoise > color sel steel blue > color sel cornflower blue > select clear > select #4/B:963 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 330 atoms, 332 bonds, 20 residues, 1 model selected > select up 356 atoms, 358 bonds, 22 residues, 1 model selected > select up 492 atoms, 494 bonds, 30 residues, 1 model selected > select up 878 atoms, 886 bonds, 53 residues, 1 model selected > select up 18734 atoms, 18908 bonds, 1153 residues, 1 model selected > select up 37613 atoms, 37931 bonds, 2321 residues, 1 model selected > select down 18734 atoms, 18908 bonds, 1153 residues, 1 model selected > color sel sky blue > color sel powder blue > color sel light blue > color sel pale turquoise > color sel light steel blue > select clear > select #4/A:240 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 394 atoms, 396 bonds, 25 residues, 1 model selected > select up 1588 atoms, 1600 bonds, 99 residues, 1 model selected > select up 1689 atoms, 1701 bonds, 105 residues, 1 model selected > select up 3902 atoms, 3925 bonds, 245 residues, 1 model selected > select up 18879 atoms, 19023 bonds, 1168 residues, 1 model selected > select up 37613 atoms, 37931 bonds, 2321 residues, 1 model selected > select down 18879 atoms, 19023 bonds, 1168 residues, 1 model selected > color sel misty rose > color sel pink > color sel light pink [Repeated 1 time(s)] > select clear > cartoon style width 4 thickness 0.5 > cartoon style width 4 thickness 1 > cartoon style width 3 thickness 1 > lighting soft > cartoon style width 5 thickness 1 > cartoon style width 4 thickness 1 > show #!3 models > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > ui mousemode right ""translate selected models"" Drag select of 306 residues, 3 pseudobonds > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.57621,0.53103,-0.62127,75.31,0.21709,0.6334,0.74275,-85.916,0.78794,-0.56286,0.24969,72.463 Drag select of 611 residues, 3 pseudobonds > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.57621,0.53103,-0.62127,-75.512,0.21709,0.6334,0.74275,-202.15,0.78794,-0.56286,0.24969,135.23 > view matrix models > #4,0.87798,-0.14383,-0.45657,-48.57,0.05193,0.97678,-0.20785,-90.829,0.47587,0.15878,0.86507,-7.7479 > view matrix models > #4,0.7877,0.10953,-0.60625,-49.458,0.015793,0.98015,0.19761,-143.86,0.61586,-0.16523,0.77033,30.621 > view matrix models > #4,0.73508,0.28865,-0.61347,-65.714,-0.016571,0.91222,0.40936,-159.99,0.67778,-0.29074,0.67534,52.687 > view matrix models > #4,0.18475,0.34588,-0.91991,48.337,-0.43716,0.86725,0.23828,-69.542,0.8802,0.35812,0.31143,-14.09 > view matrix models > #4,0.42227,-0.45645,-0.78316,106.04,-0.20567,0.79319,-0.5732,23.242,0.88283,0.40312,0.24106,-10.672 > view matrix models > #4,0.42227,-0.45645,-0.78316,117.07,-0.20567,0.79319,-0.5732,31.329,0.88283,0.40312,0.24106,-12.115 > view matrix models > #4,0.44251,-0.33887,-0.83028,104.63,-0.3772,0.76964,-0.51515,50.746,0.81358,0.54114,0.21275,-17.316 > view matrix models > #4,0.44251,-0.33887,-0.83028,114.11,-0.3772,0.76964,-0.51515,41.285,0.81358,0.54114,0.21275,-16.149 > view matrix models > #4,0.19957,-0.60072,-0.77415,176.93,-0.4871,0.62469,-0.61032,90.527,0.85024,0.49889,-0.16794,38.659 > view matrix models > #4,0.13962,-0.64055,-0.75511,188.27,-0.40213,0.66019,-0.63438,76.946,0.90487,0.39223,-0.16541,45.274 > view matrix models > #4,0.13962,-0.64055,-0.75511,198.74,-0.40213,0.66019,-0.63438,69.104,0.90487,0.39223,-0.16541,44.639 > view matrix models > #4,0.11706,-0.65133,-0.74971,202.68,-0.42301,0.65029,-0.63101,72.965,0.89853,0.391,-0.1994,50.55 > view matrix models > #4,0.11706,-0.65133,-0.74971,207.21,-0.42301,0.65029,-0.63101,75.564,0.89853,0.391,-0.1994,51.057 > view matrix models > #4,0.18868,-0.61474,-0.76583,194.24,-0.33916,0.69106,-0.63828,59.021,0.92161,0.38017,-0.078107,32.005 > ui tool show ""Side View"" > select clear > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.15719,-0.62854,-0.76173,200.05,-0.33085,0.69323,-0.64029,57.825,0.9305,0.35267,-0.098984,37.515 > view matrix models > #4,0.15719,-0.62854,-0.76173,201.47,-0.33085,0.69323,-0.64029,53.888,0.9305,0.35267,-0.098984,37.535 > view matrix models > #4,0.15719,-0.62854,-0.76173,199.54,-0.33085,0.69323,-0.64029,52.688,0.9305,0.35267,-0.098984,39.349 > view matrix models > #4,0.20568,-0.64645,-0.73471,191.27,-0.30865,0.66959,-0.67556,57.816,0.92867,0.36572,-0.061808,32.513 > view matrix models > #4,0.22322,-0.59839,-0.76948,187.07,-0.25462,0.7262,-0.6386,37.033,0.94093,0.33847,0.0097396,24.354 > view matrix models > #4,0.11707,-0.64045,-0.75902,206.52,-0.29338,0.70787,-0.64254,45.648,0.9488,0.29791,-0.10502,45.178 > select clear > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.12564,-0.66907,-0.7325,205.48,-0.28222,0.68374,-0.67294,51.724,0.95109,0.29128,-0.10293,45.471 > view matrix models > #4,0.095677,-0.56234,-0.82135,207.63,-0.32308,0.76292,-0.55997,30.509,0.94152,0.31893,-0.10869,43.826 > view matrix models > #4,0.22268,-0.51378,-0.82852,183.85,-0.22128,0.80104,-0.55621,10.209,0.94945,0.30719,0.064684,19.647 > view matrix models > #4,0.22268,-0.51378,-0.82852,179,-0.22128,0.80104,-0.55621,6.2715,0.94945,0.30719,0.064684,18.487 > view matrix models > #4,0.22268,-0.51378,-0.82852,179.22,-0.22128,0.80104,-0.55621,9.5465,0.94945,0.30719,0.064684,18.462 > view matrix models > #4,0.051693,-0.5639,-0.82422,209.88,-0.32784,0.77001,-0.54737,27.751,0.94332,0.29851,-0.14506,50.389 > select clear > open /Users/palcon/Downloads/Chimera/PDB/6VAE.pdb 6VAE.pdb title: Mono-ubiquitinated fanconi anemia id complex bound to icl DNA [more info...] Chain information for 6VAE.pdb #5 --- Chain | Description | UniProt A | fanconi anemia, complementation group I | B7ZMF2_HUMAN B | protein FACD2 | FACD2_HUMAN C D | ubiquitin | UBC_HUMAN S | DNA (29-mer) | T | DNA (29-mer) | > select add #5 42474 atoms, 42951 bonds, 19 pseudobonds, 2563 residues, 2 models selected > show sel cartoons > hide sel surfaces > hide sel atoms > cartoon style width 4 thickness 1 > select clear > select #5/S:19 33 atoms, 35 bonds, 1 residue, 1 model selected > select up 923 atoms, 995 bonds, 29 residues, 1 model selected > select up 42474 atoms, 42951 bonds, 2563 residues, 1 model selected > select down 923 atoms, 995 bonds, 29 residues, 1 model selected > delete atoms sel > delete bonds sel > select #5/T:32 32 atoms, 34 bonds, 1 residue, 1 model selected > select up 917 atoms, 988 bonds, 29 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #5/D:14 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 81 atoms, 80 bonds, 5 residues, 1 model selected > select up 1231 atoms, 1237 bonds, 76 residues, 1 model selected > hide sel cartoons > select clear > select #5/C:58 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 77 atoms, 77 bonds, 5 residues, 1 model selected > select up 1231 atoms, 1237 bonds, 76 residues, 1 model selected > hide sel cartoons > select clear > select #5/B:1023 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 483 atoms, 489 bonds, 30 residues, 1 model selected > select up 609 atoms, 617 bonds, 37 residues, 1 model selected > select up 18808 atoms, 18983 bonds, 1155 residues, 1 model selected > select up 40634 atoms, 40968 bonds, 2505 residues, 1 model selected > select down 18808 atoms, 18983 bonds, 1155 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light blue > select clear > select #5/B:810 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 500 atoms, 502 bonds, 29 residues, 1 model selected > select up 1892 atoms, 1912 bonds, 116 residues, 1 model selected > select up 1911 atoms, 1930 bonds, 117 residues, 1 model selected > select up 2414 atoms, 2440 bonds, 147 residues, 1 model selected > select up 2433 atoms, 2458 bonds, 148 residues, 1 model selected > select up 2770 atoms, 2798 bonds, 169 residues, 1 model selected > select up 18808 atoms, 18983 bonds, 1155 residues, 1 model selected > select up 40634 atoms, 40968 bonds, 2505 residues, 1 model selected > select down 18808 atoms, 18983 bonds, 1155 residues, 1 model selected > color sel sky blue > color sel light steel blue [Repeated 2 time(s)] > select clear > select #5/A:1054 18 atoms, 18 bonds, 1 residue, 1 model selected > select up 270 atoms, 272 bonds, 17 residues, 1 model selected > select up 2620 atoms, 2639 bonds, 162 residues, 1 model selected > select up 2639 atoms, 2657 bonds, 163 residues, 1 model selected > select up 6455 atoms, 6502 bonds, 401 residues, 1 model selected > select up 6488 atoms, 6535 bonds, 403 residues, 1 model selected > select up 8239 atoms, 8303 bonds, 511 residues, 1 model selected > select up 8296 atoms, 8359 bonds, 514 residues, 1 model selected > select up 10592 atoms, 10673 bonds, 654 residues, 1 model selected > select up 10692 atoms, 10773 bonds, 660 residues, 1 model selected > select up 12876 atoms, 12977 bonds, 794 residues, 1 model selected > select up 19364 atoms, 19509 bonds, 1198 residues, 1 model selected > select up 40634 atoms, 40968 bonds, 2505 residues, 1 model selected > select down 19364 atoms, 19509 bonds, 1198 residues, 1 model selected > color sel light pink > select clear > select add #5 40634 atoms, 40968 bonds, 19 pseudobonds, 2505 residues, 2 models selected > view matrix models #5,1,0,0,-108.24,0,1,0,-150.04,0,0,1,211 > view matrix models > #5,0.97897,-0.0043194,-0.20396,-77.928,-0.045164,0.97038,-0.23733,-108.65,0.19894,0.24155,0.94978,158.04 > view matrix models > #5,0.99573,0.0042728,-0.092249,-96.08,-0.014328,0.99398,-0.10861,-132.97,0.09123,0.10947,0.98979,185.2 > view matrix models > #5,0.88898,-0.086369,-0.44974,-22.263,-0.17487,0.84362,-0.50767,-38.324,0.42325,0.52995,0.73485,117.02 > view matrix models > #5,0.84799,-0.12855,-0.51418,-2.5208,-0.22912,0.78589,-0.57435,-14.39,0.47792,0.60485,0.63698,112.39 > view matrix models > #5,0.92811,-0.04802,-0.3692,-43.359,-0.12114,0.89874,-0.42142,-64.416,0.35205,0.43585,0.82831,127.06 > view matrix models > #5,0.92811,-0.04802,-0.3692,-55.108,-0.12114,0.89874,-0.42142,-66.012,0.35205,0.43585,0.82831,165.08 > view matrix models > #5,0.5072,0.62438,-0.59405,-59.222,0.74723,-0.66204,-0.057858,-20.868,-0.42941,-0.41454,-0.80235,600.71 > view matrix models > #5,0.75885,-0.0079621,-0.65122,-0.41009,0.38911,-0.7963,0.46315,-22.859,-0.52225,-0.60485,-0.60117,612.48 > view matrix models > #5,0.76688,-0.6085,0.20403,-33.113,-0.63496,-0.67311,0.37914,110.38,-0.093373,-0.4203,-0.90257,569.15 > view matrix models > #5,0.86185,-0.42224,-0.28093,-7.2276,-0.19533,-0.78756,0.58447,39.187,-0.46804,-0.44885,-0.76123,605.16 > view matrix models > #5,0.24553,-0.62499,0.74101,-30.986,0.14681,-0.73162,-0.66572,150.01,0.95821,0.27224,-0.08788,225.75 > view matrix models > #5,0.54076,-0.23901,0.80651,-131.75,0.015185,-0.95585,-0.29345,149.07,0.84104,0.17093,-0.51326,311.37 > view matrix models > #5,0.25969,-0.17326,0.95002,-121.45,-0.19929,-0.97221,-0.12283,157.87,0.9449,-0.15744,-0.287,311.81 > view matrix models > #5,0.6109,-0.60386,0.51201,-53.183,-0.78396,-0.55164,0.28477,126.61,0.11048,-0.57536,-0.8104,550.31 > view matrix models > #5,-0.072647,-0.58951,0.80449,-1.0165,-0.73953,-0.50937,-0.44004,210.39,0.6692,-0.62691,-0.39896,427.33 > view matrix models > #5,-0.51259,-0.62209,0.59182,91.037,-0.48058,-0.36331,-0.79815,202.76,0.71154,-0.69354,-0.11274,392.87 > view matrix models > #5,-0.78248,-0.6226,0.0098847,204.37,-0.022222,0.012056,-0.99968,116.51,0.62229,-0.78244,-0.023269,405.18 > view matrix models > #5,-0.90908,-0.40424,0.10081,180.06,-0.18337,0.17094,-0.96807,112.73,0.3741,-0.89854,-0.22952,481.67 > view matrix models > #5,-0.90908,-0.40424,0.10081,191.4,-0.18337,0.17094,-0.96807,123.24,0.3741,-0.89854,-0.22952,485.93 > view matrix models > #5,-0.91729,-0.38322,0.10832,188.69,-0.1595,0.10431,-0.98167,130.79,0.36489,-0.91775,-0.1568,480.19 > view matrix models > #5,-0.91729,-0.38322,0.10832,184.59,-0.1595,0.10431,-0.98167,141.58,0.36489,-0.91775,-0.1568,481.03 > hide #!4 models > view matrix models > #5,-0.91729,-0.38322,0.10832,187.15,-0.1595,0.10431,-0.98167,145.61,0.36489,-0.91775,-0.1568,480.56 > view matrix models > #5,-0.95979,-0.21713,0.17792,161.31,-0.22729,0.22909,-0.9465,133.32,0.16476,-0.94888,-0.26923,526.71 > show #!4 models > select clear > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.051693,-0.5639,-0.82422,206.51,-0.32784,0.77001,-0.54737,26.763,0.94332,0.29851,-0.14506,-61.211 > select clear > select add #5 40634 atoms, 40968 bonds, 19 pseudobonds, 2505 residues, 2 models selected > view matrix models > #5,-0.95979,-0.21713,0.17792,157.47,-0.22729,0.22909,-0.9465,137.34,0.16476,-0.94888,-0.26923,524.99 > view matrix models > #5,-0.96153,-0.21415,0.17207,158.08,-0.22121,0.23217,-0.94719,136.19,0.16289,-0.94881,-0.27061,525.42 > view matrix models > #5,-0.96333,-0.2172,0.15757,160.64,-0.20731,0.22957,-0.95096,135.15,0.17037,-0.94875,-0.26618,523.81 > view matrix models > #5,-0.94297,-0.23466,0.23609,149.89,-0.28603,0.20844,-0.93528,146.61,0.17026,-0.94947,-0.26367,523.59 > view matrix models > #5,-0.93947,-0.25247,0.23165,152.41,-0.29012,0.22641,-0.92982,144.02,0.18231,-0.94074,-0.28595,523.72 > select clear > scene one Unknown command: scene one > scene save one Unknown command: scene save one > save scene one Cannot determine format for 'scene' > scene one save Unknown command: scene one save > savepos one Unknown command: savepos one > ~savepos one Unknown command: ~savepos one > savepos one Unknown command: savepos one > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > toolshed show > save position one Cannot determine format for 'position' > save pos one Cannot determine format for 'pos' > savepos one Unknown command: savepos one > save positions 5 one Cannot determine format for 'positions' > save position 5 one Cannot determine format for 'position' > savepos #5 one Unknown command: savepos #5 one > view name pos1 > select add #3 18104 atoms, 19519 bonds, 1 pseudobond, 568 residues, 2 models selected > select subtract #3 1 model selected > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.051693,-0.5639,-0.82422,206.8,-0.32784,0.77001,-0.54737,26.154,0.94332,0.29851,-0.14506,69.854 > view matrix models > #4,0.051693,-0.5639,-0.82422,206.39,-0.32784,0.77001,-0.54737,25.835,0.94332,0.29851,-0.14506,70.894 > view name pos2 > view pos1 > view list Named views: pos1, pos2 > select clear > fly pos1 10 pos2 10 pos1 > fly pos1 20 pos2 20 pos1 > wait wait requires a frame count argument unless motion is in progress > fly pos1 20 pos2 20 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 pos2 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 2 pos2 2 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 4 pos2 4 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 1 pos2 1 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 1 pos2 1 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 100 pos2 1 pos1 > wait [Repeated 1 time(s)] wait requires a frame count argument unless motion is in progress > fly pos1 0 pos2 1 pos1 > wait > fly pos1 1 pos2 1 pos1 > wait > fly pos1 1 pos2 1 pos1 [Repeated 1 time(s)] > move pos1 1 pos2 1 pos1 Missing or invalid ""axis"" argument: Expected 3 floats or ""x"", or ""y"", or ""z"" or two atoms > move pos1 pos2 1 pos1 Missing or invalid ""axis"" argument: Expected 3 floats or ""x"", or ""y"", or ""z"" or two atoms > fly pos1 pos2 1 pos1 > fly 2 pos1 pos2 pos1 > fly 5 pos1 pos2 pos1 [Repeated 1 time(s)] > movie encode 220909_1.mp4 quality medium No frames have been recorded > movie record > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie encoding failed because no images were recorded. > movie record > fly 5 pos1 pos2 pos1 > movie encode 09052022.mp4 quality medium Movie encoding failed because no images were recorded. > movie record > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie encoding failed because no images were recorded. > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie encoding failed because no images were recorded. > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie encoding failed because no images were recorded. > movie record > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie encoding failed because no images were recorded. > movie record > fly 5 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > fly 5 pos1 pos2 pos1 > movie record > fly 25 pos1 pos2 pos1 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > hide #!5 models > view matrix models > #4,0.051693,-0.5639,-0.82422,198.42,-0.32784,0.77001,-0.54737,23.336,0.94332,0.29851,-0.14506,48.901 > view name topbound > view matrix models > #4,0.051693,-0.5639,-0.82422,199.63,-0.32784,0.77001,-0.54737,24.712,0.94332,0.29851,-0.14506,22.476 > view name topbound [Repeated 1 time(s)] > view matrix models > #4,0.051693,-0.5639,-0.82422,276.06,-0.32784,0.77001,-0.54737,-33.248,0.94332,0.29851,-0.14506,21.558 > view matrix models > #4,0.41359,-0.55085,-0.72492,208.6,0.40148,0.82496,-0.39781,-165.97,0.81716,-0.12652,0.56235,-2.3771 > view matrix models > #4,0.20234,-0.4547,-0.86736,245.65,0.5633,0.77854,-0.27672,-199.82,0.8011,-0.43259,0.41366,63.41 > view matrix models > #4,0.14822,-0.47073,-0.86974,255.91,0.53306,0.77878,-0.33066,-187.88,0.83299,-0.41462,0.36636,63.115 > view name topunbound > fly 5 topunbound topbound > view topunbound > fly 25 topunbound topbound > view topbound > view matrix models > #4,-0.063015,0.63062,-0.77353,43.522,-0.28977,0.73012,0.61884,-141.18,0.95502,0.26314,0.13672,-14.405 > view sidebound Expected an objects specifier or a view name or a keyword > view name sidebound > view topunbound > fly 25 topunbound sidebound > view matrix models > #4,-0.063015,0.63062,-0.77353,41.255,-0.28977,0.73012,0.61884,-150.38,0.95502,0.26314,0.13672,111.3 > view name sidebound1 > view matrix models > #4,-0.47145,0.03421,-0.88123,197.23,-0.88161,-0.043372,0.46997,62.065,-0.022142,0.99847,0.050608,160.97 > view sidebound1 > view matrix models > #4,-0.063015,0.63062,-0.77353,49.82,-0.28977,0.73012,0.61884,-138.76,0.95502,0.26314,0.13672,-97.318 > view sidebound2 Expected an objects specifier or a view name or a keyword > view name sidebound2 > view matrix models > #4,-0.063015,0.63062,-0.77353,49.239,-0.28977,0.73012,0.61884,-140.77,0.95502,0.26314,0.13672,-69.066 > view sidebound2 > view matrix models > #4,-0.063015,0.63062,-0.77353,51.374,-0.28977,0.73012,0.61884,-137.54,0.95502,0.26314,0.13672,-124.94 > view sidebound2 > view matrix models > #4,-0.063015,0.63062,-0.77353,49.318,-0.28977,0.73012,0.61884,-138.38,0.95502,0.26314,0.13672,-97.315 > view name zoomout1 > view matrix models > #4,-0.063015,0.63062,-0.77353,42.352,-0.28977,0.73012,0.61884,-144.13,0.95502,0.26314,0.13672,29.852 > view name zoomout2 > view matrix models > #4,-0.063015,0.63062,-0.77353,46.352,-0.28977,0.73012,0.61884,-142.05,0.95502,0.26314,0.13672,-29.044 > view name zoomout3 > view zoomout1 > view matrix models > #4,0.36379,-0.50386,-0.78344,146.89,0.11946,0.85936,-0.49722,-55.669,0.92379,0.087291,0.37282,-102.15 > view matrix models > #4,0.36379,-0.50386,-0.78344,147.65,0.11946,0.85936,-0.49722,-49.095,0.92379,0.087291,0.37282,-101.8 > view matrix models > #4,0.44154,-0.48644,-0.75394,129.97,-0.15782,0.78508,-0.59896,15.139,0.88325,0.38345,0.26987,-122.34 > view matrix models > #4,0.44154,-0.48644,-0.75394,133.96,-0.15782,0.78508,-0.59896,22.885,0.88325,0.38345,0.26987,-121.87 > view matrix models > #4,0.35847,-0.5122,-0.78048,153.13,-0.20533,0.77231,-0.60115,31.729,0.91068,0.37575,0.17168,-110.74 > view matrix models > #4,0.35847,-0.5122,-0.78048,151.59,-0.20533,0.77231,-0.60115,30.457,0.91068,0.37575,0.17168,-110.73 > view matrix models > #4,0.32744,-0.52591,-0.78498,158.55,-0.22564,0.76322,-0.60546,35.218,0.91754,0.37537,0.13124,-105.9 > view matrix models > #4,0.32744,-0.52591,-0.78498,156.26,-0.22564,0.76322,-0.60546,31.044,0.91754,0.37537,0.13124,-105.91 > view name zoomout1 > view matrix models > #4,0.32744,-0.52591,-0.78498,150.88,-0.22564,0.76322,-0.60546,15.207,0.91754,0.37537,0.13124,119.26 > view matrix models > #4,0.30555,-0.55367,-0.77465,156.36,-0.24922,0.7387,-0.62627,24.919,0.91898,0.38442,0.08772,123.99 > view name zoomout2 > view matrix models > #4,0.30555,-0.55367,-0.77465,162.46,-0.24922,0.7387,-0.62627,29.586,0.91898,0.38442,0.08772,16.172 > view matrix models > #4,0.30688,-0.56977,-0.76236,162.75,-0.24551,0.72651,-0.6418,32.953,0.91954,0.38412,0.083069,16.795 > view matrix models > #4,0.25299,-0.58584,-0.76993,173.72,-0.20328,0.74586,-0.63432,23.199,0.94587,0.31699,0.069609,24.248 > view name zoomout3 > view name zoomout4 > show #!5 models > hide #!5 models > view matrix models > #4,0.25299,-0.58584,-0.76993,165.47,-0.20328,0.74586,-0.63432,15.301,0.94587,0.31699,0.069609,187.69 > show #!5 models > hide #!5 models > view name zoomout5 > view list Named views: pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view sidebound > view sidebound1 > view topunbound > view topbound > view topunbound > movie record > fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout 5 fly: Unknown position name ""zoomout"" > movie record Already recording a movie > movie record Already recording a movie > fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > view topunbound > view name topunbound > view topbound > view name topbound > view list Named views: pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view zoomout1 > view name zoomout1 > view zoomout2 > select clear > view name zoomout2 > view zoomout3 > view zoomout2 > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.30555,-0.55367,-0.77465,159.89,-0.24922,0.7387,-0.62627,30.879,0.91898,0.38442,0.08772,25.454 Drag select of 73 residues, 1 pseudobonds > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.30555,-0.55367,-0.77465,163.63,-0.24922,0.7387,-0.62627,33.974,0.91898,0.38442,0.08772,-43.204 > view name zoomout3 > view zoomout3 > view zoomout4 > view zoomout3 > view matrix models > #4,0.30555,-0.55367,-0.77465,165.37,-0.24922,0.7387,-0.62627,35.445,0.91898,0.38442,0.08772,-75.518 > view name zoomout3 > view zoomout2 > view matrix models > #4,0.30555,-0.55367,-0.77465,164.65,-0.24922,0.7387,-0.62627,33.581,0.91898,0.38442,0.08772,-48.286 > view name zoomout3 > view name zoomout4 > view matrix models > #4,0.30555,-0.55367,-0.77465,149.16,-0.24922,0.7387,-0.62627,24.043,0.91898,0.38442,0.08772,199.84 > view matrix models > #4,0.23712,-0.58313,-0.777,163.32,-0.33327,0.70245,-0.62888,41.393,0.91253,0.40807,-0.027775,213.92 > view name junctionopen > show #!5 models > matchmaker #4 ¢5 Expected a keyword > matchmaker #4 #5 Missing required ""to"" argument > matchmaker #4 to #5 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 6VAE.pdb, chain B (#5) with 6vad.pdb, chain B (#4), sequence alignment score = 5565.9 RMSD between 635 pruned atom pairs is 1.074 angstroms; (across all 1131 pairs: 12.571) > morph #4 to #5 Expected a keyword > morph #4 #5 models have different number of chains, 2 (Morph - 6vad.pdb #/A,Morph - 6vad.pdb #/B) and 4 (6VAE.pdb #5/A,6VAE.pdb #5/B,6VAE.pdb #5/C,6VAE.pdb #5/D) > hide #!5 models > show #!5 models > hide #!4 models > select #5/B:296 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 220 atoms, 219 bonds, 13 residues, 1 model selected > select up 2998 atoms, 3018 bonds, 182 residues, 1 model selected > select up 3069 atoms, 3087 bonds, 186 residues, 1 model selected > select up 8281 atoms, 8342 bonds, 510 residues, 1 model selected > select up 8293 atoms, 8353 bonds, 511 residues, 1 model selected > select up 9875 atoms, 9955 bonds, 614 residues, 1 model selected > select up 18808 atoms, 18983 bonds, 1155 residues, 1 model selected > select up 40634 atoms, 40968 bonds, 2505 residues, 1 model selected > select up 105913 atoms, 108770 bonds, 5694 residues, 5 models selected > select down 40634 atoms, 40968 bonds, 2505 residues, 3 models selected > show sel cartoons > select clear > select #5/C:2 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 108 atoms, 108 bonds, 6 residues, 1 model selected > select up 1231 atoms, 1237 bonds, 76 residues, 1 model selected > select up 40634 atoms, 40968 bonds, 2505 residues, 1 model selected > select down 1231 atoms, 1237 bonds, 76 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #5/D:24 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 224 atoms, 223 bonds, 14 residues, 1 model selected > select up 1231 atoms, 1237 bonds, 76 residues, 1 model selected > delete atoms sel > delete bonds sel > view junctionopen > morph #4 #5 Computed 51 frame morph #6 > coordset #6 1,51 > cartoon style width 4 thickness 1 > view name junctionclosed > view list Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound [Repeated 1 time(s)] > view topbound > view topunbound > view zoomout1 > view topunbound > view topbound > show #!5 models > hide #!6 models > view list Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > show #!4 models > hide #!5 models > view topunbound > view topbound > view zoomout1 > view zoomout2 > view zoomout3 > view zoomout4 > view zoomout5 > view junctionopen > movie record > fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5 > junctionopen > view list Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > view topbound > view zoomout1 > view zoomout2 > view zoomout3 > view zoomout4 > view zoomout5 > view topunbound > view name topunbound > view topbound > view name topbound > view zoomout1 > view name zoomout1 > view zoomout2 > view name zoomout2 > view zoomout3 > view name zoomout3 > view zoomout4 > view name zoomout4 > view zoomout5 > view name zoomout5 > view junctionopen > view name junctionopen > view junctionclosed > view name junctionclosed > view topunbound > movie record Already recording a movie > movie record Already recording a movie > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > movie record > fly 25 topunbound topbound zoomout1 zoomout2 zoomout3 zoomout4 zoomout5 > junctionopen > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > view list Named views: junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topunbound, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > view topbound > view zoomout1 > view topunbound > view topbound > view topunbound > view topbound > view zoomout1 > view topbound > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.051693,-0.5639,-0.82422,205.96,-0.32784,0.77001,-0.54737,27.356,0.94332,0.29851,-0.14506,-63.261 > view name topbound1 > view matrix models > #4,0.051693,-0.5639,-0.82422,198.72,-0.32784,0.77001,-0.54737,15.567,0.94332,0.29851,-0.14506,135.75 > view name topbound2 > view matrix models > #4,0.051693,-0.5639,-0.82422,202.66,-0.32784,0.77001,-0.54737,25.713,0.94332,0.29851,-0.14506,-15.507 > view name topbound3 > view matrix models > #4,0.051693,-0.5639,-0.82422,201.55,-0.32784,0.77001,-0.54737,27.267,0.94332,0.29851,-0.14506,-23.706 > undo > view name zo1 > view matrix models > #4,0.051693,-0.5639,-0.82422,196.74,-0.32784,0.77001,-0.54737,20.935,0.94332,0.29851,-0.14506,91.214 > view name zo2 > view matrix models > #4,0.051693,-0.5639,-0.82422,200.32,-0.32784,0.77001,-0.54737,22.219,0.94332,0.29851,-0.14506,45.155 > view name zo3 > view matrix models > #4,0.051693,-0.5639,-0.82422,194.39,-0.32784,0.77001,-0.54737,10.085,0.94332,0.29851,-0.14506,236.62 > view matrix models > #4,0.13823,-0.53956,-0.83052,179.6,-0.21401,0.80248,-0.55697,-9.2463,0.967,0.25473,-0.0045496,219.3 > view matrix models > #4,0.061681,-0.51263,-0.85639,190.46,-0.30616,0.80694,-0.50509,-4.1288,0.94998,0.29334,-0.10717,230.99 > view matrix models > #4,0.083525,-0.50619,-0.85837,184.42,-0.27489,0.81625,-0.5081,-7.7796,0.95784,0.2784,-0.07097,227.94 > view matrix models > #4,0.1278,-0.6,-0.78973,181.32,-0.22977,0.75668,-0.61208,8.8344,0.96482,0.25968,-0.041161,225.3 > view matrix models > #4,0.1611,-0.58561,-0.79442,175.26,-0.18414,0.77297,-0.60714,-0.6177,0.96961,0.2441,0.016693,218.54 > view matrix models > #4,0.23587,-0.56054,-0.79382,161.06,-0.12396,0.79285,-0.59668,-13.423,0.96384,0.23915,0.11753,205.69 > view matrix models > #4,0.23587,-0.56054,-0.79382,175.63,-0.12396,0.79285,-0.59668,3.2911,0.96384,0.23915,0.11753,207.14 > view matrix models > #4,0.34499,-0.52906,-0.77529,153.1,-0.19666,0.76692,-0.61086,19.245,0.91777,0.36321,0.16054,190.42 > view matrix models > #4,0.34499,-0.52906,-0.77529,162.07,-0.19666,0.76692,-0.61086,26.643,0.91777,0.36321,0.16054,191.33 > view name jo1 > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topbound2 > view topunbound > movie record > fly 5 topunbound topbound topbound1 > topbound2 Unknown command: topbound2 > topbound3 Unknown command: topbound3 > zo1 Unknown command: zo1 > zo2 Unknown command: zo2 > zo3 Unknown command: zo3 > jo1 Unknown command: jo1 > view topunbound > view zo1 > view topunbound > movie record Already recording a movie > view topunbound > movie record Already recording a movie > view topunbound > view topbound > view topbound1 > view topbound2 > view topbound3 > view zo1 > view zo2 > view zo3 > view jo1 > view topunbound > view topbound3 > view topunbound > view zo3 > view jo1 > view zo3 > view jo1 > view topunbound > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > movie record > fly 5 topunbound topbound topbound1 topbound2 topbound3 zo1 zo2 zo3 jo1 > view topunbound > view sidebound > view topunbound [Repeated 1 time(s)] > view sidebound2 > view topunbound > view sidebound1 > view sidebound2 > view sidebound1 > view topunbound > view sidebound1 > view topunbound > view pos2 > view topunbound > view name topunbound > view topbound > view name topbound > view zoomout1 > view topbound1 > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topbound > view topunbound > view topbound > view topunbound > view topbound > view topbound1 > view name topbound1 > view topbound2 > view name topbound2 > view topbound3 > view name topbound3 > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view zo1 > view name zo1 > view zo2 > view name zo2 > view zo3 > view name zo3 > view jo1 > view name jo1 > view topunbound > select clear > movie record Already recording a movie > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topbound3 > view topunbound [Repeated 1 time(s)] > view zoomout5 > view topunbound > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > movie record > fly 5 topunbound topbound topbound1 topbound2 topbound3 zo1 zo2 zo3 jo1 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > save /Users/palcon/Desktop/220909.cxs > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > view name topunbound [Repeated 2 time(s)] > view topbound > view topunbound > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view topunbound > view matrix models > #4,0.14822,-0.47073,-0.86974,185.3,0.53306,0.77878,-0.33066,-133.96,0.83299,-0.41462,0.36636,59.764 > view matrix models > #4,0.14822,-0.47073,-0.86974,183.03,0.53306,0.77878,-0.33066,-132.16,0.83299,-0.41462,0.36636,58.823 > view matrix models > #4,0.30287,-0.58794,-0.75006,160.19,-0.3314,0.67294,-0.66131,52.62,0.89356,0.44886,0.0089741,-18.371 > view matrix models > #4,0.30287,-0.58794,-0.75006,162.12,-0.3314,0.67294,-0.66131,58.912,0.89356,0.44886,0.0089741,-16.993 > view matrix models > #4,0.30287,-0.58794,-0.75006,160.11,-0.3314,0.67294,-0.66131,55.051,0.89356,0.44886,0.0089741,-17.957 > view matrix models > #4,0.30287,-0.58794,-0.75006,165.41,-0.3314,0.67294,-0.66131,67.334,0.89356,0.44886,0.0089741,-15.048 > view matrix models > #4,0.38976,-0.54137,-0.74498,145.88,-0.17327,0.7514,-0.63669,30.463,0.90447,0.37724,0.19907,-33.75 > view matrix models > #4,0.5674,-0.45279,-0.68778,100.19,-0.31303,0.65393,-0.68876,71.256,0.76162,0.6061,0.2293,-49.371 > view matrix models > #4,0.58607,-0.45581,-0.66989,95.406,-0.28704,0.65635,-0.69772,68.496,0.75771,0.6012,0.25383,-51.629 > view matrix models > #4,0.58607,-0.45581,-0.66989,95.082,-0.28704,0.65635,-0.69772,68.704,0.75771,0.6012,0.25383,-34.943 > view matrix models > #4,0.58607,-0.45581,-0.66989,96.115,-0.28704,0.65635,-0.69772,67.769,0.75771,0.6012,0.25383,-36.009 > view matrix models > #4,0.58607,-0.45581,-0.66989,96.533,-0.28704,0.65635,-0.69772,67.383,0.75771,0.6012,0.25383,-34.977 > view matrix models > #4,0.4698,-0.52989,-0.70605,128.48,-0.18162,0.72468,-0.66472,38.225,0.86389,0.44052,0.24422,-26.499 > view matrix models > #4,0.16497,-0.67017,-0.72364,193.79,-0.24192,0.68378,-0.68842,55.84,0.95617,0.28863,-0.049321,23.15 > view matrix models > #4,0.10326,-0.68492,-0.72127,204.28,-0.18764,0.69871,-0.69036,46.324,0.9768,0.20663,-0.056366,32.56 > view matrix models > #4,0.10326,-0.68492,-0.72127,210.03,-0.18764,0.69871,-0.69036,42.095,0.9768,0.20663,-0.056366,32.666 > view matrix models > #4,0.10326,-0.68492,-0.72127,210.47,-0.18764,0.69871,-0.69036,41.415,0.9768,0.20663,-0.056366,16.55 > view name topbound Drag select of 39 residues > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.10326,-0.68492,-0.72127,259.37,-0.18764,0.69871,-0.69036,-37.784,0.9768,0.20663,-0.056366,5.2566 > view matrix models > #4,0.11734,-0.39276,-0.91212,244.12,-0.18196,0.89442,-0.40855,-105.77,0.97628,0.21391,0.033484,-8.4656 > view name topunbound > fly topunbound topbound > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > select clear > view topbound > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.10326,-0.68492,-0.72127,211.53,-0.18764,0.69871,-0.69036,40.298,0.9768,0.20663,-0.056366,-62.737 > fly topunbound topbound1 > view topunbound [Repeated 1 time(s)] > view topbound > view topunbound > view topbound > view matrix models > #4,0.10326,-0.68492,-0.72127,212.61,-0.18764,0.69871,-0.69036,38.564,0.9768,0.20663,-0.056366,-64.535 > view name topbound1 > view matrix models > #4,0.10326,-0.68492,-0.72127,210.68,-0.18764,0.69871,-0.69036,40.534,0.9768,0.20663,-0.056366,87.191 > view name topbound2 > view name topbound3 > view matrix models > #4,0.10326,-0.68492,-0.72127,210.75,-0.18764,0.69871,-0.69036,41.382,0.9768,0.20663,-0.056366,-38.145 > view name topbound4 > view matrix models > #4,0.10326,-0.68492,-0.72127,209.86,-0.18764,0.69871,-0.69036,40.843,0.9768,0.20663,-0.056366,222.23 > view name topbound5 > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topbound4, topbound5, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > fly 25 topunbound topbound topbound1 topbound2 topbound3 topbound4 topbound5 > view topunbound > movie record > fly 50 topunbound 5 topbound 5 topbound1 5 topbound2 5 topbound3 5 topbound4 > 5 topbound5 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > view topunbound > movie record > fly 50 topunbound 50 topbound 50 topbound1 50 topbound2 50 topbound3 50 > topbound4 50 topbound5 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > select clear > view topunbound > movie record > fly 20 topunbound 20 topbound 20 topbound1 20 topbound2 20 topbound3 20 > topbound4 20 topbound5 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > view list Named views: jo1, junctionclosed, junctionopen, pos1, pos2, sidebound, sidebound1, sidebound2, topbound, topbound1, topbound2, topbound3, topbound4, topbound5, topunbound, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view topunbound > view topbound > view topbound1 > view topbound2 > view topbound3 > view topunbound > movie record > fly topunbound 20 topbound 20 topbound1 20 topbound2 20 topbound3 20 > topbound4 20 topbound5 > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > fly topunbound 20 topbound > view topunbound > fly topunbound 20 topbound 20 topbound1 > fly topunbound 20 > wait 10 > fly topbound 20 > wait 10 > fly topbound1 > view topunbound > fly topunbound 20 > wait 10 > fly topbound 20 > wait 10 > fly topbound1 > fly topunbound 20 wait 10 fly topbound 20 wait 10 fly topbound1 fly: Unknown position name ""wait"" > fly topunbound 20 topbound 20 topbound1 > rock #4 y 10 Expected an axis vector or a keyword > rock y #4 y 10 Expected a number or a keyword > rock y #4 Expected a number or a keyword > rock > stop > view topunbound > fly topunbound 20 topbound 20 topbound1 > view topunbound > fly topunbound 20 topbound 20 topbound1 20 topbound2 > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.10326,-0.68492,-0.72127,291.58,-0.18764,0.69871,-0.69036,-91.31,0.9768,0.20663,-0.056366,175.92 > view matrix models > #4,0.12272,-0.36664,-0.92224,273.39,-0.17817,0.90602,-0.3839,-164.95,0.97632,0.21143,0.045863,160.78 > view matrix models > #4,-0.34564,-0.23765,-0.90778,320.17,0.58308,0.70357,-0.4062,-242.16,0.73522,-0.66971,-0.10461,338.4 > select clear > view name one > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,-0.26647,-0.22071,-0.93823,310.89,0.63114,0.69575,-0.34292,-256.93,0.72846,-0.68354,-0.0461,332.95 > view matrix models > #4,0.0014736,-0.3587,-0.93345,291.15,0.19476,0.91568,-0.35157,-223.99,0.98085,-0.18128,0.071209,210.84 > view matrix models > #4,0.0014736,-0.3587,-0.93345,214.07,0.19476,0.91568,-0.35157,-98.458,0.98085,-0.18128,0.071209,139.79 > view matrix models > #4,-0.089649,-0.26302,-0.96062,217.67,0.15891,0.94837,-0.2745,-108.84,0.98321,-0.17726,-0.043223,155.18 > view matrix models > #4,-0.0156,-0.27174,-0.96224,208.57,0.038721,0.96147,-0.27215,-93.879,0.99913,-0.041505,-0.004477,128.62 > select clear > view name two > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,-0.0156,-0.27174,-0.96224,207.25,0.038721,0.96147,-0.27215,-90.472,0.99913,-0.041505,-0.004477,-38.073 > view name three > view matrix models > #4,-0.0156,-0.27174,-0.96224,205.65,0.038721,0.96147,-0.27215,-89.391,0.99913,-0.041505,-0.004477,159.94 > view matrix models > #4,-0.0022613,-0.37577,-0.92671,213.09,0.049959,0.92551,-0.37541,-71.321,0.99875,-0.047146,0.01668,157.77 > view matrix models > #4,-0.0022613,-0.37577,-0.92671,212.53,0.049959,0.92551,-0.37541,-70.15,0.99875,-0.047146,0.01668,122.89 > view name four > view matrix models > #4,-0.0022613,-0.37577,-0.92671,213.43,0.049959,0.92551,-0.37541,-70.83,0.99875,-0.047146,0.01668,19.134 > view name five > view matrix models > #4,-0.0022613,-0.37577,-0.92671,213.73,0.049959,0.92551,-0.37541,-73.106,0.99875,-0.047146,0.01668,255.18 > view name junction > view list Named views: five, four, jo1, junction, junctionclosed, junctionopen, one, pos1, pos2, sidebound, sidebound1, sidebound2, three, topbound, topbound1, topbound2, topbound3, topbound4, topbound5, topunbound, two, zo1, zo2, zo3, zoomout1, zoomout2, zoomout3, zoomout4, zoomout5 > view one > select clear > fly 50 one two three four five junction > view one > movie record > fly 50 one > wait 10 > fly 100 two three four five junction > view one > movie record Already recording a movie > stop > save /Users/palcon/Desktop/220909.cxs ——— End of log from Fri Sep 9 15:10:40 2022 ——— opened ChimeraX session > movie record > fly 50 one 50 two > wait 10 > fly two 50 three 50 four 50 five 50 junction > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > ui tool show ""Side View"" > view onw Expected an objects specifier or a view name or a keyword > view one > fly 50 one 50 two > wait 20 > fly two 50 three 50 four 50 five 50 junction > stop > veiw onw Unknown command: veiw onw > veiw one Unknown command: veiw one > view one > fly 50 one 50 two > wait 120 > fly two 50 three 50 four 50 five 50 junction > movei record; fly 50 one 50 two; wait 110; fly two 50 three 40 four 30 five > 50 junction Unknown command: movei record; fly 50 one 50 two; wait 110; fly two 50 three 40 four 30 five 50 junction > movie record > fly 50 one 50 two > wait 110 > fly two 50 three 40 four 30 five 50 junction > movie encode 220909_1.mp4 quality medium Movie saved to 220909_1.mp4 > view one > movie record > fly 50 one 50 two > wait 50 > fly two 50 three 40 four 30 five 50 junction > view one > movie record Already recording a movie > view one > stop > save /Users/palcon/Desktop/220909.cxs ——— End of log from Fri Sep 9 15:20:29 2022 ——— opened ChimeraX session > show #!6 models > show #!5 models > hide #!5 models > hide #!6 models > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 210 > morph #4,5 Computed 51 frame morph #7 > coordset #7 1,51 > cartoon style width 4 thickness 1 > hide #!7 models > show #!4 models > view one > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 160 > hide #4 models > show #7 models > coordset #7 1,51 > view one > hide #!7 models > show #!4 models > movie record > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > view one > hide #!7 models > show #!4 models > movie encode 220909_1.mp4 quality high Movie saved to 220909_1.mp4 > ui tool show ""Side View"" > lighting full > lighting soft > movie record > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality high Movie saved to 220909_1.mp4 > view one > show #!4 models > hide #!7 models > 2dlabels text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05 y 0.1 Invalid ""text"" argument: incomplete quoted text > text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05 y 0.1 Unknown command: text 'wild-type D2-I + DNA (open)’ color black size 26 x 0.05 y 0.1 > text 'wild-type D2-I + DNA (open)’ Unknown command: text 'wild-type D2-I + DNA (open)’ > 2dlabels'wild-type D2-I + DNA (open)’ incomplete quoted text > 2dlabels text 'wild-type D2-I + DNA (open)’ Invalid ""text"" argument: incomplete quoted text > 2dlabels text 'D2-I’ Invalid ""text"" argument: incomplete quoted text > 2dlabels text 'D2-I’ Invalid ""text"" argument: incomplete quoted text > 2dlabels text 'D2-I’ Invalid ""text"" argument: incomplete quoted text > text 'D2-I’ Unknown command: text 'D2-I’ > 2dlabels text 2 > 2dlabels text D2-I > close #8.1 > view one > 2dlabels text #8.2 color blue size 26 xpos 0.62 ypos 0.1 > 2dlabels text D2-I color blue size 26 xpos 0.62 ypos 0.1 > close #8.1-3 > 2dlabels text FANCD2 color blue size 26 xpos 0.62 ypos 0.1 > 2dlabels text FANCD2 size 26 xpos 0.62 ypos 0.1 > close #9.1 > 2dlabels text FANCD2 size 26 xpos 0.22 ypos 0.1 > 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.4 > 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.7 > 2dlabels text FANCD2 size 26 xpos 0.25 ypos 0.8 > 2dlabels text FANCD2 size 26 xpos 0.3 ypos 0.9 > 2dlabels text FANCD2 size 26 xpos 0.28 ypos 0.9 > 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.9 > 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.8 > 2dlabels text FANCD2 size 26 xpos 0.35 ypos 0.85 > close #9.1-9 > 2dlabels text FANCD2 size 20 xpos 0.35 ypos 0.85 > close #9.1 > close #9.10 > 2dlabels text FANCD2 size 20 xpos 0.35 ypos 0.85 > 2dlabels text FANCI size 20 xpos 0.55 ypos 0.65 > close #10.2 > 2dlabels text FANCI size 20 xpos 0.65 ypos 0.65 > 2dlabels text FANCI size 20 xpos 0.6 ypos 0.65 > close #10.2 > wait 40 > 2dlabels change #10.1 > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > view one > show #10.3 models > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality high Movie saved to 220909_1.mp4 > view one > hide #!7 models > show #!4 models > show #10.1 models > show #10.3 models > 2dlabels text DNA loading size 20 x 0.5 y 0.6 Expected a keyword > 2dlabels text DNA loading Expected a keyword > 2dlabels text ""DNA loading"" > 2dlabels text ""DNA loading"" size 20 xpos 0.4 ypos 0.4 > 2dlabels text ""DNA loading"" size 20 xpos 0.4 ypos 0.6 > 2dlabels text ""DNA loading"" size 20 xpos 0.3 ypos 0.6 > close #10.2,4-5 > hide #10.6 models > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 models > 2dlabels change #10.6 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality high No frames have been recorded > view one > hide #!10 models > show #!4 models > hide #!7 models > show #10.1 models > show #10.3 models > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 models > 2dlabels change #10.6 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality high Movie saved to 220909_1.mp4 > view one > show #!4 models > hide #!7 models > show #10.1 models > show #10.3 models > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 models > 2dlabels change #10.6 visibility false > show #10.1 models > show #10.3 models > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 models > 2dlabels change #10.6 visibility false > show #10.1 models > show #10.3 models > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 models > 2dlabels change #10.6 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > view one > show #10.1 models > show #10.3 models > show #!4 models > show #10.6 > hide #10.6 models > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > show #10.6 > 2dlabels change #10.6 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > view one > movie encode 220909_1.mp4 quality high Movie saved to 220909_1.mp4 > close #10.6 > show #10.1 models > show #10.3 models > hide #!7 models > show #!4 models > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > 2dlabels text ""DNA loading"" size 20 xpos 0.3 ypos 0.6 > wait 60 > 2dlabels change #10.6 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > hide #10.2 models > show #10.1 models > show #10.3 models > hide #!7 models > show #!4 models > view onw Expected an objects specifier or a view name or a keyword > view one > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > 2dlabels text ""DNA loading"" size 20 xpos 0.3 ypos 0.6 > wait 60 > 2dlabels change #10.2 visibility false > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > close #10.4 > close #10.2 > 2dlabels text ""DNA loading"" size 20 xpos 0.3 ypos 0.6 > close #10.2 > show #10.1 models > show #10.3 models > hide #!7 models > show #!4 models > view one > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality highest Movie saved to 220909_1.mp4 > view one > show #10.1 models > show #10.3 models > hide #!7 models > show #!4 models > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > select clear > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.34564,-0.23765,-0.90778,315.46,0.58308,0.70357,-0.4062,-234.82,0.73522,-0.66971,-0.10461,378.21 > view save one Expected an objects specifier or a view name or a keyword > view name one > view matrix models > #4,-0.34564,-0.23765,-0.90778,237.07,0.58308,0.70357,-0.4062,-106.56,0.73522,-0.66971,-0.10461,226.51 > view matrix models > #4,0.06272,-0.37565,-0.92464,200.42,-0.081025,0.92149,-0.37986,-45.9,0.99474,0.098744,0.027359,64.486 > view matrix models > #4,0.06272,-0.37565,-0.92464,204.01,-0.081025,0.92149,-0.37986,-51.709,0.99474,0.098744,0.027359,61.51 > view name two > view matrix models > #4,0.06272,-0.37565,-0.92464,204.09,-0.081025,0.92149,-0.37986,-51.452,0.99474,0.098744,0.027359,11.818 > view name three > view matrix models > #4,0.06272,-0.37565,-0.92464,204.69,-0.081025,0.92149,-0.37986,-52.865,0.99474,0.098744,0.027359,70.237 > view name four > view matrix models > #4,0.06272,-0.37565,-0.92464,204.86,-0.081025,0.92149,-0.37986,-52.168,0.99474,0.098744,0.027359,-59.245 > view name five > view matrix models > #4,0.06272,-0.37565,-0.92464,203.69,-0.081025,0.92149,-0.37986,-52.574,0.99474,0.098744,0.027359,243.84 > view name junction > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > view matrix models > #4,0.06272,-0.37565,-0.92464,203.93,-0.081025,0.92149,-0.37986,-52.914,0.99474,0.098744,0.027359,237.26 > view name junction > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > view matrix models > #4,0.06272,-0.37565,-0.92464,203.93,-0.081025,0.92149,-0.37986,-52.832,0.99474,0.098744,0.027359,227.11 > show #!7 models > hide #!7 models > view name junction > view one > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > view one > show #10.1 models > show #10.3 models > hide #!7 models > show #!4 models > select subtract #4 Nothing selected > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality highest Movie saved to 220909_1.mp4 > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.06272,-0.37565,-0.92464,203.75,-0.081025,0.92149,-0.37986,-52.644,0.99474,0.098744,0.027359,240.56 > select up 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > select up 177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 8 models selected > select up 177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 8 models selected > select up 177971 atoms, 181442 bonds, 19 pseudobonds, 10136 residues, 11 models selected > select down 177971 atoms, 181442 bonds, 18 pseudobonds, 10136 residues, 10 models selected > select down 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 4 models selected > select clear > view name junction > show #10.1 models > show #10.3 models > hide #!7 models > view one > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality highest Movie saved to 220909_1.mp4 > show #!4 models > hide #!4 models > show #!4 models > select add #4 37613 atoms, 37931 bonds, 18 pseudobonds, 2321 residues, 2 models selected > view matrix models > #4,0.0182,-0.37787,-0.92568,210.55,-0.0088749,0.92573,-0.37807,-63.759,0.99979,0.015096,0.013495,253.38 > view matrix models > #4,0.0182,-0.37787,-0.92568,210.61,-0.0088749,0.92573,-0.37807,-63.837,0.99979,0.015096,0.013495,249.67 > view name junction > show #10.1 models > show #10.3 models > view one > select subtract #4 Nothing selected > hide #!7 models > movie record > wait 40 > 2dlabels change #10.1 visibility false > 2dlabels change #10.3 visibility false > wait 10 > fly one 50 two > wait 55 > fly two 50 three 50 four 25 five 25 junction > wait 170 > hide #4 models > show #7 models > coordset #7 1,51 > wait wait requires a frame count argument unless motion is in progress > movie encode 220909_1.mp4 quality highest Movie saved to 220909_1.mp4 > save /Users/palcon/Desktop/220909.cxs ——— End of log from Fri Sep 9 17:19:50 2022 ——— opened ChimeraX session 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: 8 L2 Cache: 16 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 1 day 3:58 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: DELL U3223QE: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes 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 Window Toolkit nonchimerax all ChimeraX